888 Citations
The G protein coupled cysteinyl leukotriene receptor CysLT R mediates inflammatory processes and plays a major role in numerous disorders including asthma allergic rhinitis cardiovascular disease and cancer Selective CysLT R antagonists are widely prescribed as antiasthmatic drugs however these drugs demonstrate low effectiveness in some patients and exhibit a variety of side effects To gain deeper understanding into the functional mechanisms of CysLTRs we determined the crystal structures of CysLT R bound to two chemically distinct antagonists zafirlukast and pranlukast The structures reveal unique ligand-binding modes and signaling mechanisms including lateral ligand access to the orthosteric pocket between transmembrane ... More
The G protein–coupled cysteinyl leukotriene receptor CysLT1R mediates inflammatory processes and plays a major role in numerous disorders, including asthma, allergic rhinitis, cardiovascular disease, and cancer. Selective CysLT1R antagonists are widely prescribed as antiasthmatic drugs; however, these drugs demonstrate low effectiveness in some patients and exhibit a variety of side effects. To gain deeper understanding into the functional mechanisms of CysLTRs, we determined the crystal structures of CysLT1R bound to two chemically distinct antagonists, zafirlukast and pranlukast. The structures reveal unique ligand-binding modes and signaling mechanisms, including lateral ligand access to the orthosteric pocket between transmembrane helices TM4 and TM5, an atypical pattern of microswitches, and a distinct four-residue–coordinated sodium site. These results provide important insights and structural templates for rational discovery of safer and more effective drugs. Less
Protein trafficking requires coat complexes that couple recognition of sorting motifs in transmembrane cargoes with biogenesis of transport carriers The mechanisms of cargo transport through the endosomal network are poorly understood Here we identify a sorting motif for endosomal recycling of cargoes including the cation-independent mannose- -phosphate receptor and semaphorin C by the membrane tubulating BAR domain-containing sorting nexins SNX and SNX Crystal structures establish that this motif folds into a -hairpin which binds a site in the SNX SNX phox homology domains Over sixty cargoes share this motif and require SNX SNX for their recycling These include cargoes involved ... More
Protein trafficking requires coat complexes that couple recognition of sorting motifs in transmembrane cargoes with biogenesis of transport carriers. The mechanisms of cargo transport through the endosomal network are poorly understood. Here, we identify a sorting motif for endosomal recycling of cargoes, including the cation-independent mannose-6-phosphate receptor and semaphorin 4C, by the membrane tubulating BAR domain-containing sorting nexins SNX5 and SNX6. Crystal structures establish that this motif folds into a β-hairpin, which binds a site in the SNX5/SNX6 phox homology domains. Over sixty cargoes share this motif and require SNX5/SNX6 for their recycling. These include cargoes involved in neuronal migration and a Drosophila snx6 mutant displays defects in axonal guidance. These studies identify a sorting motif and provide molecular insight into an evolutionary conserved coat complex, the ‘Endosomal SNX–BAR sorting complex for promoting exit 1’ (ESCPE-1), which couples sorting motif recognition to the BAR-domain-mediated biogenesis of cargo-enriched tubulo-vesicular transport carriers. Less
Protein-crystallization imaging and classification is a labor-intensive process typically performed either by humans or by instruments that currently cost well over This cost puts the use of crystallization-trial imaging outside the reach of most academic laboratories and also start-up biotechnology firms where resources are scarce An imaging system has been designed and prototyped which automatically captures images from multi-well protein-crystallization experiments using both standard and fluorescent imaging techniques at a cost times lower than current market rates The machine uses a Panowin F D printer as a base and controls it using G-code commands sent from a Python script running ... More
Protein-crystallization imaging and classification is a labor-intensive process typically performed either by humans or by instruments that currently cost well over $100 000. This cost puts the use of crystallization-trial imaging outside the reach of most academic laboratories, and also start-up biotechnology firms, where resources are scarce. An imaging system has been designed and prototyped which automatically captures images from multi-well protein-crystallization experiments using both standard and fluorescent imaging techniques at a cost 28 times lower than current market rates. The machine uses a Panowin F1 3D printer as a base and controls it using G-code commands sent from a Python script running on a desktop computer. A graphical user interface (GUI) was developed to enable users to control the machine and facilitate image capture, classification and editing. A 488 nm laser diode and a 525 nm filter were incorporated to allow in situ fluorescent imaging of proteins trace-labeled with a fluorophore, Alexa Fluor 488. The instrument was primarily designed using a 3D printer and augmented using commercially available parts, and this publication aims to serve as a guide for comparable in-laboratory robotics projects. Less
The influence of process parameters during freeze thaw FT operations is essential for the preservation of the protein stability activity during production and storage processes in the biopharmaceutical industry Process parameters such as FT ramps the final storage time and temperature affect the occurring FT stress onto the target protein in different ways FT stress includes cold denaturation freeze concentration and ice crystal formation which can result in protein aggregation To visualize the impact of variations in FT ramps descriptors such as solubility phase behavior and crystal morphology were evaluated The phase diagram-based toolbox in combination with an HTS-compatible cryo-device ... More
The influence of process parameters during freeze/thaw (FT) operations is essential for the preservation of the protein stability/activity during production and storage processes in the biopharmaceutical industry. Process parameters, such as FT ramps, the final storage time and temperature, affect the occurring FT stress onto the target protein in different ways. FT stress includes cold denaturation, freeze concentration, and ice crystal formation which can result in protein aggregation. To visualize the impact of variations in FT ramps, descriptors such as solubility, phase behavior and crystal morphology were evaluated. The phase diagram-based toolbox in combination with an HTS-compatible cryo-device allowed the identification of suitable ramping schemes during FT operations. It could be clearly shown that rapid operations are needed above the glass transition temperature of the target protein to circumvent precipitation during FT cycles. Finally, a stability index is introduced which allows ranking of the systems investigated. Less
Yersinia pestis the causative agent of bubonic plague is one of the most lethal pathogens in recorded human history Today the concern is the possible misuse of Y pestis as an agent in bioweapons and bioterrorism Current therapies for the treatment of plague include the use of a small number of antibiotics but clinical cases of antibiotic resistance have been reported in some areas of the world Therefore the discovery of new drugs is required to combat potential Y pestis infection Here the crystal structure of the Y pestis UDP-glucose pyrophosphorylase UGP a metabolic enzyme implicated in the survival of ... More
Yersinia pestis, the causative agent of bubonic plague, is one of the most lethal pathogens in recorded human history. Today, the concern is the possible misuse of Y. pestis as an agent in bioweapons and bioterrorism. Current therapies for the treatment of plague include the use of a small number of antibiotics, but clinical cases of antibiotic resistance have been reported in some areas of the world. Therefore, the discovery of new drugs is required to combat potential Y. pestis infection. Here, the crystal structure of the Y. pestis UDP-glucose pyrophosphorylase (UGP), a metabolic enzyme implicated in the survival of Y. pestis in mouse macrophages, is described at 2.17 Å resolution. The structure provides a foundation that may enable the rational design of inhibitors and open new avenues for the development of antiplague therapeutics. Less
Second harmonic generation SHG microscopy and Raman microscopy were used for qualitative and quantitative analysis of pharmaceutical materials Prototype instruments and algorithms for sampling strategies and data analyses were developed to achieve pharmaceutical materials analysis with low limits of detection and short measurement times Manufacturing an amorphous solid dispersion ASD in which an amorphous active pharmaceutical ingredient API within polymer matrix is an effective approach to improve the solubility and bioavailability of a drug However since ASDs are generally metastable materials they can often transform to produce crystalline API with higher thermodynamic stability Analytical methods with low limits of detection ... More
Second harmonic generation (SHG) microscopy and Raman microscopy were used for
qualitative and quantitative analysis of pharmaceutical materials. Prototype instruments and
algorithms for sampling strategies and data analyses were developed to achieve pharmaceutical
materials analysis with low limits of detection and short measurement times.
Manufacturing an amorphous solid dispersion (ASD), in which an amorphous active
pharmaceutical ingredient (API) within polymer matrix, is an effective approach to improve the
solubility and bioavailability of a drug. However, since ASDs are generally metastable materials,
they can often transform to produce crystalline API with higher thermodynamic stability.
Analytical methods with low limits of detection for crystalline APIs were used to assess the
stability of ASDs. With high selectivity to noncentrosymmetric crystals, SHG microscopy was
demonstrated as an analytical tool, which exhibited a limit of detection of 10 ppm for ritonavir
Form II crystals. SHG microscopy was employed for accelerated stability testing of ASDs, which
provided a four-decade dynamic range of crystallinity for kinetic modeling. An established model
was validated by investigating nucleation and crystal growth based on SHG images. To achieve in
situ accelerated stability testing, controlled environment for in situ stability testing (CEiST) was
designed and built to provide elevated temperature and humidity, which is compatible with a
commercial SHG microscope based on our research prototype. The combination of CEiST and
SHG microscopy enabled assessment of individual crystal growth rates by single-particle tracking
and nucleation rates for individual fields of view with low Poisson noise. In addition, SHG
microscopy coupled with CEiST enabled the study of heterogeneity of crystallization kinetics
within pharmaceutical materials.
Polymorphism of APIs plays an important role in drug formulation development. Different
polymorphs of identical APIs may exhibit different physiochemical properties, e.g., solubility,
stability, and bioavailability, due to their crystal structures. Moreover, polymorph transitions may take place during the manufacturing process and storage. Therefore, analytical methods with high
speed for polymorph characterization, which can provide real-time feedback for the polymorphic
transition, have broad applications in pharmaceutical materials characterization. Raman
spectroscopy is able to determine the API polymorphism, but is hampered by the long
measurement times. In this study, two analytical methods with high speed were developed to
characterize API polymorphs. One is SHG microscopy-guided Raman spectroscopy, which
achieved the speed of 10 ms/particle for clopidogrel bisulfate. Initial classification of two different
polymorphs was based on SHG images, followed acquisition of Raman spectroscopy at the
selected positions to determine the API crystal form. Another approach is implementing of
dynamic sampling into confocal Raman microscopy to accelerate Raman image acquisition for 6-
folds. Instead of raster scanning, dynamic sampling algorithm enabled acquiring Raman spectra at
the most informative locations. The reconstructed Raman image of pharmaceutical materials has
<0.5% loss of image quality with 15.8% sampling rate. Less
qualitative and quantitative analysis of pharmaceutical materials. Prototype instruments and
algorithms for sampling strategies and data analyses were developed to achieve pharmaceutical
materials analysis with low limits of detection and short measurement times.
Manufacturing an amorphous solid dispersion (ASD), in which an amorphous active
pharmaceutical ingredient (API) within polymer matrix, is an effective approach to improve the
solubility and bioavailability of a drug. However, since ASDs are generally metastable materials,
they can often transform to produce crystalline API with higher thermodynamic stability.
