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Wosicki S, Kazmierczyk M, Gilski M, Zabranska H, Pichova I, Jaskolski M. Crystal structures of inhibitor complexes of M-PMV protease with visible flap loops. Protein Sci 2021; 30:1258-1263. [PMID: 33786913 PMCID: PMC8138519 DOI: 10.1002/pro.4072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 12/05/2022]
Abstract
Mason‐Pfizer monkey virus protease (PR) was crystallized in complex with two pepstatin‐based inhibitors in P1 space group. In both crystal structures, the extended flap loops that lock the inhibitor/substrate over the active site, are visible in the electron density either completely or with only small gaps, providing the first observation of the conformation of the flap loops in dimeric complex form of this retropepsin. The H‐bond network in the active site (with D26N mutation) differs from that reported for the P21 crystal structures and is similar to a rarely occurring system in HIV‐1 PR. PDB Code(s): 7bgt and 7bgu;
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Affiliation(s)
- Stanislaw Wosicki
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Maciej Kazmierczyk
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Miroslaw Gilski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Helena Zabranska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Iva Pichova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
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2
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Abstract
For two decades, Rosetta has consistently been at the forefront of protein structure
prediction. While it has become a very large package comprising programs, scripts, and tools, for
different types of macromolecular modelling such as ligand docking, protein-protein docking,
protein design, and loop modelling, it started as the implementation of an algorithm for ab initio
protein structure prediction. The term ’Rosetta’ appeared for the first time twenty years ago in the
literature to describe that algorithm and its contribution to the third edition of the community wide
Critical Assessment of techniques for protein Structure Prediction (CASP3). Similar to the Rosetta
stone that allowed deciphering the ancient Egyptian civilisation, David Baker and his co-workers
have been contributing to deciphering ’the second half of the genetic code’. Although the focus of
Baker’s team has expended to de novo protein design in the past few years, Rosetta’s ‘fame’ is
associated with its fragment-assembly protein structure prediction approach. Following a
presentation of the main concepts underpinning its foundation, especially sequence-structure
correlation and usage of fragments, we review the main stages of its developments and highlight
the milestones it has achieved in terms of protein structure prediction, particularly in CASP.
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Affiliation(s)
- Jad Abbass
- Department of Computer Science, Lebanese International University, Bekaa, Lebanon
| | - Jean-Christophe Nebel
- Faculty of Science, Engineering and Computing, Kingston University, London, KT1 2EE, United Kingdom
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3
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Wosicki S, Gilski M, Zabranska H, Pichova I, Jaskolski M. Comparison of a retroviral protease in monomeric and dimeric states. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:904-917. [PMID: 31588922 DOI: 10.1107/s2059798319011355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/13/2019] [Indexed: 11/10/2022]
Abstract
Retroviral proteases (RPs) are of high interest owing to their crucial role in the maturation process of retroviral particles. RPs are obligatory homodimers, with a pepsin-like active site built around two aspartates (in DTG triads) that activate a water molecule, as the nucleophile, under two flap loops. Mason-Pfizer monkey virus (M-PMV) is unique among retroviruses as its protease is also stable in the monomeric form, as confirmed by an existing crystal structure of a 13 kDa variant of the protein (M-PMV PR) and its previous biochemical characterization. In the present work, two mutants of M-PMV PR, D26N and C7A/D26N/C106A, were crystallized in complex with a peptidomimetic inhibitor and one mutant (D26N) was crystallized without the inhibitor. The crystal structures were solved at resolutions of 1.6, 1.9 and 2.0 Å, respectively. At variance with the previous study, all of the new structures have the canonical dimeric form of retroviral proteases. The protomers within a dimer differ mainly in the flap-loop region, with the most extreme case observed in the apo structure, in which one flap loop is well defined while the other flap loop is not defined by electron density. The presence of the inhibitor molecules in the complex structures was assessed using polder maps, but some details of their conformations remain ambiguous. In all of the presented structures the active site contains a water molecule buried deeply between the Asn26-Thr27-Gly28 triads of the protomers. Such a water molecule is completely unique not only in retropepsins but also in aspartic proteases in general. The C7A and C106A mutations do not influence the conformation of the protein. The Cys106 residue is properly placed at the homodimer interface area for a disulfide cross-link, but the reducing conditions of the crystallization experiment prevented S-S bond formation. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:S2059798319011355.
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Affiliation(s)
- Stanislaw Wosicki
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Miroslaw Gilski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Helena Zabranska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Iva Pichova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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Wiggins A, Wilbanks J. The Rise of Citizen Science in Health and Biomedical Research. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2019; 19:3-14. [PMID: 31339831 DOI: 10.1080/15265161.2019.1619859] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Citizen science models of public participation in scientific research represent a growing area of opportunity for health and biomedical research, as well as new impetus for more collaborative forms of engagement in large-scale research. However, this also surfaces a variety of ethical issues that both fall outside of and build upon the standard human subjects concerns in bioethics. This article provides background on citizen science, examples of current projects in the field, and discussion of established and emerging ethical issues for citizen science in health and biomedical research.
