Publications

@article{noKey,

title = {Structural Insights into the DNA-Binding Mechanism of BCL11A: The Integral Role of ZnF6},

author = {Viennet, Thibault, Yin, Maolu},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10827156/},

doi = {10.1101/2024.01.17.576058},

year  = {2024},

date = {2024-01-01},

abstract = {The transcription factor BCL11A is a critical regulator of the switch from fetal hemoglobin (HbF: α 2 γ 2 ) to adult hemoglobin (HbA: α 2 β 2 ) during development. BCL11A binds at a cognate recognition site (TGACCA) in the γ-globin gene promoter and represses its expression. DNA-binding is mediated by a triple zinc finger domain, designated ZnF456. Here, we report comprehensive investigation of ZnF456, leveraging X-ray crystallography and NMR to determine the structures in both the presence and absence of DNA. We delve into the dynamics and mode of interaction with DNA. Moreover, we discovered that the last zinc finger of BCL11A (ZnF6) plays a special role in DNA binding and γ-globin gene repression. Our findings help account for some rare γ-globin gene promoter mutations that perturb BCL11A binding and lead to increased HbF in adults (hereditary persistence of fetal hemoglobin). Comprehending the DNA binding mechanism of BCL11A opens avenues for the strategic, structure-based design of novel therapeutics targeting sickle cell disease and β-thalassemia.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Lyotropic liquid crystal phases of monoolein in protic ionic liquids},

author = {Paporakis, Stefan, Brown, Stuart J.},

url = {https://pubs.aip.org/aip/jcp/article/160/2/024901/2932698},

doi = {https://doi.org/10.1063/5.0180420},

year  = {2024},

date = {2024-01-01},

abstract = {Monoolein-based liquid crystal phases are established media that are researched for various biological applications, including drug delivery. While water is the most common solvent for self-assembly, some ionic liquids (ILs) can support lipidic self-assembly. However, currently, there is limited knowledge of IL-lipid phase behavior in ILs. In this study, the lyotropic liquid crystal phase behavior of monoolein was investigated in six protic ILs known to support amphiphile self-assembly, namely ethylammonium nitrate, ethanolammonium nitrate, ethylammonium formate, ethanolammonium formate, ethylammonium acetate, and ethanolammonium acetate. These ILs were selected to identify specific ion effects on monoolein self-assembly, specifically increasing the alkyl chain length of the cation or anion, the presence of a hydroxyl group in the cation, and varying the anion. The lyotropic liquid crystal phases with 20–80 wt. % of monoolein were characterized over a temperature range from 25 to 65 °C using synchrotron small angle x-ray scattering and cross-polarized optical microscopy. These results were used to construct partial phase diagrams of monoolein in each of the six protic ILs, with inverse hexagonal, bicontinuous cubic, and lamellar phases observed. Protic ILs containing the ethylammonium cation led to monoolein forming lamellar and bicontinuous cubic phases, while those containing the ethanolammonium cation formed inverse hexagonal and bicontinuous cubic phases. Protic ILs containing formate and acetate anions favored bicontinuous cubic phases across a broader range of protic IL concentrations than those containing the nitrate anion.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {HSV-1 ICP0 dimer domain adopts a novel β-barrel fold},

author = {McCloskey, Erick, Kashipathy, Maithri},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.26673},

doi = {https://doi.org/10.1002/prot.26673},

year  = {2024},

date = {2024-01-01},

abstract = {Infected cell protein 0 (ICP0) is an immediate-early regulatory protein of herpes simplex virus 1 (HSV-1) that possesses E3 ubiquitin ligase activity. ICP0 transactivates viral genes, in part, through its C-terminal dimer domain (residues 555–767). Deletion of this dimer domain results in reduced viral gene expression, lytic infection, and reactivation from latency. Since ICP0’s dimer domain is associated with its transactivation activity and efficient viral replication, we wanted to determine the structure of this specific domain. The C-terminus of ICP0 was purified from bacteria and analyzed by X-ray crystallography to solve its structure. Each subunit or monomer in the ICP0 dimer is composed of nine β-strands and two α-helices. Interestingly, two adjacent β-strands from one monomer “reach” into the adjacent subunit during dimer formation, generating two β-barrel-like structures. Additionally, crystallographic analyses indicate a tetramer structure is formed from two β-strands of each dimer, creating a “stacking” of the β-barrels. The structural protein database searches indicate the fold or structure adopted by the ICP0 dimer is novel. The dimer is held together by an extensive network of hydrogen bonds. Computational analyses reveal that ICP0 can either form a dimer or bind to SUMO1 via its C-terminal SUMO-interacting motifs but not both. Understanding the structure of the dimer domain will provide insights into the activities of ICP0 and, ultimately, the HSV-1 life cycle.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {PRODUCTION EFFECTIVENESS OF ROCK IMAGERS WITH THE 5S METHOD AT PT. FORMULATRIX INDONESIA},

