Publications

@article{noKey,

title = {Expression, Purification, and Crystallization of the Transient Receptor Potential Channel TRPV6},

author = {Singh, Appu K., McGoldrick, Luke L.},

url = {https://pubmed.ncbi.nlm.nih.gov/31028671/},

doi = {https://doi.org/10.1007/978-1-4939-9446-5_2},

year  = {2019},

date = {2019-01-01},

abstract = {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.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Engineered variants provide new insight into the structural properties important for activity of the highly dynamic, trimeric protein disulfide isomerase ScsC from Proteus mirabilis},

author = {Furlong, Emily J., Kurth, Fabian},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450059/},

doi = {https://doi.org/10.1107/S2059798319000081},

year  = {2019},

date = {2019-01-01},

abstract = {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.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Iterative screen optimization maximizes the efficiency of macromolecular crystallization},

author = {Jones, Harrison G., Wrapp, Daniel},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360444/},

doi = {10.1107/S2053230X18017338},

year  = {2019},

date = {2019-01-01},

abstract = {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.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Design of ultra-swollen lipidic mesophases for the crystallization of membrane proteins with large extracellular domains},

author = {Tse, Alexandru Zabara, Josephine, Chong, Yin},

url = {https://www.nature.com/articles/s41467-018-02996-5},

doi = {https://doi.org/https://doi.org/10.1038/s41467-018-02996-5},

year  = {2018},

date = {2018-01-01},

abstract = {In meso crystallization of membrane proteins from lipidic mesophases is central to protein structural biology but limited to membrane proteins with small extracellular domains (ECDs), comparable to the water channels (3�5 nm) of the mesophase. Here we present a strategy expanding the scope of in meso crystallization to membrane proteins with very large ECDs. We combine monoacylglycerols and phospholipids to design thermodynamically stable ultra-swollen bicontinuous cubic phases of double-gyroid (Ia3d), double-diamond (Pn3m), and double-primitive (Im3m) space groups, with water channels five times larger than traditional lipidic mesophases, and showing re-entrant behavior upon increasing hydration, of sequences Ia3d?Pn3m?Ia3d and Pn3m?Im3m?Pn3m, unknown in lipid self-assembly. We use these mesophases to crystallize membrane proteins with ECDs inaccessible to conventional in meso crystallization, demonstrating the methodology on the Gloeobacter ligand-gated ion channel (GLIC) protein, and show substantial modulation of packing, molecular contacts and activation state of the ensued proteins crystals, illuminating a general strategy in protein structural biology.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {A Tunable Brake for HECT Ubiquitin Ligases},

author = {Chen, Zan, Jiang, Hanjie},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5489419/},

doi = {https://doi.org/10.1016/j.molcel.2017.03.020},

year  = {2018},

date = {2018-01-01},

abstract = {The HECT E3 ligases ubiquitinate numerous transcription factors and signaling molecules and their activity must be tightly controlled to prevent cancer, immune disorders, and other diseases. In this study we have found unexpectedly that peptide linkers tethering WW domains in several HECT family members are key regulatory elements of their catalytic activities. Biochemical, structural, and cellular analysis has revealed that the linkers can lock the HECT domain in an inactive conformation and block the proposed allosteric ubiquitin binding site. Such linker-mediated autoinhibition of the HECT domain can be relieved by linker post-translational modifications, but complete removal of the brake can induce hyperactive autoubiquitination and E3 self-destruction. These results clarify the mechanisms of several HECT protein cancer associated mutations and provide a new framework for understanding how HECT ubiquitin ligases must be finely tuned to ensure normal cellular behavior.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Cinder: keeping crystallographers app-y},

author = {Rosa, Nicholas, Ristic, Marko},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6038447/},

doi = {10.1107/S2053230X18008038},

year  = {2018},

date = {2018-01-01},

abstract = {The process of producing suitable crystals for X-ray diffraction analysis most often involves the setting up of hundreds (or thousands) of individual crystallization trials, each of which must be repeatedly examined for crystals or hints of crystallinity. Currently, the only real way to address this bottleneck is to use an automated imager to capture images of the trials. However, the images still need to be assessed for crystals or other outcomes. Ideally, there would exist some rapid and reliable machine-analysis tool to translate the images into a quantitative result. However, as yet no such tool exists in wide usage, despite this being a well recognized problem. One of the issues in creating robust automatic image-analysis software is the lack of reliable data for training machine-learning algorithms. Here, a mobile application, Cinder, has been developed which allows crystallization images to be scored quickly on a smartphone or tablet. The Cinder scores are inserted into the appropriate table in a crystallization database and are immediately available to the user through a more sophisticated web interface, allowing more detailed analyses. A sharp increase in the number of scored images was observed after Cinder was released, which in turn provides more data for training machine-learning tools.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Cinder : keeping crystallographers app-y},