Analytical methods with low limits of detection for crystalline APIs were used to assess the
stability of ASDs. With high selectivity to noncentrosymmetric crystals, SHG microscopy was
demonstrated as an analytical tool, which exhibited a limit of detection of 10 ppm for ritonavir
Form II crystals. SHG microscopy was employed for accelerated stability testing of ASDs, which
provided a four-decade dynamic range of crystallinity for kinetic modeling. An established model
was validated by investigating nucleation and crystal growth based on SHG images. To achieve in
situ accelerated stability testing, controlled environment for in situ stability testing (CEiST) was
designed and built to provide elevated temperature and humidity, which is compatible with a
commercial SHG microscope based on our research prototype. The combination of CEiST and
SHG microscopy enabled assessment of individual crystal growth rates by single-particle tracking
and nucleation rates for individual fields of view with low Poisson noise. In addition, SHG
microscopy coupled with CEiST enabled the study of heterogeneity of crystallization kinetics
within pharmaceutical materials.
Polymorphism of APIs plays an important role in drug formulation development. Different
polymorphs of identical APIs may exhibit different physiochemical properties, e.g., solubility,
stability, and bioavailability, due to their crystal structures. Moreover, polymorph transitions may take place during the manufacturing process and storage. Therefore, analytical methods with high
speed for polymorph characterization, which can provide real-time feedback for the polymorphic
transition, have broad applications in pharmaceutical materials characterization. Raman
spectroscopy is able to determine the API polymorphism, but is hampered by the long
measurement times. In this study, two analytical methods with high speed were developed to
characterize API polymorphs. One is SHG microscopy-guided Raman spectroscopy, which
achieved the speed of 10 ms/particle for clopidogrel bisulfate. Initial classification of two different
polymorphs was based on SHG images, followed acquisition of Raman spectroscopy at the
selected positions to determine the API crystal form. Another approach is implementing of
dynamic sampling into confocal Raman microscopy to accelerate Raman image acquisition for 6-
folds. Instead of raster scanning, dynamic sampling algorithm enabled acquiring Raman spectra at
the most informative locations. The reconstructed Raman image of pharmaceutical materials has
<0.5% loss of image quality with 15.8% sampling rate. Less
Curli amyloid fibrils secreted by Enterobacteriaceae mediate host cell adhesion and contribute to biofilm formation thereby promoting bacterial resistance to environmental stressors Here we present crystal structures of amyloid-forming segments from the major curli subunit CsgA revealing steric zipper fibrils of tightly mated -sheets demonstrating a structural link between curli and human pathological amyloids D-enantiomeric peptides originally developed to interfere with Alzheimer s disease-associated amyloid- inhibited CsgA fibrillation and reduced biofilm formation in Salmonella typhimurium Moreover as previously shown CsgA fibrils cross-seeded fibrillation of amyloid- providing support for the proposed structural resemblance and potential for cross-species amyloid interactions The presented ... More
Curli amyloid fibrils secreted by Enterobacteriaceae mediate host cell adhesion and contribute to biofilm formation, thereby promoting bacterial resistance to environmental stressors. Here, we present crystal structures of amyloid-forming segments from the major curli subunit, CsgA, revealing steric zipper fibrils of tightly mated β-sheets, demonstrating a structural link between curli and human pathological amyloids. D-enantiomeric peptides, originally developed to interfere with Alzheimer’s disease-associated amyloid-β, inhibited CsgA fibrillation and reduced biofilm formation in Salmonella typhimurium. Moreover, as previously shown, CsgA fibrils cross-seeded fibrillation of amyloid-β, providing support for the proposed structural resemblance and potential for cross-species amyloid interactions. The presented findings provide structural insights into amyloidogenic regions important for curli formation, suggest a novel strategy for disrupting amyloid-structured biofilms, and hypothesize on the formation of self-propagating prion-like species originating from a microbial source that could influence neurodegenerative diseases. Less
Phosphate acquisition by plants is an essential process that is directly implicated in the optimization of crop yields Purple acid phosphatases PAPs are ubiquitous metalloenzymes which catalyze the hydrolysis of a wide range of phosphate esters and anhydrides While some plant PAPs display a preference for ATP as the substrate others are efficient in hydrolyzing phytate or -phosphoenolpyruvate PEP PAP from red kidney bean rkbPAP is an efficient ATP- and ADPase but has no activity towards phytate The crystal structure of this enzyme in complex with an ATP analogue to resolution provides insight into the amino acid residues that play ... More
Phosphate acquisition by plants is an essential process that is directly implicated in the optimization of crop yields. Purple acid phosphatases (PAPs) are ubiquitous metalloenzymes, which catalyze the hydrolysis of a wide range of phosphate esters and anhydrides. While some plant PAPs display a preference for ATP as the substrate, others are efficient in hydrolyzing phytate or 2-phosphoenolpyruvate (PEP). PAP from red kidney bean (rkbPAP) is an efficient ATP- and ADPase, but has no activity towards phytate. The crystal structure of this enzyme in complex with an ATP analogue (to 2.20 Å resolution) provides insight into the amino acid residues that play an essential role in binding this substrate. Homology modelling was used to generate three-dimensional structures for the active sites of PAPs from tobacco (NtPAP) and Arabidopsis thaliana (AtPAP12 and AtPAP26) that are efficient in hydrolyzing phytate and PEP as substrates, respectively. In combination with substrate docking simulations and a phylogenetic analysis of 49 plant PAP sequences (including the first PAP sequences reported from Eucalyptus), several active site residues were identified that are important in defining the substrate specificities of plant PAPs. These results may inform bioengineering studies aimed at identifying and incorporating suitable plant PAP genes into crops to improve phosphorus use efficiency. Organic phosphorus sources increasingly supplement or replace inorganic fertilizer, and efficient phosphorus use of crops will lower the environmental footprint of agriculture while enhancing food production. Less
The CC chemokine receptor CCR balances immunity and tolerance by homeostatic trafficking of immune cells In cancer CCR -mediated trafficking leads to lymph node metastasis suggesting the receptor as a promising therapeutic target Here we present the crystal structure of human CCR fused to the protein Sialidase NanA by using data up to resolution The structure shows the ligand Cmp bound to an intracellular allosteric binding pocket A sulfonamide group characteristic for various chemokine receptor ligands binds to a patch of conserved residues in the Gi protein binding region between transmembrane helix and helix We demonstrate how structural data can ... More
The CC chemokine receptor 7 (CCR7) balances immunity and tolerance by homeostatic trafficking of immune cells. In cancer, CCR7-mediated trafficking leads to lymph node metastasis, suggesting the receptor as a promising therapeutic target. Here, we present the crystal structure of human CCR7 fused to the protein Sialidase NanA by using data up to 2.1 Å resolution. The structure shows the ligand Cmp2105 bound to an intracellular allosteric binding pocket. A sulfonamide group, characteristic for various chemokine receptor ligands, binds to a patch of conserved residues in the Gi protein binding region between transmembrane helix 7 and helix 8. We demonstrate how structural data can be used in combination with a compound repository and automated thermal stability screening to identify and modulate allosteric chemokine receptor antagonists. We detect both novel (CS-1 and CS-2) and clinically relevant (CXCR1-CXCR2 phase-II antagonist Navarixin) CCR7 modulators with implications for multi-target strategies against cancer. Less
A H N virus predominated recent influenza seasons which has resulted in the rigorous investigation of haemagglutinin but whether neuraminidase NA has undergone antigenic change and contributed to the predominance of A H N virus is unknown Here we show that the NA of the circulating A H N viruses has experienced significant antigenic drift since compared with the A Hong Kong vaccine strain This antigenic drift was mainly caused by amino acid mutations at NA residues S N S T introducing an N-linked glycosylation site at residue and As a result the binding of the NA of A H ... More
A(H3N2) virus predominated recent influenza seasons, which has resulted in the rigorous investigation of haemagglutinin, but whether neuraminidase (NA) has undergone antigenic change and contributed to the predominance of A(H3N2) virus is unknown. Here, we show that the NA of the circulating A(H3N2) viruses has experienced significant antigenic drift since 2016 compared with the A/Hong Kong/4801/2014 vaccine strain. This antigenic drift was mainly caused by amino acid mutations at NA residues 245, 247 (S245N/S247T; introducing an N-linked glycosylation site at residue 245) and 468. As a result, the binding of the NA of A(H3N2) virus by some human monoclonal antibodies, including those that have broad reactivity to the NA of the 1957 A(H2N2) and 1968 A(H3N2) reference pandemic viruses as well as contemporary A(H3N2) strains, was reduced or abolished. This antigenic drift also reduced NA-antibody-based protection against in vivo virus challenge. X-ray crystallography showed that the glycosylation site at residue 245 is within a conserved epitope that overlaps the NA active site, explaining why it impacts antibody binding. Our findings suggest that NA antigenic drift impacts protection against influenza virus infection, thus highlighting the importance of including NA antigenicity for consideration in the optimization of influenza vaccines. Less
We previously generated rotavirus-specific RV-specific recombinant monoclonal antibodies mAbs derived from B cells isolated from human intestinal resections Twenty-four of these mAbs were specific for the VP fragment of RV VP and most of were non-neutralizing when tested in the conventional MA cell based assay We reexamined the ability of these mAbs to neutralize RVs in human intestinal epithelial cells including ileal enteroids and HT- cells Most of of the non-neutralizing VP mAbs efficiently neutralized human RV in HT- cells or enteroids Serum RV neutralization titers in adults and infants were significantly higher in HT- than MA cells and adsorption ... More
We previously generated 32 rotavirus-specific (RV-specific) recombinant monoclonal antibodies (mAbs) derived from B cells isolated from human intestinal resections. Twenty-four of these mAbs were specific for the VP8* fragment of RV VP4, and most (20 of 24) were non-neutralizing when tested in the conventional MA104 cell–based assay. We reexamined the ability of these mAbs to neutralize RVs in human intestinal epithelial cells, including ileal enteroids and HT-29 cells. Most (18 of 20) of the “non-neutralizing” VP8* mAbs efficiently neutralized human RV in HT-29 cells or enteroids. Serum RV neutralization titers in adults and infants were significantly higher in HT-29 than MA104 cells and adsorption of these sera with recombinant VP8* lowered the neutralization titers in HT-29 but not MA104 cells. VP8* mAbs also protected suckling mice from diarrhea in an in vivo challenge model. X-ray crystallographic analysis of one VP8* mAb (mAb9) in complex with human RV VP8* revealed that the mAb interaction site was distinct from the human histo-blood group antigen binding site. Since MA104 cells are the most commonly used cell line to detect anti-RV neutralization activity, these findings suggest that prior vaccine and other studies of human RV neutralization responses may have underestimated the contribution of VP8* antibodies to the overall neutralization titer. Less
Image-based protein phase diagram analysis is key for understanding and exploiting protein phase behavior in the biopharmaceutical field However required data analysis has become a notorious time-consuming task since high-throughput screening approaches were implemented A variety of computational tools have been developed to support analysis but these tools primarily use end point visible light images This study investigates the combined effect of end point and time-dependent image features obtained from cross-polarized and ultraviolet light features supplementary to visible light on protein phase diagram image classification In addition external validation was performed to evaluate the classification algorithm s applicability to support ... More