author = {SUSILO, DIDIK},

url = {http://repository.unissula.ac.id/27761/},

doi = {Thesis},

year  = {2023},

date = {2023-01-01},

abstract = {PT. Formulatrix is ​​one of the industries that produce automation tools or robots, therefore companies are required to produce automation products that meet the needs of the world market. PT. Formulatrix has 2 production divisions LH (Liquid Handling) and RI (Rock Imager). Examples of the production of automation equipment include, NT8, Formulator for liquid handling and RI 1000, RI 182, RI 54 for rock imagers. The difference lies in the shape and function of each product. The problem focuses on the rock imager production process, where production is made with a make to order system and the assembly process is parallel, making the assembly not smooth because you have to choose components, waiting for replacement components because they are damaged or missing to assemble. To improve the effective and efficient production process, replace the better production process. While production in liquid handling is said to be smooth because the production is small and the product is small compared to the rock imager. Assembling in parallel makes assemblers a hassle when assembling robots, because they have to sort out robot components in one container. Making assembly inefficient and ineffective. After collecting 5S data to support the kitting process in the rock imager assembling division, the process of assembling a one-table robot with components. As for the application of the 5S method applied at PT. Formulatrix Indonesia. The seiri method is applied to every division without exception, because in each division many mechanical equipment is found scattered on tables or on the floor. Seiton is a continuation of seiri, where the sorting results that have been carried out will be followed by the process of arranging the sorted equipment. Seiso at this stage, what is being done is the cleaning process. The cleaning that is done is cleaning the work area, such as the floor of the equipment used for the production process. At this stage it is more directed at the process of monitoring the 5S method that has been implemented. This stage is the last part of the 5S method. This section focuses more on how to get used to the application of this method. With the kitting process and the 5S method, it is hoped that assembling robots will be more efficient and effective, because waiting, sorting out parts, and looking for tools to assemble will be more optimal than the old process. With the kitting process, the efficiency value is better than the old process, from the previous 83% to 92%, which the researchers got from a trial at PT. Formulatrix Indonesia. Keywords: Rock Imager production process, 5S, Kitting.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {IgE binding epitope mapping with TL1A tagged peptides},

author = {Zhang, Yuzhu, Bhardwaj, Shilpa R.},

url = {https://www.sciencedirect.com/science/article/pii/S0161589022004916?casa_token=EnIlP_M19NEAAAAA:DjZJVO_yB2h3fwV8BPQV9-bSxfD3CBIzXl2PTNDqqA_OY1biqkepQ_k8B4EexI58_j1mI880MsJY},

doi = {https://doi.org/10.1016/j.molimm.2022.12.001},

year  = {2023},

date = {2023-01-01},

abstract = {Linear IgE epitopes play essential roles in persistent allergies, including peanut and tree nut allergies. Using chemically synthesized peptides attached to membranes and microarray experiments is one approach for determining predominant epitopes that has seen success. However, the overall expense of this approach and the inherent challenges in scaling up the production and purification of synthetic peptides precludes the general application of this approach. To overcome this problem, we have constructed a plasmid vector for expressing peptides sandwiched between an N-terminal His-tag and a trimeric protein. The vector was used to make overlapping peptides derived from peanut allergens Ara h 2. All the peptides were successfully expressed and purified. The resulting peptides were applied to identify IgE binding epitopes of Ara h 2 using four sera samples from individuals with known peanut allergies. New and previously defined dominant IgE binding epitopes of Ara h 2 were identified. This system may be readily applied to produce agents for component- and epitope-resolved food allergy diagnosis.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Structural basis of regulated m7G tRNA modification by METTL1–WDR4},