author = {Rosa, N., Ristic, M.},

url = {http://scripts.iucr.org/cgi-bin/paper?S2053230X18008038},

doi = {https://doi.org/10.1107/S2053230X18008038},

year  = {2018},

date = {2018-01-01},

abstract = {The process of producing suitable crystals for X-ray diffraction analysis most often involves the setting up of hundreds (or thousands) of individual crystallization trials, each of which must be repeatedly examined for crystals or hints of crystallinity. Currently, the only real way to address this bottleneck is to use an automated imager to capture images of the trials. However, the images still need to be assessed for crystals or other outcomes. Ideally, there would exist some rapid and reliable machine-analysis tool to translate the images into a quantitative result. However, as yet no such tool exists in wide usage, despite this being a well recognized problem. One of the issues in creating robust automatic image-analysis software is the lack of reliable data for training machine-learning algorithms. Here, a mobile application, Cinder, has been developed which allows crystallization images to be scored quickly on a smartphone or tablet. The Cinder scores are inserted into the appropriate table in a crystallization database and are immediately available to the user through a more sophisticated web interface, allowing more detailed analyses. A sharp increase in the number of scored images was observed after Cinder was released, which in turn provides more data for training machine-learning tools.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Structural Basis for Apelin Control of the Human Apelin Receptor},

author = {Ma, Yingli, Yue, Yang},

url = {https://www.cell.com/structure/fulltext/S0969-2126(17)30126-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0969212617301260%3Fshowall%3Dtrue},

doi = {https://doi.org/10.1016/j.str.2017.04.008},

year  = {2017},

date = {2017-01-01},

abstract = {Apelin receptor (APJR) is a key regulator of human cardiovascular function and is activated by two different endogenous peptide ligands, apelin and Elabela, each with different isoforms diversified by length and amino acid sequence. Here we report the 2.6-� resolution crystal structure of human APJR in complex with a designed 17-amino-acid apelin mimetic peptide agonist. The structure reveals that the peptide agonist adopts a lactam constrained curved two-site ligand binding mode. Combined with mutation analysis and molecular dynamics simulations with apelin-13 binding to the wild-type APJR, this structure provides a mechanistic understanding of apelin recognition and binding specificity. Comparison of this structure with that of other peptide receptors suggests that endogenous peptide ligands with a high degree of conformational flexibility may bind and modulate the receptors via a similar two-site binding mechanism.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Assembly of Francisella novicida Cpf1 endonuclease in complex with guide RNA and target DNA},

author = {Alco´n, Pablo, Montoya, Guillermo},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5505246/},

doi = {https://doi.org/10.1107/S2053230X1700838X},

year  = {2017},

date = {2017-01-01},

abstract = {Bacteria and archaea use the CRISPR�Cas system as an adaptive response 

against infection by foreign nucleic acids. Owing to its remarkable flexibility, this 

mechanism has been harnessed and adopted as a powerful tool for genome 

editing. The CRISPR�Cas system includes two classes that are subdivided into 

six types and 19 subtypes according to conservation of the cas gene and loci 

organization. Recently, a new protein with endonuclease activity belonging to 

class 2 type V has been identified. This endonuclease, termed Cpf1, in complex 

with a single CRISPR RNA (crRNA) is able to recognize and cleave a target 

DNA preceded by a 50 

-TTN-30 protospacer-adjacent motif (PAM) complementary to the RNA guide. To obtain structural insight into the inner workings of 

Cpf1, the crystallization of an active complex containing the full extent of the 

crRNA and a 31-nucleotide dsDNA target was attempted. The gene encoding 

Cpf1 from Francisella novicida was cloned, overexpressed and purified. 