Image-based protein phase diagram analysis is key for understanding and exploiting protein phase behavior in the biopharmaceutical field. However, required data analysis has become a notorious time-consuming task since high-throughput screening approaches were implemented. A variety of computational tools have been developed to support analysis, but these tools primarily use end point visible light images. This study investigates the combined effect of end point and time-dependent image features obtained from cross-polarized and ultraviolet light features, supplementary to visible light, on protein phase diagram image classification. In addition, external validation was performed to evaluate the classification algorithm’s applicability to support protein phase diagram scoring. The predicted protein phase behavior classes were subsequently used to automatically construct multidimensional protein phase diagrams to prevent image information loss without complicating the used image classification algorithm. Combining end point and time-dependent features from 3 light sources resulted in a balanced accuracy of 86.4 ± 4.3%, which is comparable to or better than more complex classifiers reported in literature. External validation resulted in a correct formulation classification rate of 91.7%. Subsequent automated construction of the multidimensional protein phase diagrams, using predicted classes, allowed visualization of details such as crystallization rate and protein phase behavior type coexistence. Less
Human anti-HIV- broadly neutralizing antibodies bNAbs protect against infection in animal models However bNAbs have not been elicited by vaccination in diverse wild-type animals or humans in part because B cells expressing the precursors of these antibodies do not recognize most HIV- envelopes Envs Immunogens have been designed that activate these B cell precursors in vivo but they also activate competing off-target responses Here we report on a complementary approach to expand specific B cells using an anti-idiotypic antibody iv that selects for naive human B cells expressing immunoglobulin light chains with amino acid complementarity determining region s a key ... More
Human anti-HIV-1 broadly neutralizing antibodies (bNAbs) protect against infection in animal models. However, bNAbs have not been elicited by vaccination in diverse wild-type animals or humans, in part because B cells expressing the precursors of these antibodies do not recognize most HIV-1 envelopes (Envs). Immunogens have been designed that activate these B cell precursors in vivo, but they also activate competing off-target responses. Here we report on a complementary approach to expand specific B cells using an anti-idiotypic antibody, iv8, that selects for naive human B cells expressing immunoglobulin light chains with 5–amino acid complementarity determining region 3s, a key feature of anti-CD4 binding site (CD4bs)–specific VRC01-class antibodies. In mice, iv8 induced target cells to expand and mature in the context of a polyclonal immune system and produced serologic responses targeting the CD4bs on Env. In summary, the results demonstrate that an anti-idiotypic antibody can specifically recognize and expand rare B cells that express VRC01-class antibodies against HIV-1. Less
Detection and activation of HIV broadly neutralizing antibody precursor B cells using anti-idiotypes
Many tested vaccines fail to provide protection against disease despite the induction of antibodies that bind the pathogen of interest In light of this there is much interest in rationally designed subunit vaccines that direct the antibody response to protective epitopes Here we produced a panel of anti-idiotype antibodies able to specifically recognize the inferred germline version of the human immunodeficiency virus HIV- broadly neutralizing antibody b iglb We determined the crystal structure of two anti-idiotypes in complex with iglb and used these anti-idiotypes to identify rare naive human B cells expressing B cell receptors with similarity to iglb Immunization ... More
Many tested vaccines fail to provide protection against disease despite the induction of antibodies that bind the pathogen of interest. In light of this, there is much interest in rationally designed subunit vaccines that direct the antibody response to protective epitopes. Here, we produced a panel of anti-idiotype antibodies able to specifically recognize the inferred germline version of the human immunodeficiency virus 1 (HIV-1) broadly neutralizing antibody b12 (iglb12). We determined the crystal structure of two anti-idiotypes in complex with iglb12 and used these anti-idiotypes to identify rare naive human B cells expressing B cell receptors with similarity to iglb12. Immunization with a multimerized version of this anti-idiotype induced the proliferation of transgenic murine B cells expressing the iglb12 heavy chain in vivo, despite the presence of deletion and anergy within this population. Together, our data indicate that anti-idiotypes are a valuable tool for the study and induction of potentially protective antibodies. Less
Balanced fusion and fission are key for the proper function and physiology of mitochondria Remodelling of the mitochondrial inner membrane is mediated by the dynamin-like protein mitochondrial genome maintenance Mgm in fungi or the related protein optic atrophy OPA in animals Mgm is required for the preservation of mitochondrial DNA in yeast whereas mutations in the OPA gene in humans are a common cause of autosomal dominant optic atrophy a genetic disorder that affects the optic nerve Mgm and OPA are present in mitochondria as a membrane-integral long form and a short form that is soluble in the intermembrane space ... More
Balanced fusion and fission are key for the proper function and physiology of mitochondria1,2. Remodelling of the mitochondrial inner membrane is mediated by the dynamin-like protein mitochondrial genome maintenance 1 (Mgm1) in fungi or the related protein optic atrophy 1 (OPA1) in animals3,4,5. Mgm1 is required for the preservation of mitochondrial DNA in yeast6, whereas mutations in the OPA1 gene in humans are a common cause of autosomal dominant optic atrophy—a genetic disorder that affects the optic nerve7,8. Mgm1 and OPA1 are present in mitochondria as a membrane-integral long form and a short form that is soluble in the intermembrane space. Yeast strains that express temperature-sensitive mutants of Mgm19,10 or mammalian cells that lack OPA1 display fragmented mitochondria11,12, which suggests that Mgm1 and OPA1 have an important role in inner-membrane fusion. Consistently, only the mitochondrial outer membrane—not the inner membrane—fuses in the absence of functional Mgm113. Mgm1 and OPA1 have also been shown to maintain proper cristae architecture10,14; for example, OPA1 prevents the release of pro-apoptotic factors by tightening crista junctions15. Finally, the short form of OPA1 localizes to mitochondrial constriction sites, where it presumably promotes mitochondrial fission16. How Mgm1 and OPA1 perform their diverse functions in membrane fusion, scission and cristae organization is at present unknown. Here we present crystal and electron cryo-tomography structures of Mgm1 from Chaetomium thermophilum. Mgm1 consists of a GTPase (G) domain, a bundle signalling element domain, a stalk, and a paddle domain that contains a membrane-binding site. Biochemical and cell-based experiments demonstrate that the Mgm1 stalk mediates the assembly of bent tetramers into helical filaments. Electron cryo-tomography studies of Mgm1-decorated lipid tubes and fluorescence microscopy experiments on reconstituted membrane tubes indicate how the tetramers assemble on positively or negatively curved membranes. Our findings convey how Mgm1 and OPA1 filaments dynamically remodel the mitochondrial inner membrane. Less
The -oxopurine phosphoribosyltransferases PRTs are drug targets for the treatment of parasitic diseases This is due to the fact that parasites are auxotrophic for the -oxopurine bases relying on salvage enzymes for the synthesis of their -oxopurine nucleoside monophosphates In Trypanosoma brucei the parasite that is the aetiological agent for sleeping sickness there are three -oxopurine PRT isoforms Two are specific for hypoxanthine and guanine whilst the third characterized here uses all three naturally occurring bases with similar efficiency Here we have determined crystal structures for TbrHGXPRT in complex with GMP XMP and IMP to investigate the structural basis for ... More
The 6-oxopurine phosphoribosyltransferases (PRTs) are drug targets for the treatment of parasitic diseases. This is due to the fact that parasites are auxotrophic for the 6-oxopurine bases relying on salvage enzymes for the synthesis of their 6-oxopurine nucleoside monophosphates. In Trypanosoma brucei, the parasite that is the aetiological agent for sleeping sickness, there are three 6-oxopurine PRT isoforms. Two are specific for hypoxanthine and guanine, whilst the third, characterized here, uses all three naturally occurring bases with similar efficiency. Here, we have determined crystal structures for TbrHGXPRT in complex with GMP, XMP and IMP to investigate the structural basis for substrate specificity. The results show that Y201 and E208, not commonly observed within the purine binding pocket of 6-oxopurine PRTs, contribute to the versatility of this enzyme. The structures further show that a nearby water can act as an adaptor to facilitate the binding of XMP and GMP. When GMP binds, a water can accept a proton from the 2-amino group but when XMP binds, the equivalent water can donate its proton to the 2-oxo group. However, when IMP is bound, no water molecule is observed at that location. Less
The structure of BgaR a transcriptional regulator of the lactose operon in Clostridium perfringens has been solved by SAD phasing using a mercury derivative BgaR is an exquisite sensor of lactose with a binding affinity in the low-micromolar range This sensor and regulator has been captured bound to lactose and to lactulose as well as in a nominal apo form and was compared with AraC another saccharide-binding transcriptional regulator It is shown that the saccharides bind in the N-terminal region of a jelly-roll fold but that part of the saccharide is exposed to bulk solvent This differs from the classical ... More
The structure of BgaR, a transcriptional regulator of the lactose operon in�Clostridium perfringens, has been solved by SAD phasing using a mercury derivative. BgaR is an exquisite sensor of lactose, with a binding affinity in the low-micromolar range. This sensor and regulator has been captured bound to lactose and to lactulose as well as in a nominal apo form, and was compared with AraC, another saccharide-binding transcriptional regulator. It is shown that the saccharides bind in the N-terminal region of a jelly-roll fold, but that part of the saccharide is exposed to bulk solvent. This differs from the classical AraC saccharide-binding site, which is mostly sequestered from the bulk solvent. The structures of BgaR bound to lactose and to lactulose highlight how specific and nonspecific interactions lead to a higher binding affinity of BgaR for lactose compared with lactulose. Moreover, solving multiple structures of BgaR in different space groups, both bound to saccharides and unbound, verified that the dimer interface along a C-terminal helix is similar to the dimer interface observed in AraC. Less
Designing peptides that fold and assemble in response to metal ions tests our understanding of how peptide folding and metal binding influence one another Here histidine residues are introduced into the hydrophobic core of a coiled-coil trimer generating a peptide that self-assembles upon the addition of metal ions HisAD the resulting peptide is unstructured in the absence of metal and folds selectively to form an -helical construct upon complexation with Cu II and Ni II but not Co II or Zn II The structure and metal-binding ability of HisAD is probed using a combination of circular dichroism CD spectroscopy analytical ... More
Designing peptides that fold and assemble in response to metal ions tests our understanding of how peptide folding and metal binding influence one another. Here, histidine residues are introduced into the hydrophobic core of a coiled-coil trimer, generating a peptide that self-assembles upon the addition of metal ions. HisAD, the resulting peptide, is unstructured in the absence of metal and folds selectively to form an α-helical construct upon complexation with Cu(II) and Ni(II) but not Co(II) or Zn(II). The structure, and metal-binding ability, of HisAD is probed using a combination of circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AUC), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. These show the peptide is trimeric and binds to both Cu(II) and Ni(II) in a 1 : 1 ratio with the histidine residues involved in the metal coordination, as designed. The X-ray crystal structure of the HisAD-Cu(II) complex reveals the trimeric HisAD peptide coordinates three Cu(II) ions; this is the first example of such a structure. Additionally, HisAD demonstrates an unprecedented discrimination between transition metal ions, the basis of which is likely to be related to the stability of the peptide-metal complexes formed. Less
Transient receptor potential TRP channels are polymodal sensory transducers that respond to chemicals temperature mechanical stress and membrane voltage and are involved in vision taste olfaction hearing touch thermal perception and nociception TRP channels are implicated in numerous devastating diseases including various forms of cancer and represent important drug targets The large sizes low expression levels and conformational dynamics of TRP channels make them challenging targets for structural biology Here we present the methodology used in structural studies of TRPV a TRP channel that is highly selective for calcium and mediates Ca uptake in epithelial tissues We provide a protocol ... More