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Cooper S, Sterling ALR, Kleffner R, Silversmith WM, Siegel JB. Repurposing Citizen Science Games as Software Tools for Professional Scientists. FDG : PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON FOUNDATIONS OF DIGITAL GAMES. INTERNATIONAL CONFERENCE ON THE FOUNDATIONS OF DIGITAL GAMES 2018; 2018:39. [PMID: 30465045 PMCID: PMC6241531 DOI: 10.1145/3235765.3235770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Scientific software is often developed with professional scientists in mind, resulting in complex tools with a steep learning curve. Citizen science games, however, are designed for citizen scientists- members of the general public. These games maintain scientific accuracy while placing design goals such as usability and enjoyment at the forefront. In this paper, we identify an emerging use of game-based technology, in the repurposing of citizen science games to be software tools for professional scientists in their work. We discuss our experience in two such repurposings: Foldit, a protein folding and design game, and Eyewire, a web-based 3D neuron reconstruction game. Based on this experience, we provide evidence that the software artifacts produced for citizen science can be useful for professional scientists, and provide an overview of key design principles we found to be useful in the process of repurposing.
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Baaden M, Delalande O, Ferey N, Pasquali S, Waldispühl J, Taly A. Ten simple rules to create a serious game, illustrated with examples from structural biology. PLoS Comput Biol 2018. [PMID: 29518072 PMCID: PMC5843163 DOI: 10.1371/journal.pcbi.1005955] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Marc Baaden
- Laboratoire de Biochimie Théorique, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Olivier Delalande
- Institut de Génétique et Développement de Rennes, Univ. Rennes 1, Rennes, France
| | | | - Samuela Pasquali
- Laboratoire de Cristallographie et RMN Biologiques, Faculté des sciences pharmaceutiques et biologiques, Université Paris Descartes et Université Sorbonne Paris Cité, Paris, France
| | | | - Antoine Taly
- Laboratoire de Biochimie Théorique, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- * E-mail:
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DiMaio F. Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems. Methods Mol Biol 2017; 1607:455-466. [PMID: 28573585 DOI: 10.1007/978-1-4939-7000-1_19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular replacement (MR), a method for solving the crystallographic phase problem using phases derived from a model of the target structure, has proven extremely valuable, accounting for the vast majority of structures solved by X-ray crystallography. However, when the resolution of data is low, or the starting model is very dissimilar to the target protein, solving structures via molecular replacement may be very challenging. In recent years, protein structure prediction methodology has emerged as a powerful tool in model building and model refinement for difficult molecular replacement problems. This chapter describes some of the tools available in Rosetta for model building and model refinement specifically geared toward difficult molecular replacement cases.
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Affiliation(s)
- Frank DiMaio
- Department of Biochemistry, Institute of Protein Design, University of Washington, Seattle, WA, USA
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8
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Walsh SR, Gerpe MCR, Wootton SK. Construction of a molecular clone of ovine enzootic nasal tumor virus. Virol J 2016; 13:209. [PMID: 28038674 PMCID: PMC5203713 DOI: 10.1186/s12985-016-0660-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Enzootic nasal tumor virus (ENTV-1) is an ovine betaretrovirus that has been linked to enzootic nasal adenocarcinoma (ENA), a contagious tumor of the ethmoid turbinates of sheep. Transmission experiments performed using virus isolated from cell free nasal tumor homogenates suggest that ENTV-1 is the causative agent of ENA; however, this etiological relationship has not been conclusively proven due to the fact that the virus cannot be propagated in vitro nor is there an infectious molecular clone of the virus. METHODS Here we report construction of a molecular clone of ENTV-1 and demonstrate that transfection of this molecular clone into HEK 293T cells produces mature virus particles. RESULTS Analysis of recombinant virus particles derived from the initial molecular clone revealed a defect in the proteolytic processing of Gag; however, this defect could be corrected by co-expression of the Gag-Pro-Pol polyprotein from the highly related Jaagsiekte sheep retrovirus (JSRV) suggesting that the polyprotein cleavage sites in the ENTV-1 molecular clone were functional. Mutagenesis of the molecular clone to correct amino acid variants identified within the pro gene did not restore proteolytic processing; whereas deletion of one proline residue from a polyproline tract located in variable region 1 (VR1) of the matrix resulted in production of CA protein of the mature (cleaved) size strongly suggesting that normal virion morphogenesis and polyprotein cleavage took place. Finally, electron microscopy revealed the presence of spherical virus particles with an eccentric capsid and an average diameter of about 100 nm. CONCLUSION In summary, we have constructed the first molecular clone of ENTV-1 from which mature virus particles can be produced. Future experiments using virus produced from this molecular clone can now be conducted to fulfill Koch's postulates and demonstrate that ENTV-1 is necessary and sufficient to induce ENA in sheep.