The crRNA was transcribed and purified in vitro. Finally, the ternary 

FnCpf1�crRNA�DNA complex was assembled and purified by preparative 

electrophoresis before crystallization. Crystals belonging to space group C2221, 

with unit-cell parameters a = 85.2, b = 137.6, c = 320.5 A� , were obtained and 

subjected to preliminary diffraction experiments.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {A new method to reconstruct the structure from crystal images},

author = {Li, Y.},

url = {https://openaccess.leidenuniv.nl/bitstream/handle/1887/48877/FullText.pdf?sequence=1},

doi = {undefined},

year  = {2017},

date = {2017-01-01},

abstract = {Biological molecules, especially the proteins, have a special and important function. We study their structure to understand their functions, and further make application, like the medical research. The routine method is diffraction, but not work for molecules which cannot grow into crystal and molecules which their crystal are too small. Cryo-EM technique provides another way to solve their structures through their images, it does not need crystals. Meanwhile, electron diffraction can work small crystals (micro- and nano-crystals) after the sample preparation was improved. Hence, we try to build a method that can restore the structure from the crystal�s image. We collect images of protein nano-crystal, and these images were processed to enhance their contrast. The key step is to find the orientations of these images in the procedure of reconstruction, therefore, we create a method that calculates these orientations. Nano-crystals, which cannot be used in diffraction method, then can be used in this method.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Studies on low pH-activated HA2 from Influenza haemagglutinin},

author = {Wiktoria Ogrodowicz, Roksana},

url = {https://discovery.ucl.ac.uk/id/eprint/1540872/1/FINAL_RPS_REDUCED.pdf},

doi = {undefined},

year  = {2017},

date = {2017-01-01},

abstract = {Influenza A haemagglutinin is a surface glycoprotein of Influenza virus, 

responsible for the initial attachment of the virus to the target cell and, at a later 

stage, for viral membrane fusion. At the acidic pH of the endosome, the HA 

molecule undergoes an irreversible structural rearrangement. In consequence, the 

hydrophobic terminal segments of HA2 are moved to the same end of the refolded 

molecule, promoting membrane fusion. 

16 haemagglutinin subtypes (H1-H16) identified to date can be divided into two 

groups based on characteristic structural features. The low pH-induced structures 

of proteolytically prepared and E.coli-expressed fragments of influenza A H3 HA2 

(group 2 HA) were previously determined by X-ray crystallography. 

This study presents structures of proteolytically prepared and recombinantlyexpressed fragments of H1 HA2 in a postfusion conformation. Refolded H1 HA2, 

belonging to group 1 HA, adopts a hairpin-like conformation, similar to that of a 

rearranged H3 HA2. Structures were compared to the known structures of low pHactivated HA2, to gain a better understanding of the structural differences between 

the two groups of HA. 

The data show the structures of the refolded HA2 to be conserved between the HA 

groups with minor differences. 

These structural data are supplemented with functional studies involving the 

cross-reactive FI6 antibody. FI6 antibody binds near the conserved fusion 

subdomain of the HA molecule and thus interferes with the low pH-triggered 

conformational change of HA. Additional methods employed in this study, such as 

limited proteolysis, electron microscopy, biolayer interferometry and MDCK1 cell 

infection, give insight into the mechanism of FI6 antibody-mediated neutralization, 

and highlight the differences in infectivity of H1N1 and H3N2 viruses neutralized 

by the FI6 antibody.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Renaissance of protein crystallization and precipitation in biopharmaceuticals purification},

author = {Santos, Raqueldos, Carvalho, Ana Luísa},

url = {https://www.sciencedirect.com/science/article/abs/pii/S0734975016301513?via%3Dihub},

doi = {https://doi.org/10.1016/j.biotechadv.2016.11.005},

year  = {2016},

date = {2016-01-01},

abstract = {The current chromatographic approaches used in protein purification are not keeping pace with the increasing biopharmaceutical market demand. With the upstream improvements, the bottleneck shifted towards the downstream process. New approaches rely in Anything But Chromatography methodologies and revisiting former techniques with a bioprocess perspective. Protein crystallization and precipitation methods are already implemented in the downstream process of diverse therapeutic biological macromolecules, overcoming the current chromatographic bottlenecks. Promising work is being developed in order to implement crystallization and precipitation in the purification pipeline of high value therapeutic molecules. This review focuses in the role of these two methodologies in current industrial purification processes, and highlights their potential implementation in the purification pipeline of high value therapeutic molecules, overcoming chromatographic holdups.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Characterization of the NTPR and BD1 interacting domains of the human PICH�BEND3 complex},

author = {Pitchai, Ganesha P., Hickson, Ian D.},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973307/},