Transient receptor potential (TRP) channels are polymodal sensory transducers that respond to chemicals, temperature, mechanical stress, and membrane voltage and are involved in vision, taste, olfaction, hearing, touch, thermal perception, and nociception. TRP channels are implicated in numerous devastating diseases, including various forms of cancer, and represent important drug targets. The large sizes, low expression levels, and conformational dynamics of TRP channels make them challenging targets for structural biology. Here, we present the methodology used in structural studies of TRPV6, a TRP channel that is highly selective for calcium and mediates Ca2+ uptake in epithelial tissues. We provide a protocol for the expression, purification, and crystallization of TRPV6. Similar approaches can be used to determine crystal structures of other membrane proteins, including different members of the TRP channel family. Less
The universally conserved N -threonylcarbamoyladenosine t A modification of tRNA is essential for translational fidelity In bacteria t A biosynthesis starts with the TsaC TsaC -catalyzed synthesis of the intermediate threonylcarbamoyl adenylate TC AMP followed by transfer of the threonylcarbamoyl TC moiety to adenine- of tRNA by the TC-transfer complex comprised of TsaB TsaD and TsaE subunits and possessing an ATPase activity required for multi-turnover of the t A cycle We report a - crystal structure of the T maritima TC-transfer complex TmTsaB D E bound to Mg -ATP in the ATPase site and substrate analog carboxy-AMP in the TC-transfer ... More
The universally conserved N6-threonylcarbamoyladenosine (t6A) modification of tRNA is essential for translational fidelity. In bacteria, t6A biosynthesis starts with the TsaC/TsaC2-catalyzed synthesis of the intermediate threonylcarbamoyl adenylate (TC–AMP), followed by transfer of the threonylcarbamoyl (TC) moiety to adenine-37 of tRNA by the TC-transfer complex comprised of TsaB, TsaD and TsaE subunits and possessing an ATPase activity required for multi-turnover of the t6A cycle. We report a 2.5-Å crystal structure of the T. maritima TC-transfer complex (TmTsaB2D2E2) bound to Mg2+-ATP in the ATPase site, and substrate analog carboxy-AMP in the TC-transfer site. Site directed mutagenesis results show that residues in the conserved Switch I and Switch II motifs of TsaE mediate the ATP hydrolysis-driven reactivation/reset step of the t6A cycle. Further, SAXS analysis of the TmTsaB2D2-tRNA complex in solution reveals bound tRNA lodged in the TsaE binding cavity, confirming our previous biochemical data. Based on the crystal structure and molecular docking of TC–AMP and adenine-37 in the TC-transfer site, we propose a model for the mechanism of TC transfer by this universal biosynthetic system. Less
Toxin-antitoxin TA gene pairs have been identified in nearly all bacterial genomes sequenced to date and are thought to facilitate persistence and antibiotic tolerance TA loci are classified into various types based upon the characteristics of their antitoxins with those in type II expressing proteic antitoxins Many toxins from type II modules are ribonucleases that maintain a PilT N-terminal PIN domain containing conserved amino acids considered essential for activity The vapBC virulence-associated protein TA system is the largest subfamily in this class and has been linked to pathogenesis of nontypeable Haemophilus influenzae NTHi In this study the crystal structure of ... More
Toxin-antitoxin (TA) gene pairs have been identified in nearly all bacterial genomes sequenced to date and are thought to facilitate persistence and antibiotic tolerance. TA loci are classified into various types based upon the characteristics of their antitoxins, with those in type II expressing proteic antitoxins. Many toxins from type II modules are ribonucleases that maintain a PilT N-terminal (PIN) domain containing conserved amino acids considered essential for activity. The vapBC (virulence-associated protein) TA system is the largest subfamily in this class and has been linked to pathogenesis of nontypeable Haemophilus influenzae (NTHi). In this study, the crystal structure of the VapBC-1 complex from NTHi was determined to 2.20 Å resolution. Based on this structure, aspartate-to-asparagine and glutamate-to-glutamine mutations of four conserved residues in the PIN domain of the VapC-1 toxin were constructed and the effects of the mutations on protein-protein interactions, growth of Escherichia coli, and pathogenesis ex vivo were tested. Finally, a novel model system was designed and utilized that consists of an NTHi ΔvapBC-1 strain complemented in cis with the TA module containing a mutated or wild-type toxin at an ectopic site on the chromosome. This enabled the analysis of the effect of PIN domain toxin mutants in tandem with their wild-type antitoxin under the control of the vapBC-1 native promoter and in single copy. This is the first report of a system facilitating the study of TA mutant operons in the background of NTHi during infections of primary human tissues ex vivo. Less
The HLA-A -restricted decapeptide EAAGIGILTV derived from melanoma antigen recognized by T-cells- MART- protein represents one of the best-studied tumor associated T-cell epitopes but clinical results targeting this peptide have been disappointing This limitation may reflect the dominance of the nonapeptide AAGIGILTV at the melanoma cell surface The decapeptide and nonapeptide are presented in distinct conformations by HLA-A and TCRs from clinically relevant T-cell clones recognize the nonapeptide poorly Here we studied the MEL TCR that potently recognizes the nonapeptide The structure of the MEL -HLA-A -AAGIGILTV complex revealed an induced fit mechanism of antigen recognition involving altered peptide MHC ... More
The HLA-A*02:01-restricted decapeptide EAAGIGILTV, derived from melanoma antigen recognized by T-cells-1 (MART-1) protein, represents one of the best-studied tumor associated T-cell epitopes, but clinical results targeting this peptide have been disappointing. This limitation may reflect the dominance of the nonapeptide, AAGIGILTV, at the melanoma cell surface. The decapeptide and nonapeptide are presented in distinct conformations by HLA-A*02:01 and TCRs from clinically relevant T-cell clones recognize the nonapeptide poorly. Here, we studied the MEL5 TCR that potently recognizes the nonapeptide. The structure of the MEL5-HLA-A*02:01-AAGIGILTV complex revealed an induced fit mechanism of antigen recognition involving altered peptide–MHC anchoring. This “flexing” at the TCR–peptide–MHC interface to accommodate the peptide antigen explains previously observed incongruences in this well-studied system and has important implications for future therapeutic approaches. Finally, this study expands upon the mechanisms by which molecular plasticity can influence antigen recognition by T cells. Less
The human protein tyrosine phosphatase non-receptor type PTPN is a PDZ PSD- Dlg ZO- domain-containing phosphatase with a tumor-suppressive or a tumor-promoting role in many cancers Interestingly the high-risk genital human papillomavirus HPV types and target the PDZ domain of PTPN The presence of a PDZ binding motif PBM on E confers interaction with a number of different cellular PDZ domain-containing proteins and is a marker of high oncogenic potential Here we report the molecular basis of interaction between the PDZ domain of PTPN and the PBM of the HPV E protein We combined biophysical NMR and X-ray experiments to ... More
The human protein tyrosine phosphatase non-receptor type 3 (PTPN3) is a PDZ (PSD-95/Dlg/ZO-1) domain-containing phosphatase with a tumor-suppressive or a tumor-promoting role in many cancers. Interestingly, the high-risk genital human papillomavirus (HPV) types 16 and 18 target the PDZ domain of PTPN3. The presence of a PDZ binding motif (PBM) on E6 confers interaction with a number of different cellular PDZ domain-containing proteins and is a marker of high oncogenic potential. Here, we report the molecular basis of interaction between the PDZ domain of PTPN3 and the PBM of the HPV E6 protein. We combined biophysical, NMR and X-ray experiments to investigate the structural and functional properties of the PDZ domain of PTPN3. We showed that the C-terminal sequences from viral proteins encompassing a PBM interact with PTPN3-PDZ with similar affinities to the endogenous PTPN3 ligand MAP kinase p38γ. PBM binding stabilizes the PDZ domain of PTPN3. We solved the X-ray structure of the PDZ domain of PTPN3 in complex with the PBM of the HPV E6 protein. The crystal structure and the NMR chemical shift mapping of the PTPN3-PDZ/peptide complex allowed us to pinpoint the main structural determinants of recognition of the C-terminal sequence of the E6 protein and the long-range perturbations induced upon PBM binding. Less
The polymerase of negative-stranded RNA viruses consists of the large protein L and the phosphoprotein P the latter serving both as a chaperon and a cofactor for L We mapped within measles virus MeV P the regions responsible for binding and stabilizing L and showed that the coiled-coil multimerization domain MD of P is required for gene expression MeV MD is kinked as a result of the presence of a stammer Both restoration of the heptad regularity and displacement of the stammer strongly decrease or abrogate activity in a minigenome assay By contrast P activity is rather tolerant of substitutions ... More
The polymerase of negative-stranded RNA viruses consists of the large protein (L) and the phosphoprotein (P), the latter serving both as a chaperon and a cofactor for L. We mapped within measles virus (MeV) P the regions responsible for binding and stabilizing L and showed that the coiled-coil multimerization domain (MD) of P is required for gene expression. MeV MD is kinked as a result of the presence of a stammer. Both restoration of the heptad regularity and displacement of the stammer strongly decrease or abrogate activity in a minigenome assay. By contrast, P activity is rather tolerant of substitutions within the stammer. Single substitutions at the “a” or “d” hydrophobic anchor positions with residues of variable hydrophobicity revealed that P functionality requires a narrow range of cohesiveness of its MD. Results collectively indicate that, beyond merely ensuring P oligomerization, the MD finely tunes viral gene expression through its cohesiveness. Less
Melatonin N-acetyl- -methoxytryptamine is a neurohormone that maintains circadian rhythms by synchronization to environmental cues and is involved in diverse physiological processes such as the regulation of blood pressure and core body temperature oncogenesis and immune function Melatonin is formed in the pineal gland in a light-regulated manner by enzymatic conversion from -hydroxytryptamine -HT or serotonin and modulates sleep and wakefulness by activating two high-affinity G-protein-coupled receptors type A MT and type B MT Shift work travel and ubiquitous artificial lighting can disrupt natural circadian rhythms as a result sleep disorders affect a substantial population in modern society and pose ... More
Melatonin (N-acetyl-5-methoxytryptamine) is a neurohormone that maintains circadian rhythms1 by synchronization to environmental cues and is involved in diverse physiological processes2 such as the regulation of blood pressure and core body temperature, oncogenesis, and immune function3. Melatonin is formed in the pineal gland in a light-regulated manner4 by enzymatic conversion from 5-hydroxytryptamine (5-HT or serotonin), and modulates sleep and wakefulness5 by activating two high-affinity G-protein-coupled receptors, type 1A (MT1) and type 1B (MT2)3,6. Shift work, travel, and ubiquitous artificial lighting can disrupt natural circadian rhythms; as a result, sleep disorders affect a substantial population in modern society and pose a considerable economic burden7. Over-the-counter melatonin is widely used to alleviate jet lag and as a safer alternative to benzodiazepines and other sleeping aids8,9, and is one of the most popular supplements in the United States10. Here, we present high-resolution room-temperature X-ray free electron laser (XFEL) structures of MT1 in complex with four agonists: the insomnia drug ramelteon11, two melatonin analogues, and the mixed melatonin–serotonin antidepressant agomelatine12,13. The structure of MT2 is described in an accompanying paper14. Although the MT1 and 5-HT receptors have similar endogenous ligands, and agomelatine acts on both receptors, the receptors differ markedly in the structure and composition of their ligand pockets; in MT1, access to the ligand pocket is tightly sealed from solvent by extracellular loop 2, leaving only a narrow channel between transmembrane helices IV and V that connects it to the lipid bilayer. The binding site is extremely compact, and ligands interact with MT1 mainly by strong aromatic stacking with Phe179 and auxiliary hydrogen bonds with Asn162 and Gln181. Our structures provide an unexpected example of atypical ligand entry for a non-lipid receptor, lay the molecular foundation of ligand recognition by melatonin receptors, and will facilitate the design of future tool compounds and therapeutic agents, while their comparison to 5-HT receptors yields insights into the evolution and polypharmacology of G-protein-coupled receptors. Less