author = {Li, Jiazhi, Wang, Longfei},

url = {https://www.nature.com/articles/s41586-022-05566-4#citeas},

doi = {https://doi.org/10.1038/s41586-022-05566-4},

year  = {2023},

date = {2023-01-01},

abstract = {Chemical modifications of RNA have key roles in many biological processes1,2,3. N7-methylguanosine (m7G) is required for integrity and stability of a large subset of tRNAs4,5,6,7. The methyltransferase 1–WD repeat-containing protein 4 (METTL1–WDR4) complex is the methyltransferase that modifies G46 in the variable loop of certain tRNAs, and its dysregulation drives tumorigenesis in numerous cancer types8,9,10,11,12,13,14. Mutations in WDR4 cause human developmental phenotypes including microcephaly15,16,17. How METTL1–WDR4 modifies tRNA substrates and is regulated remains elusive18. Here we show,  through structural, biochemical and cellular studies of human METTL1–WDR4, that WDR4 serves as a scaffold for METTL1 and the tRNA T-arm. Upon tRNA binding, the αC region of METTL1 transforms into a helix, which together with the α6 helix secures both ends of the tRNA variable loop. Unexpectedly, we find that the predicted disordered N-terminal region of METTL1 is part of the catalytic pocket and essential for methyltransferase activity. Furthermore, we reveal that S27 phosphorylation in the METTL1 N-terminal region inhibits methyltransferase activity by locally disrupting the catalytic centre. Our results provide a molecular understanding of tRNA substrate recognition and phosphorylation-mediated regulation of METTL1–WDR4, and reveal the presumed disordered N-terminal region of METTL1 as a nexus of methyltransferase activity.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding},

author = {Rodarte, Justas V., Baehr, Carly},

url = {https://www.sciencedirect.com/science/article/abs/pii/S0969212622004579},

doi = {https://doi.org/10.1016/j.str.2022.11.008},

year  = {2023},

date = {2023-01-01},

abstract = {Opioid-related fatal overdoses have reached epidemic proportions. Because existing treatments for opioid use disorders offer limited long-term protection, accelerating the development of newer approaches is critical. Monoclonal antibodies (mAbs) are an emerging treatment strategy that targets and sequesters selected opioids in the bloodstream, reducing drug distribution across the blood-brain barrier, thus preventing or reversing opioid toxicity. We previously identified a series of murine mAbs with high affinity and selectivity for oxycodone, morphine, fentanyl, and nicotine. To determine their binding mechanism, we used X-ray crystallography to solve the structures of mAbs bound to their respective targets, to 2.2 Å resolution or higher. Structural analysis showed a critical convergent hydrogen bonding mode that is dependent on a glutamic acid residue in the mAbs’ heavy chain and a tertiary amine of the ligand. Characterizing drug-mAb complexes represents a significant step toward rational antibody engineering and future manufacturing activities to support clinical evaluation.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Biochemical Studies of Systemic Lupus Erythematosus-Associated Mutations in Nonreceptor Tyrosine Kinases Ack1 and Brk},

author = {Kan, Yagmur, Paung, YiTing},

url = {https://pubs.acs.org/doi/full/10.1021/acs.biochem.2c00685},

doi = {https://doi.org/10.1021/acs.biochem.2c00685},

year  = {2023},

date = {2023-01-01},

abstract = {Tyrosine kinases (TKs) play essential roles in signaling processes that regulate cell survival, migration, and proliferation. Dysregulation of tyrosine kinases underlies many disorders, including cancer, cardiovascular and developmental diseases, as well as pathologies of the immune system. Ack1 and Brk are nonreceptor tyrosine kinases (NRTKs) best known for their roles in cancer. Here, we have biochemically characterized novel Ack1 and Brk mutations identified in patients with systemic lupus erythematosus (SLE). These mutations are the first SLE-linked polymorphisms found among NRTKs. We show that two of the mutants are catalytically inactive, while the other three have reduced activity. To understand the structural changes associated with the loss-of-function phenotype, we solved the crystal structure of one of the Ack1 kinase mutants, K161Q. Furthermore, two of the mutated residues (Ack1 A156 and K161) critical for catalytic activity are highly conserved among other TKs, and their substitution in other members of the kinase family could have implications in cancer. In contrast to canonical gain-of-function mutations in TKs observed in many cancers, we report loss-of-function mutations in Ack1 and Brk, highlighting the complexity of TK involvement in human diseases.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Structural Basis for Binding of Neutralizing Antibodies to Clostridioides difficile Binary Toxin},

