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Sánchez Rodríguez F, Chojnowski G, Keegan RM, Rigden DJ. Using deep-learning predictions of inter-residue distances for model validation. Acta Crystallogr D Struct Biol 2022; 78:1412-1427. [PMID: 36458613 PMCID: PMC9716559 DOI: 10.1107/s2059798322010415] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/28/2022] [Indexed: 11/27/2022] Open
Abstract
Determination of protein structures typically entails building a model that satisfies the collected experimental observations and its deposition in the Protein Data Bank. Experimental limitations can lead to unavoidable uncertainties during the process of model building, which result in the introduction of errors into the deposited model. Many metrics are available for model validation, but most are limited to consideration of the physico-chemical aspects of the model or its match to the experimental data. The latest advances in the field of deep learning have enabled the increasingly accurate prediction of inter-residue distances, an advance which has played a pivotal role in the recent improvements observed in the field of protein ab initio modelling. Here, new validation methods are presented based on the use of these precise inter-residue distance predictions, which are compared with the distances observed in the protein model. Sequence-register errors are particularly clearly detected and the register shifts required for their correction can be reliably determined. The method is available in the ConKit package (https://www.conkit.org).
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Affiliation(s)
- Filomeno Sánchez Rodríguez
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Ronan M. Keegan
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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2
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Chojnowski G, Pereira J, Lamzin VS. Sequence assignment for low-resolution modelling of protein crystal structures. Acta Crystallogr D Struct Biol 2019; 75:753-763. [PMID: 31373574 PMCID: PMC6677015 DOI: 10.1107/s2059798319009392] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/30/2019] [Indexed: 01/08/2023] Open
Abstract
The performance of automated model building in crystal structure determination usually decreases with the resolution of the experimental data, and may result in fragmented models and incorrect side-chain assignment. Presented here are new methods for machine-learning-based docking of main-chain fragments to the sequence and for their sequence-independent connection using a dedicated library of protein fragments. The combined use of these new methods noticeably increases sequence coverage and reduces fragmentation of the protein models automatically built with ARP/wARP.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Joana Pereira
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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3
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. J Appl Crystallogr 2019; 52:495-497. [PMID: 31236090 PMCID: PMC6557178 DOI: 10.1107/s1600576719005922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, UK
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
- The European Extreme Light Infrastructure, Institute of Physics, AS CR, Na Slovance 2, Prague 18221 8, Czech Republic
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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4
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. IUCRJ 2019; 6:341-343. [PMID: 31098014 PMCID: PMC6503929 DOI: 10.1107/s2052252519005918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, United Kingdom
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
- The European Extreme Light Infrastructure, Institute of Physics, AS CR, Na Slovance 2, Prague 18221 8, Czech Republic
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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5
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. Acta Crystallogr F Struct Biol Commun 2019; 75:321-323. [PMID: 31045560 PMCID: PMC6497101 DOI: 10.1107/s2053230x19005909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, United Kingdom
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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6
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. Acta Crystallogr D Struct Biol 2019; 75:455-457. [PMID: 31063147 PMCID: PMC6503765 DOI: 10.1107/s2059798319004844] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, United Kingdom
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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7
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Helliwell JR, McMahon B, Guss JM, Kroon-Batenburg LMJ. The science is in the data. IUCRJ 2017; 4:714-722. [PMID: 29123672 PMCID: PMC5668855 DOI: 10.1107/s2052252517013690] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/24/2017] [Indexed: 05/22/2023]
Abstract
Understanding published research results should be through one's own eyes and include the opportunity to work with raw diffraction data to check the various decisions made in the analyses by the original authors. Today, preserving raw diffraction data is technically and organizationally viable at a growing number of data archives, both centralized and distributed, which are empowered to register data sets and obtain a preservation descriptor, typically a 'digital object identifier'. This introduces an important role of preserving raw data, namely understanding where we fail in or could improve our analyses. Individual science area case studies in crystallography are provided.
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Affiliation(s)
- John R. Helliwell
- School of Chemistry, University of Manchester, Manchester M13 9PL, England
| | - Brian McMahon
- International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
| | - J. Mitchell Guss
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Loes M. J. Kroon-Batenburg
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, CH 3584 Utrecht, The Netherlands
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8
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Helliwell JR. New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences. Biosci Rep 2017; 37:BSR20170204. [PMID: 28572170 PMCID: PMC6434086 DOI: 10.1042/bsr20170204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
Abstract
Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography's role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.
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9
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Raimer AC, Gray KM, Matera AG. SMN - A chaperone for nuclear RNP social occasions? RNA Biol 2017; 14:701-711. [PMID: 27648855 PMCID: PMC5519234 DOI: 10.1080/15476286.2016.1236168] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/01/2016] [Accepted: 09/09/2016] [Indexed: 12/24/2022] Open
Abstract
Survival Motor Neuron (SMN) protein localizes to both the nucleus and the cytoplasm. Cytoplasmic SMN is diffusely localized in large oligomeric complexes with core member proteins, called Gemins. Biochemical and cell biological studies have demonstrated that the SMN complex is required for the cytoplasmic assembly and nuclear transport of Sm-class ribonucleoproteins (RNPs). Nuclear SMN accumulates with spliceosomal small nuclear (sn)RNPs in Cajal bodies, sub-domains involved in multiple facets of snRNP maturation. Thus, the SMN complex forms stable associations with both nuclear and cytoplasmic snRNPs, and plays a critical role in their biogenesis. In this review, we focus on potential functions of the nuclear SMN complex, with particular emphasis on its role within the Cajal body.