The three members of the endocrine fibroblast growth factor FGF family designated FGF FGF and FGF mediate their pleiotropic cellular effects by binding to and activating binary complexes composed of an FGF receptor FGFR bound to either -Klotho or -Klotho receptors Structural analyses of ligandoccupied Klotho extracellular domains have provided important insights concerning mechanisms underlying the binding specificities of FGF and FGF to -Klotho or -Klotho respectively They have also demonstrated that Klotho proteins function as primary high-affinity receptors while FGFRs function as the catalytic subunits that mediate intracellular signaling Here we describe the crystal structure the C-terminal tail of ... More
The three members of the endocrine fibroblast growth factor (FGF) family designated FGF19, FGF21, and FGF23 mediate their pleiotropic cellular effects by binding to and activating binary complexes composed of an FGF receptor (FGFR) bound to either α-Klotho or β-Klotho receptors. Structural analyses of ligandoccupied Klotho extracellular domains have provided important insights concerning mechanisms underlying the binding specificities of FGF21 and FGF23 to β-Klotho or α-Klotho, respectively. They have also demonstrated that Klotho proteins function as primary high-affinity receptors while FGFRs function as the catalytic subunits that mediate intracellular signaling. Here we describe the crystal structure the C-terminal tail of FGF19 (FGF19CT) bound to sKLB and demonstrate that FGF19CT and FGF21CT bind to the same binding site on sKLB, via a multiturn D-P motif to site 1 and via a SP-S motif to the pseudoglycoside hydrolase region (site 2). Binding affinities to sKLB and cellular stimulatory activities of FGF19CT, FGF21CT, and a variety of chimeric mutants to cells expressing β-Klotho together with FGFR1c or FGFR4 were also analyzed. These experiments as well as detailed comparison of the structures of free and ligand-occupied sKLB to the structure of ligandoccupied sKLA reveal a general mechanism for recognition of endocrine FGFs by Klotho proteins and regulatory interactions with FGFRs that control their pleiotropic cellular responses. Less
The human MT and MT melatonin receptors are G protein-coupled receptors GPCRs involved in the regulation of circadian rhythm and sleep patterns Drug development efforts target both receptors for treatment of insomnia circadian rhythm and mood disorders and cancer while MT has also been implicated in type diabetes T D Here we report the X-ray Free Electron Laser XFEL structures of the human MT receptor in complex with agonists -phenylmelatonin -pmt and ramelteon at resolutions of and respectively along with two structures of function-related mutants H A superscripts represent the Ballesteros-Weinstein residue numbering nomenclature and N D obtained in complex ... More
The human MT11 and MT22 melatonin receptors are G protein-coupled receptors (GPCRs) involved in the regulation of circadian rhythm and sleep patterns3. Drug development efforts target both receptors for treatment of insomnia, circadian rhythm and mood disorders, and cancer3, while MT2 has also been implicated in type 2 diabetes (T2D)4,5. Here we report the X-ray Free Electron Laser (XFEL) structures of the human MT2 receptor in complex with agonists 2-phenylmelatonin (2-pmt) and ramelteon6 at resolutions of 2.8 Å and 3.3 Å, respectively, along with two structures of function-related mutants, H2085.46A (superscripts represent the Ballesteros-Weinstein residue numbering nomenclature7) and N862.50D, obtained in complex with 2-pmt. Comparison of the MT2 structures with MT18 reveals that, despite the fact that the orthosteric ligand-binding site residues are conserved, there are notable conformational variations as well as differences in [3H]-melatonin dissociation kinetics that provide new insights into the selectivity between melatonin receptor subtypes. In addition to the membrane-buried lateral ligand entry channel that is also observed in MT1, the MT2 structures reveal a narrow opening towards the solvent in the extracellular part of the receptor. We provide functional and kinetic data supporting a prominent role for the intramembrane ligand entry in both receptors, while simultaneously suggesting the possibility of an extracellular entry path in MT2. Our findings contribute to a molecular understanding of melatonin receptor subtype selectivity and ligand access modes, which are essential for the design of highly selective melatonin tool compounds and therapeutic agents. Less
The three members of the endocrine fibroblast growth factor FGF family designated FGF FGF and FGF mediate their pleiotropic cellular effects by binding to and activating binary complexes composed of an FGF receptor FGFR bound to either -Klotho or -Klotho receptors Structural analyses of ligand-occupied Klotho extracellular domains have provided important insights concerning mechanisms underlying the binding specificities of FGF and FGF to -Klotho or -Klotho respectively They have also demonstrated that Klotho proteins function as primary high-affinity receptors while FGFRs function as the catalytic subunits that mediate intracellular signaling Here we describe the crystal structure the C-terminal tail of ... More
The three members of the endocrine fibroblast growth factor (FGF) family designated FGF19, FGF21, and FGF23 mediate their pleiotropic cellular effects by binding to and activating binary complexes composed of an FGF receptor (FGFR) bound to either α-Klotho or β-Klotho receptors. Structural analyses of ligand-occupied Klotho extracellular domains have provided important insights concerning mechanisms underlying the binding specificities of FGF21 and FGF23 to β-Klotho or α-Klotho, respectively. They have also demonstrated that Klotho proteins function as primary high-affinity receptors while FGFRs function as the catalytic subunits that mediate intracellular signaling. Here we describe the crystal structure the C-terminal tail of FGF19 (FGF19CT) bound to sKLB and demonstrate that FGF19CT and FGF21CT bind to the same binding site on sKLB, via a multiturn D-P motif to site 1 and via a S-P-S motif to the pseudoglycoside hydrolase region (site 2). Binding affinities to sKLB and cellular stimulatory activities of FGF19CT, FGF21CT, and a variety of chimeric mutants to cells expressing β-Klotho together with FGFR1c or FGFR4 were also analyzed. These experiments as well as detailed comparison of the structures of free and ligand-occupied sKLB to the structure of ligand-occupied sKLA reveal a general mechanism for recognition of endocrine FGFs by Klotho proteins and regulatory interactions with FGFRs that control their pleiotropic cellular responses. Less
Many long-standing image processing problems in applied science domains are finding solutions through the application of deep learning approaches to image processing Here we present one such application the case of classifying images of protein crystallisation droplets The Collaborative Crystallisation Centre in Melbourne Australia is a medium throughput service facility that produces between five and twenty thousand images per day This submission outlines a reliable and robust machine learning pipeline that autonomously classifies these images using CSIRO s high-performance computing facilities Our pipeline achieves improved accuracies over existing implementations and delivers these results in real time We discuss the specific ... More
Many long-standing image processing problems in applied science domains are finding solutions through the application of deep learning approaches to image processing. Here we present one such application; the case of classifying images of protein crystallisation droplets. The Collaborative Crystallisation Centre in Melbourne, Australia is a medium throughput service facility that produces between five and twenty thousand images per day. This submission outlines a reliable and robust machine learning pipeline that autonomously classifies these images using CSIRO’s high-performance computing facilities. Our pipeline achieves improved accuracies over existing implementations and delivers these results in real time. We discuss the specific tools and techniques used to construct the pipeline, as well as the methodologies for testing and validating externally developed classification models. Less
Rhodopsins are the most universal biological light-energy transducers and abundant phototrophic mechanisms that evolved on Earth and have a remarkable diversity and potential for biotechnological applications Recently the first sodium-pumping rhodopsin KR from Krokinobacter eikastus was discovered and characterized However the existing structures of KR are contradictory and the mechanism of Na pumping is not yet understood Here we present a structure of the cationic non H light-driven pump at physiological pH in its pentameric form We also present atomic structures and functional data on the KR and its mutants including potassium pumps which show that oligomerization of the microbial ... More
Rhodopsins are the most universal biological light-energy transducers and abundant phototrophic mechanisms that evolved on Earth and have a remarkable diversity and potential for biotechnological applications. Recently, the first sodium-pumping rhodopsin KR2 from Krokinobacter eikastus was discovered and characterized. However, the existing structures of KR2 are contradictory, and the mechanism of Na+ pumping is not yet understood. Here, we present a structure of the cationic (non H+) light-driven pump at physiological pH in its pentameric form. We also present 13 atomic structures and functional data on the KR2 and its mutants, including potassium pumps, which show that oligomerization of the microbial rhodopsin is obligatory for its biological function. The studies reveal the structure of KR2 at nonphysiological low pH where it acts as a proton pump. The structure provides new insights into the mechanisms of microbial rhodopsins and opens the way to a rational design of novel cation pumps for optogenetics. Less
Phox homology PX domains are membrane interacting domains that bind to phosphatidylinositol phospholipids or phosphoinositides markers of organelle identity in the endocytic system Although many PX domains bind the canonical endosome-enriched lipid PtdIns P others interact with alternative phosphoinositides and a precise understanding of how these specificities arise has remained elusive Here we systematically screen all human PX domains for their phospholipid preferences using liposome binding assays biolayer interferometry and isothermal titration calorimetry These analyses define four distinct classes of human PX domains that either bind specifically to PtdIns P non-specifically to various di- and tri-phosphorylated phosphoinositides bind both PtdIns ... More
Phox homology (PX) domains are membrane interacting domains that bind to phosphatidylinositol phospholipids or phosphoinositides, markers of organelle identity in the endocytic system. Although many PX domains bind the canonical endosome-enriched lipid PtdIns3P, others interact with alternative phosphoinositides, and a precise understanding of how these specificities arise has remained elusive. Here we systematically screen all human PX domains for their phospholipid preferences using liposome binding assays, biolayer interferometry and isothermal titration calorimetry. These analyses define four distinct classes of human PX domains that either bind specifically to PtdIns3P, non-specifically to various di- and tri-phosphorylated phosphoinositides, bind both PtdIns3P and other phosphoinositides, or associate with none of the lipids tested. A comprehensive evaluation of PX domain structures reveals two distinct binding sites that explain these specificities, providing a basis for defining and predicting the functional membrane interactions of the entire PX domain protein family. Less
The hyperthermophilic crenarchaeon Ignicoccus hospitalis KIN I possesses at least putative genes encoding enzymes that belong to the -hydrolase superfamily One of those genes the metallo-hydrolase-encoding igni was cloned and heterologously expressed in Pichia pastoris The enzyme produced was purified in its catalytically active form The recombinant enzyme was successfully crystallized and the crystal diffracted to a resolution of The crystal belonged to space group R with unit-cell parameters a b c It is suggested that it contains one monomer of Igni within the asymmetric unit
Inosine- -monophosphate dehydrogenase IMPDH is an essential enzyme in many bacterial pathogens and is considered as a potential drug target for the development of new antibacterial agents Our recent work has revealed the crucial role of one of the two structural domains i e Bateman domain in the regulation of the quaternary structure and enzymatic activity of bacterial IMPDHs Thus we have screened chemical libraries to search for compounds targeting the Bateman domain and identified first in-class allosteric inhibitors of a bacterial IMPDH These inhibitors were shown to counteract the activation by the natural positive effector MgATP and to block ... More