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Affiliation(s)
- Scott R Walsh
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - María Carla Rosales Gerpe
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Sarah K Wootton
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada.
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Power to the People: Addressing Big Data Challenges in Neuroscience by Creating a New Cadre of Citizen Neuroscientists. Neuron 2016; 92:658-664. [DOI: 10.1016/j.neuron.2016.10.045] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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May JC, McLean JA. Advanced Multidimensional Separations in Mass Spectrometry: Navigating the Big Data Deluge. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:387-409. [PMID: 27306312 PMCID: PMC5763907 DOI: 10.1146/annurev-anchem-071015-041734] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Hybrid analytical instrumentation constructed around mass spectrometry (MS) is becoming the preferred technique for addressing many grand challenges in science and medicine. From the omics sciences to drug discovery and synthetic biology, multidimensional separations based on MS provide the high peak capacity and high measurement throughput necessary to obtain large-scale measurements used to infer systems-level information. In this article, we describe multidimensional MS configurations as technologies that are big data drivers and review some new and emerging strategies for mining information from large-scale datasets. We discuss the information content that can be obtained from individual dimensions, as well as the unique information that can be derived by comparing different levels of data. Finally, we summarize some emerging data visualization strategies that seek to make highly dimensional datasets both accessible and comprehensible.
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Affiliation(s)
- Jody C May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235;
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235;
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11
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Minor W, Dauter Z, Jaskolski M. The young person's guide to the PDB. Postepy Biochem 2016; 62:242-249. [PMID: 28132477 PMCID: PMC5610703 DOI: 10.18388/pb.2016_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 07/06/2016] [Indexed: 06/06/2023]
Abstract
The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120, 000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview.
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Affiliation(s)
- Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Zbigniew Dauter
- Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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12
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Jaskolski M, Miller M, Mohana Rao JK, Gustchina A, Wlodawer A. Elucidation of the structure of retroviral proteases: a reminiscence. FEBS J 2015; 282:4059-66. [PMID: 26258480 DOI: 10.1111/febs.13397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/21/2015] [Accepted: 07/29/2015] [Indexed: 12/01/2022]
Abstract
Determinations of only a very few protein structures had consequences comparable to the impact exerted by the structure of the protease encoded by HIV-1, published just over 25 years ago. The structure of this relatively small protein and its cousins from other retroviruses provided a clear target for a spectacularly successful structure-assisted drug design effort that offered new hope for controlling the then-escalating AIDS epidemic. This reminiscence is limited primarily to work conducted at the National Cancer Institute, and is not meant to be a comprehensive history of the field, but is rather an attempt to provide a very personal account of how the structures of this most thoroughly studied crystallographic target were determined.
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Affiliation(s)
- Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University and Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Maria Miller
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - J K Mohana Rao
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Alla Gustchina
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
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Harbeck N, Wuerstlein R, Schinkoethe T. Improved patient management using eHealth tools: potential and pitfalls. BREAST CANCER MANAGEMENT 2015. [DOI: 10.2217/bmt.14.53] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Nadia Harbeck
- Breast Center, Department of OB&GYN, University of Munich, 81377 Munich, Germany
| | - Rachel Wuerstlein
- Breast Center, Department of OB&GYN, University of Munich, 81377 Munich, Germany
| | - Time Schinkoethe
- Breast Center, Department of OB&GYN, University of Munich, 81377 Munich, Germany
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14
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Domagalski MJ, Zheng H, Zimmerman MD, Dauter Z, Wlodawer A, Minor W. The quality and validation of structures from structural genomics. Methods Mol Biol 2014; 1091:297-314. [PMID: 24203341 DOI: 10.1007/978-1-62703-691-7_21] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Quality control of three-dimensional structures of macromolecules is a critical step to ensure the integrity of structural biology data, especially those produced by structural genomics centers. Whereas the Protein Data Bank (PDB) has proven to be a remarkable success overall, the inconsistent quality of structures reveals a lack of universal standards for structure/deposit validation. Here, we review the state-of-the-art methods used in macromolecular structure validation, focusing on validation of structures determined by X-ray crystallography. We describe some general protocols used in the rebuilding and re-refinement of problematic structural models. We also briefly discuss some frontier areas of structure validation, including refinement of protein-ligand complexes, automation of structure redetermination, and the use of NMR structures and computational models to solve X-ray crystal structures by molecular replacement.
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Affiliation(s)
- Marcin J Domagalski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
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15
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Wlodawer A, Minor W, Dauter Z, Jaskolski M. Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination. FEBS J 2013; 280:5705-36. [PMID: 24034303 DOI: 10.1111/febs.12495] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/12/2013] [Accepted: 08/20/2013] [Indexed: 12/28/2022]
Abstract
The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation.
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Affiliation(s)
- Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD, USA
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