author = {Goldsmith, Jory A., Dewar, Vincent},

url = {https://journals.asm.org/doi/full/10.1128/jb.00456-22},

doi = {https://doi.org/10.1128/jb.00456-22},

year  = {2023},

date = {2023-01-01},

abstract = {Clostridioides difficile is a Gram-positive opportunistic human pathogen that causes 15,000 deaths annually in the United States, prompting a need for vaccine development. In addition to the important toxins TcdA and TcdB, binary toxin (CDT) plays a significant role in the pathogenesis of certain C. difficile ribotypes by catalyzing the ADP-ribosylation of actin in host cells. However, the mechanisms of CDT neutralization by antibodies have not been studied, limiting our understanding of key epitopes for CDT antigen design. Therefore, we isolated neutralizing monoclonal antibodies against CDT and characterized their mechanisms of neutralization structurally and biochemically. Here, 2.5-Å and 2.6-Å resolution X-ray crystal structures of the antibodies BINTOXB/22 and BINTOXB/9, respectively, in complex with CDTb—the CDT subunit that forms a heptameric pore for the delivery of toxic CDTa enzyme into the host cytosol—showed that both antibodies sterically clash with adjacent protomers in the assembled heptamer. Assessment of trypsin-induced oligomerization of the purified CDTb protoxin in vitro showed that BINTOXB/22 and BINTOXB/9 prevented the assembly of di-heptamers upon prodomain cleavage. This work suggests that the CDT oligomerization process can be effectively targeted by antibodies, which will aid in the development of C. difficile vaccines and therapeutics.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Structural insights into DarT toxin neutralization by cognate DarG antitoxin: ssDNA mimicry by DarG C-terminal domain keeps the DarT toxin inhibited},

author = {Deep, Amar, Singh, Latika},

url = {https://www.cell.com/structure/pdf/S0969-2126(23)00131-4.pdf},

doi = {https://doi.org/10.1016/j.str.2023.04.008},

year  = {2023},

date = {2023-01-01},

abstract = {In the DarTG toxin-antitoxin system, the DarT toxin ADP-ribosylates single-stranded DNA (ssDNA), which stalls DNA replication and plays a crucial role in controlling bacterial growth and bacteriophage infection. This toxic activity is reversed by the N-terminal macrodomain of the cognate antitoxin DarG. DarG also binds DarT, but the role of these interactions in DarT neutralization is unknown. Here, we report that the C-terminal domain of DarG (DarG toxin-binding domain [DarGTBD]) interacts with DarT to form a 1:1 stoichiometric heterodimeric complex. We determined the 2.2 Å resolution crystal structure of the Mycobacterium tuberculosis DarT-DarGTBD complex. The comparative structural analysis reveals that DarGTBD interacts with DarT at the DarT/ssDNA interaction interface, thus sterically occluding substrate ssDNA binding and consequently inactivating toxin by direct protein-protein interactions. Our data support a unique two-layered DarT toxin neutralization mechanism of DarG, which is important in keeping the toxin molecules in check under normal growth conditions.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Two distinct mechanisms of flavoprotein spectral tuning revealed by low-temperature and time-dependent spectroscopy},

author = {Nikolaev, Andrey, Tropina, Elena V.},

url = {https://onlinelibrary.wiley.com/doi/full/10.1002/pro.4851?casa_token=p3r7cddnZj8AAAAA%3AVFBZm6WIKWnMN37ocmyeSsOIVJwe-xXuoFGn7dnYmTyUjlQx46pnbbPuwC1_kkuFW4gaKjZPOxeXDBLB},

doi = {https://doi.org/10.1002/pro.4851},

year  = {2023},

date = {2023-01-01},

abstract = {Flavins such as flavin mononucleotide or flavin adenine dinucleotide are bound by diverse proteins, yet have very similar spectra when in the oxidized state. Recently, we developed new variants of flavin-binding protein CagFbFP exhibiting notable blue (Q148V) or red (I52V A85Q) shifts of fluorescence emission maxima. Here, we use time-resolved and low-temperature spectroscopy to show that whereas the chromophore environment is static in Q148V, an additional protein-flavin hydrogen bond is formed upon photoexcitation in the I52V A85Q variant. Consequently, in Q148V, excitation, emission, and phosphorescence spectra are shifted, whereas in I52V A85Q, excitation and low-temperature phosphorescence spectra are relatively unchanged, while emission spectrum is altered. We also determine the x-ray structures of the two variants to reveal the flavin environment and complement the spectroscopy data. Our findings illustrate two distinct color-tuning mechanisms of flavin-binding proteins and could be helpful for the engineering of new variants with improved optical properties.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Key roles of β-glucosidase BglA for the catabolism of both laminaribiose and cellobiose in the lignocellulolytic bacterium Clostridium thermocellum},