Inosine-5‘-monophosphate dehydrogenase (IMPDH) is an essential enzyme in many bacterial pathogens and is considered as a potential drug target for the development of new antibacterial agents. Our recent work has revealed the crucial role of one of the two structural domains (i.e. Bateman domain) in the regulation of the quaternary structure and enzymatic activity of bacterial IMPDHs. Thus, we have screened chemical libraries to search for compounds targeting the Bateman domain and identified first in-class allosteric inhibitors of a bacterial IMPDH. These inhibitors were shown to counteract the activation by the natural positive effector, MgATP, and to block the enzyme in its apo conformation (low affinity for IMP). Our structural studies demonstrate the versatility of the Bateman domain to accommodate totally unrelated chemical scaffolds and pave the way for the development of allosteric inhibitors, an avenue little explored until now. Less
Poor solubility is a common challenge encountered during the development of high concentration monoclonal antibody mAb formulations but there are currently no methods that can provide predictive information on high-concentration behavior of mAbs in early discovery We explored the utility of methodologies used for determining extrapolated solubility as a way to rank-order mAbs based on their relative solubility properties We devised two approaches to accomplish this vapor diffusion technique utilized in traditional protein crystallization practice and polyethylene glycol PEG -induced precipitation and quantitation by turbidity Using a variety of in-house mAbs with known high-concentration behavior we demonstrated that both approaches ... More
Poor solubility is a common challenge encountered during the development of high concentration monoclonal antibody (mAb) formulations, but there are currently no methods that can provide predictive information on high-concentration behavior of mAbs in early discovery. We explored the utility of methodologies used for determining extrapolated solubility as a way to rank-order mAbs based on their relative solubility properties. We devised two approaches to accomplish this: 1) vapor diffusion technique utilized in traditional protein crystallization practice, and 2) polyethylene glycol (PEG)-induced precipitation and quantitation by turbidity. Using a variety of in-house mAbs with known high-concentration behavior, we demonstrated that both approaches exhibited reliable predictability of the relative solubility properties of these mAbs. Optimizing the latter approach, we developed a format that is capable of screening a large panel of mAbs in multiple pH and buffer conditions. This simple, material-saving, high-throughput approach enables the selection of superior molecules and optimal formulation conditions much earlier in the antibody discovery process, prior to time-consuming and material intensive high-concentration studies. Less
HheG from Ilumatobacter coccineus is a halohydrin dehalogenase with synthetically useful activity in the ring opening of cyclic epoxides with various small anionic nucleophiles This enzyme provides access to chiral -substituted alcohols that serve as building blocks in the pharmaceutical industry Wild-type HheG suffers from low thermostability which poses a significant drawback for potential applications In an attempt to thermostabilize HheG by protein engineering several single mutants at position were identified which displayed up to C increased apparent melting temperatures and up to three-fold higher activity Aromatic amino acids at position resulted even in a slightly higher enantioselectivity Crystal structures ... More
HheG from Ilumatobacter coccineus is a halohydrin dehalogenase with synthetically useful activity in the ring opening of cyclic epoxides with various small anionic nucleophiles. This enzyme provides access to chiral β-substituted alcohols that serve as building blocks in the pharmaceutical industry. Wild-type HheG suffers from low thermostability, which poses a significant drawback for potential applications. In an attempt to thermostabilize HheG by protein engineering, several single mutants at position 123 were identified which displayed up to 14 °C increased apparent melting temperatures and up to three-fold higher activity. Aromatic amino acids at position 123 resulted even in a slightly higher enantioselectivity. Crystal structures of variants T123W and T123G revealed a flexible loop opposite to amino acid 123. In variant T123G, this loop adopted two different positions resulting in an open or partially closed active site. Classical molecular dynamics simulations confirmed a high mobility of this loop. Moreover, in variant T123G this loop adopted a position much closer to residue 123 resulting in denser packing and increased buried surface area. Our results indicate an important role for position 123 in HheG and give first structural and mechanistic insight into the thermostabilizing effect of mutations T123W and T123G. Less
NEMO is an essential component in the activation of the canonical NF- B pathway and exerts its function by recruiting the I B kinases IKK to the IKK complex Inhibition of the NEMO IKKs interaction is an attractive therapeutic paradigm for diseases related to NF- B mis-regulation but a difficult endeavor because of the extensive protein-protein interface Here we report the high-resolution structure of the unbound IKK -binding domain of NEMO that will greatly facilitate the design of NEMO IKK inhibitors The structures of unbound NEMO show a closed conformation that partially occludes the three binding hot-spots and suggest a ... More
NEMO is an essential component in the activation of the canonical NF-?B pathway and exerts its function by recruiting the I?B kinases (IKK) to the IKK complex. Inhibition of the NEMO/IKKs interaction is an attractive therapeutic paradigm for diseases related to NF-?B mis-regulation, but a difficult endeavor because of the extensive protein-protein interface. Here we report the high-resolution structure of the unbound IKK�-binding domain of NEMO that will greatly facilitate the design of NEMO/IKK inhibitors. The structures of unbound NEMO show a closed conformation that partially occludes the three binding hot-spots and suggest a facile transition to an open state that can accommodate ligand binding. By fusing coiled-coil adaptors to the IKK�-binding domain of NEMO, we succeeded in creating a protein with improved solution behavior, IKK�-binding affinity and crystallization compatibility, which will enable the structural characterization of new NEMO/inhibitor complexes. Less
Suppressor of copper sensitivity protein C from Proteus mirabilis PmScsC is a homotrimeric disulfide isomerase that plays a role in copper tolerance which is a key virulence trait of this uropathogen Each protomer of the enzyme has an N-terminal trimerization stem residues containing a flexible linker residues connected to a thioredoxin-fold-containing catalytic domain residues Here two PmScsC variants PmScsC N and PmScsC Linker are characterized PmScsC N is an N-terminally truncated form of the protomer with two helices of the trimerization stem removed generating a protein with dithiol oxidase rather than disulfide isomerase activity The crystal structure of PmScsC N ... More
Suppressor of copper sensitivity protein C from Proteus mirabilis (PmScsC) is a homotrimeric disulfide isomerase that plays a role in copper tolerance, which is a key virulence trait of this uropathogen. Each protomer of the enzyme has an N-terminal trimerization stem (59 residues) containing a flexible linker (11 residues) connected to a thioredoxin-fold-containing catalytic domain (163 residues). Here, two PmScsC variants, PmScsC?N and PmScsC?Linker, are characterized. PmScsC?N is an N-terminally truncated form of the protomer with two helices of the trimerization stem removed, generating a protein with dithiol oxidase rather than disulfide isomerase activity. The crystal structure of PmScsC?N reported here reveals, as expected, a monomer that is structurally similar to the catalytic domain of native PmScsC. The second variant, PmScsC?Linker, was designed to remove the 11-amino-acid linker, and it is shown that it generates a protein that has neither disulfide isomerase nor dithiol oxidase activity. The crystal structure of PmScsC?Linker reveals a trimeric arrangement, with the catalytic domains packed together very closely. Small-angle X-ray scattering analysis found that native PmScsC is predominantly trimeric in solution even at low concentrations, whereas PmScsC?Linker exists as an equilibrium between monomeric, dimeric and trimeric states, with the monomeric form dominating at low concentrations. These findings increase the understanding of disulfide isomerase activity, showing how (i) oligomerization, (ii) the spacing between and (iii) the dynamic motion of catalytic domains in PmScsC all contribute to its native function. Less
Upon triggering by their inducer signal transduction ATPases with numerous domains STANDs initially in monomeric resting forms multimerize into large hubs that activate target macromolecules This process requires conversion of the STAND conserved core the NOD from a closed form encasing an ADP molecule to an ATP-bound open form prone to multimerize In the absence of inducer autoinhibitory interactions maintain the NOD closed In particular in resting STAND proteins with an LRR- or WD -type sensor domain the latter establishes interactions with the NOD that are disrupted in the multimerization-competent forms Here we solved the first crystal structure of a ... More
Upon triggering by their inducer, signal transduction ATPases with numerous domains (STANDs), initially in monomeric resting forms, multimerize into large hubs that activate target macromolecules. This process requires conversion of the STAND conserved core (the NOD) from a closed form encasing an ADP molecule to an ATP-bound open form prone to multimerize. In the absence of inducer, autoinhibitory interactions maintain the NOD closed. In particular, in resting STAND proteins with an LRR- or WD40-type sensor domain, the latter establishes interactions with the NOD that are disrupted in the multimerization-competent forms. Here, we solved the first crystal structure of a STAND with a tetratricopeptide repeat sensor domain, PH0952 from Pyrococcus horikoshii, revealing analogous NOD-sensor contacts. We use this structural information to experimentally demonstrate that similar interactions also exist in a PH0952 homolog, the MalT STAND archetype, and actually contribute to the MalT autoinhibition in vitro and in vivo. We propose that STAND activation occurs by stepwise release of autoinhibitory contacts coupled to the unmasking of inducer-binding determinants. The MalT example suggests that STAND weak autoinhibitory interactions could assist the binding of inhibitory proteins by placing in register inhibitor recognition elements born by two domains. Less
Sodium ions are endogenous allosteric modulators of many G protein-coupled receptors GPCRs Mutation of key residues in the sodium binding motif causes a striking effect on G protein signaling We report the crystal structures of agonist complexes for two variants in the first sodium coordination shell of the human A A adenosine receptor A AAR D N and S A Both structures present an overall active-like conformation however the variants show key changes in the activation motif NPxxY Changes in the hydrogen bonding network in this microswitch suggest a possible mechanism for modified G protein signaling and enhanced thermal stability ... More
Sodium ions are endogenous allosteric modulators of many G protein-coupled receptors (GPCRs). Mutation of key residues in the sodium binding motif causes a striking effect on G protein signaling. We report the crystal structures of agonist complexes for two variants in the first sodium coordination shell of the human A2A adenosine receptor (A2AAR), D522.50N and S913.39A. Both structures present an overall active-like conformation; however, the variants show key changes in the activation motif NPxxY. Changes in the hydrogen bonding network in this microswitch suggest a possible mechanism for modified G protein signaling and enhanced thermal stability. These structures, signaling data, and thermal stability analysis with a panel of pharmacological ligands provide a basis for understanding the role of the sodium-coordinating residues on stability and G protein signaling. Utilizing the D2.50N variant is a promising method for stabilizing class A GPCRs to accelerate structural efforts and drug discovery. Less
Nramp family transporters expressed in organisms from bacteria to humans enable uptake of essential divalent transition metals via an alternating-access mechanism that also involves proton transport We present high-resolution structures of Deinococcus radiodurans Dra Nramp in multiple conformations to provide a thorough description of the Nramp transport cycle by identifying the key intramolecular rearrangements and changes to the metal coordination sphere Strikingly while metal transport requires cycling from outward- to inward-open states efficient proton transport still occurs in outward-locked but not inward-locked DraNramp We propose a model in which metal and proton enter the transporter via the same external pathway ... More