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Affiliation(s)
- Amanda C. Raimer
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kelsey M. Gray
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - A. Gregory Matera
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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10
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Christensen EM, Patel SM, Korasick DA, Campbell AC, Krause KL, Becker DF, Tanner JJ. Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1. J Biol Chem 2017; 292:7233-7243. [PMID: 28258219 PMCID: PMC5409489 DOI: 10.1074/jbc.m117.780288] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 02/27/2017] [Indexed: 01/22/2023] Open
Abstract
Pyrroline-5-carboxylate reductase (PYCR) is the final enzyme in proline biosynthesis, catalyzing the NAD(P)H-dependent reduction of Δ1-pyrroline-5-carboxylate (P5C) to proline. Mutations in the PYCR1 gene alter mitochondrial function and cause the connective tissue disorder cutis laxa. Furthermore, PYCR1 is overexpressed in multiple cancers, and the PYCR1 knock-out suppresses tumorigenic growth, suggesting that PYCR1 is a potential cancer target. However, inhibitor development has been stymied by limited mechanistic details for the enzyme, particularly in light of a previous crystallographic study that placed the cofactor-binding site in the C-terminal domain rather than the anticipated Rossmann fold of the N-terminal domain. To fill this gap, we report crystallographic, sedimentation-velocity, and kinetics data for human PYCR1. Structures of binary complexes of PYCR1 with NADPH or proline determined at 1.9 Å resolution provide insight into cofactor and substrate recognition. We see NADPH bound to the Rossmann fold, over 25 Å from the previously proposed site. The 1.85 Å resolution structure of a ternary complex containing NADPH and a P5C/proline analog provides a model of the Michaelis complex formed during hydride transfer. Sedimentation velocity shows that PYCR1 forms a concentration-dependent decamer in solution, consistent with the pentamer-of-dimers assembly seen crystallographically. Kinetic and mutational analysis confirmed several features seen in the crystal structure, including the importance of a hydrogen bond between Thr-238 and the substrate as well as limited cofactor discrimination.
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Affiliation(s)
| | - Sagar M Patel
- the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588
| | | | | | - Kurt L Krause
- the Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand, and
| | - Donald F Becker
- the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588
| | - John J Tanner
- From the Departments of Chemistry and
- Biochemistry University of Missouri, Columbia, Missouri 65211
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11
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Hatti K, Biswas A, Chaudhary S, Dadireddy V, Sekar K, Srinivasan N, Murthy MRN. Structure determination of contaminant proteins using the MarathonMR procedure. J Struct Biol 2017; 197:372-378. [PMID: 28167161 DOI: 10.1016/j.jsb.2017.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/21/2017] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
Abstract
In the recent decades, essential steps of protein structure determination such as phasing by multiple isomorphous replacement and multi wave length anomalous dispersion, molecular replacement, refinement of the structure determined and its validation have been fully automated. Several computer program suites that execute all these steps as a pipeline operation have been made available. In spite of these great advances, determination of a protein structure may turn out to be a challenging task for a variety of reasons. It might be difficult to obtain multiple isomorphous replacement or multi wave length anomalous dispersion data or the crystal may have defects such as twinning or pseudo translation. Apart from these usual difficulties, more frequent difficulties have been encountered in recent years because of the large number of projects handled by structural biologists. These new difficulties usually result from contamination of the protein of interest by other proteins or presence of proteins from pathogenic organisms that could withstand the antibiotics used to prevent bacterial contamination. It could also be a result of poor book keeping. Recently, we have developed a procedure called MarathonMR that has the power to resolve some of these problems automatically. In this communication, we describe how the MarathonMR was used to determine four different protein structures that had remained elusive for several years. We describe the plausible reasons for the difficulties encountered in determining these structures and point out that the method presented here could be a validation tool for protein structures deposited in the protein data bank.
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Affiliation(s)
- Kaushik Hatti
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India; Vittal Mallya Scientific Research Foundation, Kanakapura Road, Bengaluru, Karnataka 560062, India
| | - Ansuman Biswas
- Physics Department, Indian Institute of Science, Bengaluru, Karnataka 560062, India
| | - Santosh Chaudhary
- Physics Department, Indian Institute of Science, Bengaluru, Karnataka 560062, India
| | | | - Kanagaraj Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka 560062, India
| | | | - Mathur R N Murthy
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India.
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12
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Hungler A, Momin A, Diederichs K, Arold ST. ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants. J Appl Crystallogr 2016; 49:2252-2258. [PMID: 27980519 PMCID: PMC5140001 DOI: 10.1107/s1600576716014965] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/21/2016] [Indexed: 01/22/2023] Open
Abstract
Solving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown. A webserver (ContaMiner) and a contaminant database (ContaBase) have been established, to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. The web-based ContaMiner (available at http://strube.cbrc.kaust.edu.sa/contaminer/) currently produces results in 5 min to 4 h. The program is also available in a github repository and can be installed locally. ContaMiner enables screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for 'crystallization and preliminary X-ray analysis' publications. Thus, in addition to potentially saving X-ray crystallographers much time and effort, ContaMiner might considerably lower the risk of publishing erroneous data.
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Affiliation(s)
- Arnaud Hungler
- King Abdullah University of Science and Technology (KAUST), Center for Computational Bioscience Research (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Afaque Momin
- King Abdullah University of Science and Technology (KAUST), Center for Computational Bioscience Research (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Kay Diederichs
- Fachbereich Biologie, Universität Konstanz, M647, D-78457 Konstanz, Germany
| | - Stefan, T. Arold
- King Abdullah University of Science and Technology (KAUST), Center for Computational Bioscience Research (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Thuwal, 23955-6900, Saudi Arabia
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