doi = {https://doi.org/10.1107/S2053230X16010724},

year  = {2016},

date = {2016-01-01},

abstract = {Chromosome integrity depends on DNA structure-specific processing complexes that resolve DNA entanglement between sister chromatids. If left unresolved, these entanglements can generate either chromatin bridging or ultrafine DNA bridging in the anaphase of mitosis. These bridge structures are defined by the presence of the PICH protein, which interacts with the BEND3 protein in mitosis. To obtain structural insights into PICH�BEND3 complex formation at the atomic level, their respective NTPR and BD1 domains were cloned, overexpressed and crystallized using 1.56 M ammonium sulfate as a precipitant at pH 7.0. The protein complex readily formed large hexagonal crystals belonging to space group P6122, with unit-cell parameters a = b = 47.28, c = 431.58 � and with one heterodimer in the asymmetric unit. A complete multiwavelength anomalous dispersion (MAD) data set extending to 2.2 � resolution was collected from a selenomethionine-labelled crystal at the Swiss Light Source.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Novel detectors and algorithms for electron nano-crystallography},

author = {Genderen, Eric van},

url = {https://hdl.handle.net/1887/36598},

doi = {undefined},

year  = {2015},

date = {2015-01-01},

abstract = {In the past decade, advances in structure determination with electron microscopy of organic, beam sensitive, materials have been significant. The newly developed techniques, triggered by new microscope systems and new cameras, made it possible to acquire 3D structural information from these samples to a resolution which was impossible to achieve before. Knowledge is required to improve structure solution and every aspect of the process involved, from treatment of radiation sensitive materials, sample preparation, TEM imaging and diffraction systems all the way to how data must be interpreted. In this thesis I explained multiple new techniques and methods developed by us, using both new microscopes as well as a new type of detector: Timepix. I describe how these tools can help to overcome (what were) the most important problems and bottlenecks in detection of very low dose electron diffraction.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Sent packing: protein engineering generates a new crystal form of Pseudomonas aeruginosa DsbA1 with increased catalytic surface accessibility},

author = {McMahon, Roisin M., Coinçon, Mathieu},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667283/},

doi = {https://doi.org/10.1107/S1399004715018519},

year  = {2015},

date = {2015-01-01},

abstract = {Pseudomonas aeruginosa is an opportunistic human pathogen for which new antimicrobial drug options are urgently sought. P. aeruginosa disulfide-bond protein A1 (PaDsbA1) plays a pivotal role in catalyzing the oxidative folding of multiple virulence proteins and as such holds great promise as a drug target. As part of a fragment-based lead discovery approach to PaDsbA1 inhibitor development, the identification of a crystal form of PaDsbA1 that was more suitable for fragment-soaking experiments was sought. A previously identified crystallization condition for this protein was unsuitable, as in this crystal form of PaDsbA1 the active-site surface loops are engaged in the crystal packing, occluding access to the target site. A single residue involved in crystal-packing interactions was substituted with an amino acid commonly found at this position in closely related enzymes, and this variant was successfully used to generate a new crystal form of PaDsbA1 in which the active-site surface is more accessible for soaking experiments. The PaDsbA1 variant displays identical redox character and in vitro activity to wild-type PaDsbA1 and is structurally highly similar. Two crystal structures of the PaDsbA1 variant were determined in complex with small molecules bound to the protein active site. These small molecules (MES, glycerol and ethylene glycol) were derived from the crystallization or cryoprotectant solutions and provide a proof of principle that the reported crystal form will be amenable to co-crystallization and soaking with small molecules designed to target the protein active-site surface.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Molecular blueprint of allosteric binding sites in a homologue of the agonist-binding domain of the a7 nicotinic acetylcholine receptor},

author = {Spurny, Radovan, Debaveye, Sarah},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4434711/},

doi = {https://doi.org/10.1073/pnas.1418289112},

year  = {2015},

date = {2015-01-01},

abstract = {In this study we take advantage of a recently described chimera of the a7 nicotinic acetylcholine receptor (nAChR) and acetylcholine binding protein (AChBP), termed a7-AChBP. To date, more than 70 crystal structures have been determined for AChBP in complex with ligands that occupy the orthosteric binding site. Here, we use an innovative screening strategy to discover molecular fragments that occupy allosteric binding sites. In combination with X-ray crystallography we determine a molecular blueprint of three different allosteric sites in a7-AChBP. Using electrophysiological recordings on the human a7 nAChR we demonstrate that each of the three sites is involved in allosteric modulation of the receptor. Our study contributes to understanding the sites of allosteric binding in ion channels.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {From osmotic second virial coefficient (B 22) to phase behavior of a monoclonal antibody},