Nramp family transporters—expressed in organisms from bacteria to humans—enable uptake of essential divalent transition metals via an alternating-access mechanism that also involves proton transport. We present high-resolution structures of Deinococcus radiodurans (Dra)Nramp in multiple conformations to provide a thorough description of the Nramp transport cycle by identifying the key intramolecular rearrangements and changes to the metal coordination sphere. Strikingly, while metal transport requires cycling from outward- to inward-open states, efficient proton transport still occurs in outward-locked (but not inward-locked) DraNramp. We propose a model in which metal and proton enter the transporter via the same external pathway to the binding site, but follow separate routes to the cytoplasm, which could facilitate the co-transport of two cationic species. Our results illustrate the flexibility of the LeuT fold to support a broad range of substrate transport and conformational change mechanisms. Less
Many drugs target the serotonin A receptor -HT AR including second-generation antipsychotics that also target the dopamine D receptor D R These drugs often produce severe side effects due to non-selective binding to other aminergic receptors Here we report the structures of human -HT AR in complex with the second-generation antipsychotics risperidone and zotepine These antipsychotics effectively stabilize the inactive conformation by forming direct contacts with the residues at the bottom of the ligand-binding pocket the movements of which are important for receptor activation -HT AR is structurally similar to -HT CR but possesses a unique side-extended cavity near the ... More
Many drugs target the serotonin 2A receptor (5-HT2AR), including second-generation antipsychotics that also target the dopamine D2 receptor (D2R). These drugs often produce severe side effects due to non-selective binding to other aminergic receptors. Here, we report the structures of human 5-HT2AR in complex with the second-generation antipsychotics risperidone and zotepine. These antipsychotics effectively stabilize the inactive conformation by forming direct contacts with the residues at the bottom of the ligand-binding pocket, the movements of which are important for receptor activation. 5-HT2AR is structurally similar to 5-HT2CR but possesses a unique side-extended cavity near the orthosteric binding site. A docking study and mutagenic studies suggest that a highly 5-HT2AR-selective antagonist binds the side-extended cavity. The conformation of the ligand-binding pocket in 5-HT2AR significantly differs around extracellular loops 1 and 2 from that in D2R. These findings are beneficial for the rational design of safer antipsychotics and 5-HT2AR-selective drugs. Less
Purple acid phosphatases PAPs are members of the large family of metallohydrolases a group of enzymes that perform a wide range of biological functions while employing a highly conserved catalytic mechanism PAPs are found in plants animals and fungi in humans they play an important role in bone turnover and are thus of interest for developing treatments for osteoporosis The majority of metallohydrolases use a metal-bound hydroxide to initiate catalysis which leads to the formation of a proposed five-coordinate oxyphosphorane species in the transition state In this work we crystallized PAP from red kidney beans rkbPAP in the presence of ... More
Purple acid phosphatases (PAPs) are members of the large family of metallohydrolases, a group of enzymes that perform a wide range of biological functions, while employing a highly conserved catalytic mechanism. PAPs are found in plants, animals and fungi; in humans they play an important role in bone turnover and are thus of interest for developing treatments for osteoporosis. The majority of metallohydrolases use a metal-bound hydroxide to initiate catalysis, which leads to the formation of a proposed five-coordinate oxyphosphorane species in the transition state. In this work, we crystallized PAP from red kidney beans (rkbPAP) in the presence of both adenosine and vanadate. The in crystallo-formed vanadate analogue of ADP provides detailed insight into the binding mode of a PAP substrate, captured in a structure that mimics the putative fivecoordinate transition state. Our observations not only provide unprecedented insight into the mechanism of metallohydrolases, but might also guide the structure-based design of inhibitors for application in the treatment of several human illnesses. Less
Advances in X-ray crystallography have streamlined the process of determining high-resolution three-dimensional macromolecular structures However a rate-limiting step in this process continues to be the generation of crystals that are of sufficient size and quality for subsequent diffraction experiments Here iterative screen optimization ISO a highly automated process in which the precipitant concentrations of each condition in a crystallization screen are modified based on the results of a prior crystallization experiment is described After designing a novel high-throughput crystallization screen to take full advantage of this method the value of ISO is demonstrated by using it to successfully crystallize a ... More
Advances in X-ray crystallography have streamlined the process of determining high-resolution three-dimensional macromolecular structures. However, a rate-limiting step in this process continues to be the generation of crystals that are of sufficient size and quality for subsequent diffraction experiments. Here, iterative screen optimization (ISO), a highly automated process in which the precipitant concentrations of each condition in a crystallization screen are modified based on the results of a prior crystallization experiment, is described. After designing a novel high-throughput crystallization screen to take full advantage of this method, the value of ISO is demonstrated by using it to successfully crystallize a panel of six diverse proteins. The results suggest that ISO is an effective method to obtain macromolecular crystals, particularly for proteins that crystallize under a narrow range of precipitant concentrations. Less
Knowledge of protein behavior stability during freeze thaw FT operations is essential for storage and production processes in the biopharmaceutical industry FT stress involves freeze concentration cold denaturation and ice crystals formation which can result in protein aggregation Therefore it is important to understand the ongoing FT processes and the influence of different solution parameters In order to evaluate the ongoing processes during FT up to C phase diagrams with lysozyme from chicken egg white and sodium chloride were generated Thereby three different buffer systems with varying buffer substances and ionic strengths at pH and pH were investigated As indicators ... More
Knowledge of protein behavior/stability during freeze/thaw (FT) operations is essential for storage and production processes in the biopharmaceutical industry. FT stress involves freeze concentration, cold denaturation, and ice crystals formation which can result in protein aggregation. Therefore, it is important to understand the ongoing FT processes, and the influence of different solution parameters. In order to evaluate the ongoing processes during FT (up to −80°C), phase diagrams with lysozyme from chicken egg white and sodium chloride were generated. Thereby, three different buffer systems with varying buffer substances and ionic strengths at pH 3 and pH 5 were investigated. As indicators for the ongoing FT processes, the phase behavior, crystal morphology and solubility were used. An increased number of cycles led, for example, to the formation of micro crystals, sea urchin crystals – indicating LLPS and/or high supersaturation – and precipitate. Furthermore, the buffer substances had a more distinct influence on the phase behavior and morphology compared to the ionic strength differences. The solubility line itself was only shifted when distinct changes in the phase behavior could be observed. In summary, a tool was developed for using the phase behavior and especially the crystal morphology as indicator for underlying processes during FT operations. Less
Mycobacterium tuberculosis Mtb the main causative agent of tuberculosis TB is naturally resistant to -lactam antibiotics due to the production of the extended spectrum -lactamase BlaC -Lactam -lactamase inhibitor combination therapies can circumvent the BlaC-mediated resistance of Mtb and are promising treatment options against TB However still little is known of the exact mechanism of BlaC inhibition by the -lactamase inhibitors currently approved for clinical use clavulanic acid sulbactam tazobactam and avibactam Here we present the X-ray diffraction crystal structures of the acyl-enzyme adducts of wild-type BlaC with the four inhibitors The Da adduct derived from clavulanate and the trans-enamine ... More
Mycobacterium tuberculosis (Mtb), the main causative agent of tuberculosis (TB), is naturally resistant to β-lactam antibiotics due to the production of the extended spectrum β-lactamase BlaC. β-Lactam/β-lactamase inhibitor combination therapies can circumvent the BlaC-mediated resistance of Mtb and are promising treatment options against TB. However, still little is known of the exact mechanism of BlaC inhibition by the β-lactamase inhibitors currently approved for clinical use, clavulanic acid, sulbactam, tazobactam, and avibactam. Here, we present the X-ray diffraction crystal structures of the acyl-enzyme adducts of wild-type BlaC with the four inhibitors. The +70 Da adduct derived from clavulanate and the trans-enamine acylation adducts of sulbactam and tazobactam are reported. BlaC in complex with avibactam revealed two inhibitor conformations. Preacylation binding could not be observed because inhibitor binding was not detected in BlaC variants carrying a substitution of the active site serine 70 to either alanine or cysteine, by crystallography, ITC or NMR. These results suggest that the catalytic serine 70 is necessary not only for enzyme acylation but also for increasing BlaC affinity for inhibitors in the preacylation state. The structure of BlaC with the serine to cysteine mutation showed a covalent linkage of the cysteine 70 Sγ atom to the nearby amino group of lysine 73. The differences of adduct conformations between BlaC and other β-lactamases are discussed. Less
Rab proteins belong to the ras superfamily of small GTPases and play important roles in the regulation of vesicular transport within the eukaryaotic cell The central mechanistic hallmark of all GTPases is their ability to bind the nucleotide GTP and to hydrolyze it to GDP Dependent on the nucleotide state small GTPases can take specific conformations which serve different roles GTP-bound small GTPases can interact with so called effector proteins and thereby actively mediate a specific function whereas in their GDP-bound state they are inactive Due to their ability to cycle between an active and inactive state small GTPases are ... More
Rab proteins belong to the ras superfamily of small GTPases and play important roles in the regulation of vesicular transport within the eukaryaotic cell. The central mechanistic hallmark of all GTPases is their ability to bind the nucleotide GTP and to hydrolyze it to GDP. Dependent on the nucleotide state small GTPases can take specific conformations which serve different roles: GTP-bound small GTPases can interact with so called effector proteins and thereby actively mediate a specific function, whereas in their GDP-bound state, they are inactive. Due to their ability to cycle between an active and inactive state, small GTPases are often called „molecular switches“. In order to control their activity in a spatially and temporally exact manner, additional proteins are necessary: guanine nucleotide exchange factors (short: GEFs) and GTPase activating proteins (short: GAPs). While GEFs facilitate the exchange of GDP for GTP and thereby activate the associated GTPase, GAPs stimulate the hydrolysis of GTP to GDP and thereby inactivate the GTPase. As for any GTPase the knowledge of the regulatory context of a Rab protein is thus crucial to fully understand how it exerts its function. However, although over 60 human Rab proteins have been identified so far, comparatively little is known about the regulation of Rab proteins by their GEFs, since only few Rab-GEFs have been identified. The main reason for this is that the identification of Rab-GEFs by in silico approaches which search for cognate genes has been hampered by the huge diversity of structures and sequences of Rab-GEFs. In order to facilitate the identification of new GEFs for Rab proteins this dissertation presents a protocol that has been adapted and optimized to perform specific pull-down experiments for GEFs. It exploits the enzymatic mechanism of GEFs by stabilizing an intermediate, nucleotide-free state of GTPases in which they have a very high affinity towards their GEF, favoring their enrichment in the pull-down experiments. Evidence of the protocol’s applicability is given within this dissertation using the known Rab/GEFcouple Sec4/Sec2 as an example. To correlate experimental observations of G-proteins with a defined nucleotide state in vitro, one can use non-hydrolyzable nucleotide analogs such as GppNHp. In vivo, however, these analogs are prone to be exchanged with intracellular nucleotides. Alternative strategies for creating constitutive active or inactive G-proteins are often of dubious efficiency or charged with artefacts. In order to gain definitive control over a G-protein’s nucleotide state, the research group of Prof. Roger Goody has developed a new kind of nucleotide analogs which can be covalently linked to the G-protein. The covalent bond prevents nucleotide exchange and ensures a defined nucleotide state. Based on x-ray crystallographic analyses it is shown within this thesis that the modification of the small GTPase Ypt7 with the GTP variant of this new kind of nucleotides does not disturb the structure of Ypt7. Less