author = {Xiao, Yan, Dong, Sheng},

url = {https://www.sciencedirect.com/science/article/pii/S0141813023031227?casa_token=NazPwnu5Vc0AAAAA:CTMilPc-maLxIPtSqrbRj77hcwYipr7t2EOZzkvjbJPCcaPue5XPdAOh1_Vdv2HTL8tiXIDX},

doi = {https://doi.org/10.1016/j.ijbiomac.2023.126226},

year  = {2023},

date = {2023-01-01},

abstract = {The thermophilic bacterium Clostridium thermocellum efficiently degrades polysaccharides into oligosaccharides. The metabolism of β-1,4-linked cello-oligosaccharides is initiated by three enzymes, i.e., the cellodextrin phosphorylase (Cdp), the cellobiose phosphorylase (Cbp), and the β-glucosidase A (BglA), in C. thermocellum. In comparison, how the oligosaccharides containing other kinds of linkage are utilized is rarely understood. In this study, we found that BglA could hydrolyze the β-1,3-disaccharide laminaribiose with much higher activity than that against the β-1,4-disaccharide cellobiose. The structural basis of the substrate specificity was analyzed by crystal structure determination and molecular docking. Genetic deletions of BglA and Cbp, respectively, and enzymatic analysis of cell extracts demonstrated that BglA is the key enzyme responsible for laminaribiose metabolism. Furthermore, the deletion of BglA can suppress the expression of Cbp and the deletion of Cbp can up-regulate the expression of BglA, indicating that BglA and Cbp have cross-regulation and BglA is also critical for cellobiose metabolism. These insights pave the way for both a fundamental understanding of metabolism and regulation in C. thermocellum and emphasize the importance of the degradation and utilization of polysaccharides containing β-1,3-linked glycosidic bonds in lignocellulose biorefinery.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Cost-Effective Protein Production in CHO Cells Following Polyethylenimine-Mediated Gene Delivery Showcased by the Production and Crystallization of Antibody Fabs},

author = {Meskova, Klaudia, Martonova, Katarina},

url = {https://www.mdpi.com/2073-4468/12/3/51},

doi = {https://doi.org/10.3390/antib12030051},

year  = {2023},

date = {2023-01-01},

abstract = {Laboratory production of recombinant mammalian proteins, particularly antibodies, requires an expression pipeline assuring sufficient yield and correct folding with appropriate posttranslational modifications. Transient gene expression (TGE) in the suspension-adapted Chinese Hamster Ovary (CHO) cell lines has become the method of choice for this task. The antibodies can be secreted into the media, which facilitates subsequent purification, and can be glycosylated. However, in general, protein production in CHO cells is expensive and may provide variable outcomes, namely in laboratories without previous experience. While achievable yields may be influenced by the nucleotide sequence, there are other aspects of the process which offer space for optimization, like gene delivery method, cultivation process or expression plasmid design. Polyethylenimine (PEI)-mediated gene delivery is frequently employed as a low-cost alternative to liposome-based methods. In this work, we are proposing a TGE platform for universal medium-scale production of antibodies and other proteins in CHO cells, with a novel expression vector allowing fast and flexible cloning of new genes and secretion of translated proteins. The production cost has been further reduced using recyclable labware. Nine days after transfection, we routinely obtain milligrams of antibody Fabs or human lactoferrin in a 25 mL culture volume. Potential of the platform is established based on the production and crystallization of antibody Fabs and their complexes.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site},