author = {Rakel, Natalie, Bauer, Katharina Christin},

url = {http://scripts.iucr.org/cgi-bin/paper?S0907444913002734},

doi = {https://doi.org/10.1002/btpr.2065},

year  = {2015},

date = {2015-01-01},

abstract = {Antibodies are complex macromolecules and their phase behavior as well as interactions within different solvents and precipitants are still not understood. To shed some light into the processes on a molecular dimension, the occurring self-interactions between antibody molecules were analyzed by means of the osmotic second virial coefficient (B22). The determined B22 follows qualitatively the phenomenological Hofmeister series describing the aggregation probability of antibodies for the various solvent compositions. However, a direct correlation between crystallization probability and B22 in form of a crystallization slot does not seem to be feasible for antibodies since the phase behavior is strongly dependent on their anisotropy. Kinetic parameters have to be taken into account due to the molecular size and complexity of the molecules. This is confirmed by a comparison of experimental data with a theoretical phase diagram. On the other hand the solubility is thermodynamically driven and therefore the B22 could be used to establish a universal solubility line for the monoclonal antibody mAb04c and different solvent compositions by using thermodynamic models. � 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:438�451, 2015},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Moving through three-dimensional phase diagrams of monoclonal antibodies},

author = {Rakel, Natalie, Baum, Miriam},

url = {https://aiche.onlinelibrary.wiley.com/doi/10.1002/btpr.1947},

doi = {https://doi.org/10.1002/btpr.1947},

year  = {2014},

date = {2014-01-01},

abstract = {Protein phase behavior characterization is a multivariate problem due to the high amount of influencing parameters and the diversity of the proteins. Single influences on the protein are not understood and fundamental knowledge remains to be obtained. For this purpose, a systematic screening method was developed to characterize the influence of fluid phase conditions on the phase behavior of proteins in three-dimensional phase diagrams. This approach was applied to three monoclonal antibodies to investigate influences of pH, protein and salt concentrations, with five different salts being tested. Although differences exist between the antibodies, this extensive study confirmed the general applicability of the Hofmeister series over the broad parameter range analyzed. The influence of the different salts on the aggregation (crystallization and precipitation) probability was described qualitatively using this Hofmeister series, with a differentiation between crystallization and precipitation being impossible, however. � 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1103�1113, 2014},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Automation in biological crystallization},

author = {Stewarta, Patrick Shaw, Dieckmannb, Jochen Mueller},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4051518/},

doi = {https://doi.org/10.1107/S2053230X14011601},

year  = {2014},

date = {2014-01-01},

abstract = {Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}

@article{noKey,

title = {Transforming biomedical and structural data into information and knowledge},

author = {Zimmerman, M., Cooper, D.},

url = {http://scripts.iucr.org/cgi-bin/paper?S2053273314095072},

doi = {https://doi.org/10.1107/S2053273314095072},

year  = {2014},

date = {2014-01-01},

abstract = {The LabDB laboratory information management system (LIMS) tracks, organizes and analyzes data from chemical and solution management, protein production, crystallization, diffraction, structure solution, and in vitro biochemical and biophysical experiments. The system is comprised of multiple modules specialized for different tasks, such as the Xtaldb system for crystallization or the hkldb module of the HKL-3000 suite for diffraction data collection and structure solution. The biochemical/biophysical experiments tracked by LabDB include spectrophotometric binding and kinetics, thermal shift binding, isothermal titration calorimetry (ITC) and protein quantitation. These tools associate functional and structural experiments, for example, for selecting likely substrates for co-crystallization and soaking experiments. Whenever possible, the system harvests data with no or minimal user intervention from laboratory hardware. Devices that may connect to or import data into LabDB include crystal observation (Rigaku Minstrel HT and Formulatrix Rock Imager), liquid handling (Formulatrix Rock Maker and Emerald Opti-Matrix Maker), chromatography (GE Healthcare AKTA), quantitation (Caliper LabChip GX II and Bio-Rad Gel Doc EZ), RT-PCR (Applied Biosystems 7900HT and Bio-Rad C1000/CFX96) and ITC (MicroCal iTC-200) systems. LabDB is used by two high-throughput PSI:Biology centers (MCSG and NYSGRC) as well as other major NIH consortia (the Center for Structural Genomics of Infectious Diseases and the Enzyme Function Initiative), and track millions of experiments on tens of thousands of targets.[1] The system also provides extensive data mining and analysis tools for translating raw experimental data into information and knowledge. We present examples of analyses generated by the system useful in designing new experiments.},

keywords = {ROCKMAKER},

pubstate = {published},

tppubtype = {article}

}