VMXi is a new high-flux microfocus macromolecular crystallography beamline at Diamond Light Source The beamline dedicated to fully automated and fully remote data collection of macromolecular crystals in situ allows rapid screening of hundreds of crystallization plates from multiple user groups Its main purpose is to give fast feedback at the complex stages of crystallization and crystal optimization but it also enables data collection of small and delicate samples that are particularly difficult to harvest using conventional cryo-methods crystals grown in the lipidic cubic phase and allows for multi-crystal data collections in drug discovery programs The beamline is equipped with ... More
VMXi is a new high-flux microfocus macromolecular crystallography beamline at Diamond Light Source. The beamline, dedicated to fully automated and fully remote data collection of macromolecular crystals in situ, allows rapid screening of hundreds of crystallization plates from multiple user groups. Its main purpose is to give fast feedback at the complex stages of crystallization and crystal optimization, but it also enables data collection of small and delicate samples that are particularly difficult to harvest using conventional cryo-methods, crystals grown in the lipidic cubic phase, and allows for multi-crystal data collections in drug discovery programs. The beamline is equipped with two monochromators: one with a narrow band-pass and fine energy resolution (optimal for regular oscillation experiments), and one with a wide band-pass and a high photon flux (optimal for fast screening). The beamline has a state-of-the-art detector and custom goniometry that allows fast data collection. This paper describes the beamline design, current status and future plans. Less
With the advent of X-Ray free electron lasers FELs the field of serial femtosecond crystallography SFX was borne allowing a stream of nanocrystals to be measured individually and diffraction data to be collected and merged to form a complete crystallographic data set This allows submicron to micron crystals to be utilized in an experiment when they were once at best only an intermediate result towards larger usable crystals SFX and its variants have opened new possibilities in structural biology including studies with increased temporal resolution extending to systems with irreversible reactions and minimizing artifacts related to local radiation damage Perhaps ... More
With the advent of X-Ray free electron lasers (FELs), the field of serial femtosecond crystallography (SFX) was borne, allowing a stream of nanocrystals to be measured individually and diffraction data to be collected and merged to form a complete crystallographic data set. This allows submicron to micron crystals to be utilized in an experiment when they were once, at best, only an intermediate result towards larger, usable crystals. SFX and its variants have opened new possibilities in structural biology, including studies with increased temporal resolution, extending to systems with irreversible reactions, and minimizing artifacts related to local radiation damage. Perhaps the most profound aspect of this newly established field is that �molecular movies,� in which the dynamics and kinetics of biomolecules are studied as a function of time, are now an attainable commodity for a broad variety of systems, as discussed in Chaps. 11 and 12. However, one of the historic challenges in crystallography has always been crystallogenesis and this is no exception when preparing samples for serial crystallography methods. In the following chapter, we focus on some of the specific characteristics and considerations inherent in preparing a suitable sample for successful serial crystallographic approaches. Less
Binding between DIP and Dpr neuronal-recognition proteins has been proposed to regulate synaptic connections between lamina and medulla neurons in the Drosophila visual system Each lamina neuron was previously shown to express many Dprs Here we demonstrate by contrast that their synaptic partners typically express one or two DIPs with binding specificities matched to the lamina neuron-expressed Dprs A deeper understanding of the molecular logic of DIP Dpr interaction requires quantitative studies on the properties of these proteins We thus generated a quantitative affinity-based DIP Dpr interactome for all DIP Dpr protein family members This revealed a broad range of ... More
Binding between DIP and Dpr neuronal-recognition proteins has been proposed to regulate synaptic connections between lamina and medulla neurons in the Drosophila visual system. Each lamina neuron was previously shown to express many Dprs. Here, we demonstrate, by contrast, that their synaptic partners typically express one or two DIPs, with binding specificities matched to the lamina neuron-expressed Dprs. A deeper understanding of the molecular logic of DIP/Dpr interaction requires quantitative studies on the properties of these proteins. We thus generated a quantitative affinity-based DIP/Dpr interactome for all DIP/Dpr protein family members. This revealed a broad range of affinities and identified homophilic binding for some DIPs and some Dprs. These data, along with full-length ectodomain DIP/Dpr and DIP/DIP crystal structures, led to the identification of molecular determinants of DIP/Dpr specificity. This structural knowledge, along with a comprehensive set of quantitative binding affinities, provides new tools for functional studies in vivo. Less
Virtually all terrestrial habitats are dominated by angiosperms or flowering plants Their success in colonizing new habitats and supplanting other species is due to the advent of a complex reproductive structure the flower The flower unites the male and female organs into one compact structure and encloses the seed Flowering plants are not only the dominant type of land plants but also are the primary source of food and habitat for all animals including humans In evolutionary terms flowers are considered a recent development and have been a subject of speculation from the time of Charles Darwin who termed the ... More
Virtually all terrestrial habitats are dominated by angiosperms, or flowering plants. Their
success in colonizing new habitats and supplanting other species is due to the advent of a
complex reproductive structure � the flower. The flower unites the male and female organs
into one compact structure and encloses the seed. Flowering plants are not only the dominant
type of land plants, but also are the primary source of food and habitat for all animals,
including humans. In evolutionary terms, flowers are considered a recent development and
have been a subject of speculation from the time of Charles Darwin who termed the dominant
rise and diversification of flowering plants as �an abominable mystery�* due to the lack of a
smooth transition from non-flowering to flowering plants in the fossil record. With the
sequencing of multiple genomes from gymnosperms (non-flowering seed plants), basal
angiosperms and higher flowering plants, certain gene families have been identified which
play a central role in the development and evolution of the flower. My research focuses on
one such family of high-level regulators, the MADS transcription factor (TF) family. This TF
family helps to orchestrate flower development among other functions. As such, there is great
interest in understanding the molecular mechanisms of the MADS family and how these
proteins are able to control complex reproductive pathways.
This project integrates different biophysical techniques including x-ray crystallography,
small angle x-ray scattering (SAXS) and atomic force microscopy (AFM) to investigate
protein-protein and protein-DNA interactions of MADS TFs. No studies to date have
investigated the molecular mechanisms of MADS TFs using this integrated structural
approach.
One important hurdle in the study of the MADS TFs has been recombinant protein
expression and purification. In this project, recombinant purification protocols for several
full length MADS TFs were established, allowing the structural and biochemical
characterisation of the proteins. The crystal structure of the oligomerisation domain of the
MADS family protein SEPALLATA3 (SEP3) is presented and used as a template for
understanding the oligomerisation patterns of the larger family and the molecular basis for
protein-protein interactions. Investigation of solution structures, derived from SAXS studies,
of AGAMOUS (AG) and SHORT VEGETATIVE PHASE (SVP) along with biochemical
characterisation of their oligomerisation states are also presented.
In order to study protein-DNA interactions, complementary methods were used. An
important putative property of the MADS TFs is their ability to change the structure of DNA
through the formation of DNA loops. MADS TFs are hypothesized to oligomerise and bind
DNA at two different sites, potentiating looping of DNA. Using AFM, the first direct
evidence of DNA looping by SEP3 is described. The DNA binding characteristics of SVP
were studied using electrophoretic mobility shift assay (EMSA), microscale thermophoresis
(MST) and AFM. Unlike SEP3, SVP is dimeric and thus exhibits different DNA-binding
patterns.
The data presented here provide an atomic and structural basis for MADS TF function.
Based on this work, we now are beginning to understand some of the oligomerisation and
DNA-binding specificity determinants. These studies demonstrate how the MADS TFs
oligomerise and the results show that we can disrupt oligomerisation and potentially DNAbinding very specifically through the introduction of point mutations. Future work will
investigate the in vivo consequences of altered oligomerisation and how this affects different
developmental programs in plant reproduction and floral organ morphogenesis. Less
success in colonizing new habitats and supplanting other species is due to the advent of a
complex reproductive structure � the flower. The flower unites the male and female organs
into one compact structure and encloses the seed. Flowering plants are not only the dominant
type of land plants, but also are the primary source of food and habitat for all animals,
including humans. In evolutionary terms, flowers are considered a recent development and
have been a subject of speculation from the time of Charles Darwin who termed the dominant
rise and diversification of flowering plants as �an abominable mystery�* due to the lack of a
smooth transition from non-flowering to flowering plants in the fossil record. With the
sequencing of multiple genomes from gymnosperms (non-flowering seed plants), basal
angiosperms and higher flowering plants, certain gene families have been identified which
play a central role in the development and evolution of the flower. My research focuses on
one such family of high-level regulators, the MADS transcription factor (TF) family. This TF
family helps to orchestrate flower development among other functions. As such, there is great
interest in understanding the molecular mechanisms of the MADS family and how these
proteins are able to control complex reproductive pathways.
This project integrates different biophysical techniques including x-ray crystallography,
small angle x-ray scattering (SAXS) and atomic force microscopy (AFM) to investigate
protein-protein and protein-DNA interactions of MADS TFs. No studies to date have
investigated the molecular mechanisms of MADS TFs using this integrated structural
approach.
One important hurdle in the study of the MADS TFs has been recombinant protein
expression and purification. In this project, recombinant purification protocols for several
full length MADS TFs were established, allowing the structural and biochemical
characterisation of the proteins. The crystal structure of the oligomerisation domain of the
MADS family protein SEPALLATA3 (SEP3) is presented and used as a template for
understanding the oligomerisation patterns of the larger family and the molecular basis for
protein-protein interactions. Investigation of solution structures, derived from SAXS studies,
of AGAMOUS (AG) and SHORT VEGETATIVE PHASE (SVP) along with biochemical
characterisation of their oligomerisation states are also presented.
In order to study protein-DNA interactions, complementary methods were used. An
important putative property of the MADS TFs is their ability to change the structure of DNA
through the formation of DNA loops. MADS TFs are hypothesized to oligomerise and bind
DNA at two different sites, potentiating looping of DNA. Using AFM, the first direct
evidence of DNA looping by SEP3 is described. The DNA binding characteristics of SVP
were studied using electrophoretic mobility shift assay (EMSA), microscale thermophoresis
(MST) and AFM. Unlike SEP3, SVP is dimeric and thus exhibits different DNA-binding
patterns.
The data presented here provide an atomic and structural basis for MADS TF function.
Based on this work, we now are beginning to understand some of the oligomerisation and
DNA-binding specificity determinants. These studies demonstrate how the MADS TFs
oligomerise and the results show that we can disrupt oligomerisation and potentially DNAbinding very specifically through the introduction of point mutations. Future work will
investigate the in vivo consequences of altered oligomerisation and how this affects different
developmental programs in plant reproduction and floral organ morphogenesis. Less