author = {Mohammad Ghafoori, Seyed, Petersen, Gayle F.},

url = {https://www.nature.com/articles/s41598-023-33529-w},

doi = {https://doi.org/10.1038/s41598-023-33529-w},

year  = {2023},

date = {2023-01-01},

abstract = {Influenza virus (IV) causes several outbreaks of the flu each year resulting in an economic burden to the healthcare system in the billions of dollars. Several influenza pandemics have occurred during the last century and estimated to have caused 100 million deaths. There are four genera of IV, A (IVA), B (IVB), C (IVC), and D (IVD), with IVA being the most virulent to the human population. Hemagglutinin (HA) is an IVA surface protein that allows the virus to attach to host cell receptors and enter the cell. Here we have characterised the high-resolution structures of seven IVA HAs, with one in complex with the anti-influenza head-binding antibody C05. Our analysis revealed conserved receptor binding residues in all structures, as seen in previously characterised IV HAs. Amino acid conservation is more prevalent on the stalk than the receptor binding domain (RBD; also called the head domain), allowing the virus to escape from antibodies targeting the RBD. The equivalent site of C05 antibody binding to A/Denver/57 HA appears hypervariable in the other H1N1 IV HAs. Modifications within this region appear to disrupt binding of the C05 antibody, as these HAs no longer bind the C05 antibody by analytical SEC. Our study brings new insights into the structural and functional recognition of IV HA proteins and can contribute to further development of anti-influenza vaccines.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Structure of Rhizobium sp. 4-9 histamine dehydrogenase and analysis of the electron transfer pathway to an abiological electron acceptor},

author = {Goyal, Priyanka, Deay III, Dwight},

url = {https://www.sciencedirect.com/science/article/abs/pii/S000398612300111X?casa_token=vjpTR2UNVq4AAAAA:oAQ7nE157_dbJwcWZ_CKX_DrS1Jeudu_09XZoDbsUrGXdUObvPQZWdbf0lPzEVo3kLiRBGlr},

doi = {https://doi.org/10.1016/j.abb.2023.109612},

year  = {2023},

date = {2023-01-01},

abstract = {Histamine dehydrogenase from the gram-negative bacterium Rhizobium sp. 4-9 (HaDHR) is a member of a small family of dehydrogenases containing a covalently attached FMN, and the only member so far identified to date that does not exhibit substrate inhibition. In this study, we present the 2.1 Å resolution crystal structure of HaDHR. This new structure allowed for the identification of the internal electron transfer pathway to abiological ferrocene-based mediators. Alanine 437 was identified as the exit point of electrons from the Fe4S4 cluster. The enzyme was modified with a Ser436Cys mutation to facilitate covalent attachment of a ferrocene moiety. When modified with Fc-maleimide, this new construct demonstrated direct electron transfer from the enzyme to a gold electrode in a histamine concentration-dependent manner without the need for any additional electron mediators.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Heterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme},

author = {Kalkan, Özlem, Kantamneni, Sravya},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10427876/},

doi = {10.3389/fchem.2023.1220543},

year  = {2023},

date = {2023-01-01},

abstract = {The Dictyostelium discoideum dye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of DdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the DdDyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of DdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native DdDyP active site and its implication on DyP catalysis.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Crystal packing reveals rapamycin-mediated homodimerization of an FK506-binding domain},

author = {Kumar Singha, Ajit, Saharan, Ketul},

url = {https://www.sciencedirect.com/science/article/pii/S0141813022003543?casa_token=njcENZOfLLAAAAAA:U8vTqUq0p8zbAO4AyyImIqEVFP-nZNJv74Iy-1Hs8HwM-aoVpKgITYecCzkey2rUde65U6kkdbE},

doi = {https://doi.org/10.1016/j.ijbiomac.2022.02.107},

year  = {2022},

date = {2022-01-01},

abstract = {Chemically induced dimerization (CID) is used to induce proximity and result in artificial complex formation between a pair of proteins involved in biological processes in cells to investigate and regulate these processes. The induced heterodimerization of FKBP fusion proteins by rapamycin and FK506 has been extensively exploited as a chemically induced dimerization system to regulate and understand highly dynamic cellular processes. Here, we report the crystal structure of the AtFKBP53 FKBD in complex with rapamycin. The crystal packing reveals an unusual feature whereby two rapamycin molecules appear to mediate homodimerization of the FKBD. The triene arm of rapamycin appears to play a significant role in forming this dimer. This forms the first structural report of rapamycin-mediated homodimerization of an FKBP. The structural information on the rapamycin-mediated FKBD dimerization may be employed to design and synthesize covalently linked dimeric rapamycin, which may subsequently serve as a chemically induced dimerization system for the regulation and characterization of cellular processes.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Characterization of a vaccine-elicited human antibody with sequence homology to VRC01-class antibodies that binds the C1C2 gp120 domain},

author = {GRAY, MATTHEW D., FENG, JUNLI},

url = {https://www.science.org/doi/full/10.1126/sciadv.abm3948},

doi = {https://doi.org/10.1126/sciadv.abm39},

year  = {2022},

date = {2022-01-01},

abstract = {Broadly HIV-1–neutralizing VRC01-class antibodies bind the CD4-binding site of Env and contain VH1-2*02–derived heavy chains paired with light chains expressing five–amino acid–long CDRL3s. Their unmutated germline forms do not recognize HIV-1 Env, and their lack of elicitation in human clinical trials could be due to the absence of activation of the corresponding naïve B cells by the vaccine immunogens. To address this point, we examined Env-specific B cell receptor sequences from participants in the HVTN 100 clinical trial. Of all the sequences analyzed, only one displayed homology to VRC01-class antibodies, but the corresponding antibody (FH1) recognized the C1C2 gp120 domain. For FH1 to switch epitope recognition to the CD4-binding site, alterations in the CDRH3 and CDRL3 were necessary. Only germ line–targeting Env immunogens efficiently activated VRC01 B cells, even in the presence of FH1 B cells. Our findings support the use of these immunogens to activate VRC01 B cells in humans.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {High-Throughput Evaluation of Emission and Structure in Reduced- Dimensional Perovskites},

author = {Anwar, Husna, Johnston, Andrew},

url = {https://pubs.acs.org/doi/10.1021/acscentsci.2c00041},

doi = {https://doi.org/10.1021/acscentsci.2c00041},

year  = {2022},

date = {2022-01-01},

abstract = {High-throughput experimentation (HTE) seeks to accelerate the exploration of materials space by uniting robotics, combinatorial methods, and parallel processing. HTE is particularly relevant to metal halide perovskites (MHPs), a diverse class of optoelectronic materials with a large chemical space. Here we develop an HTE workflow to synthesize and characterize light-emitting MHP single crystals, allowing us to generate the first reported data set of experimentally derived photoluminescence spectra for low-dimensional MHPs. We leverage the accelerated workflow to optimize the synthesis and emission of a new MHP, methoxy-phenethylammonium lead iodide ((4-MeO-PEAI)2-PbI2). We then synthesize 16 000 MHP single crystals and measure their photoluminescence to study the effects of synthesis parameters and compositional engineering on the emission intensity of 54 distinct MHPs: we achieve an acceleration factor of more than 100 times over previously reported HTE MHP synthesis and characterization methods. Using insights derived from this analysis, we screen an existing database for new, potentially emissive MHPs. On the basis of the Tanimoto similarity of the bright available emitters, we present our top candidates for future exploration. As a proof of concept, we use one of these (3,4-difluorophenylmethanamine) to synthesize an MHP which we find has a photoluminescence quantum yield of 10%.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Structural and functional studies of signaling molecules in axon guidance},

author = {Knapp, Kryštof},

url = {https://dspace.cuni.cz/handle/20.500.11956/175227},

doi = {Thesis},

year  = {2022},

date = {2022-01-01},

abstract = {This work aims to determine a model of the autoinhibition mechanism of MICAL proteins using biochemical, biophysical, and bioinformatical approaches. MICAL proteins are a group of flavin monooxygenases that play a key role in various cellular processes, as they facilitate the reorganization of the actin cytoskeleton. MICAL-1 has long been known for its vital role in axon guidance as an effector of repulsive signaling through oxidative destabilization of actin filaments. However, recent findings indicate that MICAL-1 can also serve as a signaling molecule, using localized hydrogen peroxide production to regulate other downstream effectors. Despite the consensus that MICAL-1 activity must be strictly regulated, the exact molecular mechanism of this regulation has not yet been described. In this work, we provide a novel model of MICAL-1 autoinibiton mechanism based on a comparison of steady-state kinetic experiments and molecular dynamics simulations between full-length MICAL-1 from Coturnix japonica and its truncated form lacking the C-terminal domain. In our model, we conclude that changes in MICAL-1 activity are the result of intramolecular protein interactions between the C-terminal and the monooxygenase domain. Furthermore, we rule out the role of MICAL-1 oligomerization in its activity regulation. Our work provides the basis for further research that will need to focus on a more detailed investigation of intramolecular interactions between the MICAL-1 domains.},

keywords = {NT8},

pubstate = {published},

tppubtype = {article}

}