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Alnabati E, Esquivel-Rodriguez J, Terashi G, Kihara D. MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field. Front Mol Biosci 2022; 9:935411. [PMID: 35959463 PMCID: PMC9358042 DOI: 10.3389/fmolb.2022.935411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
An increasing number of protein complex structures are determined by cryo-electron microscopy (cryo-EM). When individual protein structures have been determined and are available, an important task in structure modeling is to fit the individual structures into the density map. Here, we designed a method that fits the atomic structures of proteins in cryo-EM maps of medium to low resolutions using Markov random fields, which allows probabilistic evaluation of fitted models. The accuracy of our method, MarkovFit, performed better than existing methods on datasets of 31 simulated cryo-EM maps of resolution 10 Å , nine experimentally determined cryo-EM maps of resolution less than 4 Å , and 28 experimentally determined cryo-EM maps of resolution 6 to 20 Å .
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Affiliation(s)
- Eman Alnabati
- Department of Computer Science, Purdue University, West Lafayette, IN, United States
| | | | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, United States
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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2
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Gromiha MM, Orengo CA, Sowdhamini R, Thornton AJM. Srinivasan (1962-2021) in Bioinformatics and beyond. Bioinformatics 2022; 38:2377-2379. [PMID: 35134112 PMCID: PMC9004639 DOI: 10.1093/bioinformatics/btac054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 02/05/2023] Open
Affiliation(s)
- M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Christine A Orengo
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (NCBS-TIFR), GKVK Campus, Bangalore, Karnataka 560065, India,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India,Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
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Malhotra S, Joseph AP, Thiyagalingam J, Topf M. Assessment of protein-protein interfaces in cryo-EM derived assemblies. Nat Commun 2021; 12:3399. [PMID: 34099703 PMCID: PMC8184972 DOI: 10.1038/s41467-021-23692-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/14/2021] [Indexed: 02/05/2023] Open
Abstract
Structures of macromolecular assemblies derived from cryo-EM maps often contain errors that become more abundant with decreasing resolution. Despite efforts in the cryo-EM community to develop metrics for map and atomistic model validation, thus far, no specific scoring metrics have been applied systematically to assess the interface between the assembly subunits. Here, we comprehensively assessed protein-protein interfaces in macromolecular assemblies derived by cryo-EM. To this end, we developed Protein Interface-score (PI-score), a density-independent machine learning-based metric, trained using the features of protein-protein interfaces in crystal structures. We evaluated 5873 interfaces in 1053 PDB-deposited cryo-EM models (including SARS-CoV-2 complexes), as well as the models submitted to CASP13 cryo-EM targets and the EM model challenge. We further inspected the interfaces associated with low-scores and found that some of those, especially in intermediate-to-low resolution (worse than 4 Å) structures, were not captured by density-based assessment scores. A combined score incorporating PI-score and fit-to-density score showed discriminatory power, allowing our method to provide a powerful complementary assessment tool for the ever-increasing number of complexes solved by cryo-EM.
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Affiliation(s)
- Sony Malhotra
- grid.4464.20000 0001 2161 2573Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK ,grid.14467.30Scientific Computing Department, Science and Technology Facilities Council, Didcot, UK
| | - Agnel Praveen Joseph
- grid.14467.30Scientific Computing Department, Science and Technology Facilities Council, Didcot, UK
| | - Jeyan Thiyagalingam
- grid.14467.30Scientific Computing Department, Science and Technology Facilities Council, Didcot, UK
| | - Maya Topf
- grid.4464.20000 0001 2161 2573Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK ,grid.13648.380000 0001 2180 3484Centre for Structural Systems Biology, Leibniz-Institut für Experimentelle Virologie and Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany
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Alnabati E, Kihara D. Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps. Molecules 2019; 25:molecules25010082. [PMID: 31878333 PMCID: PMC6982917 DOI: 10.3390/molecules25010082] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 01/16/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) has now become a widely used technique for structure determination of macromolecular complexes. For modeling molecular structures from density maps of different resolutions, many algorithms have been developed. These algorithms can be categorized into rigid fitting, flexible fitting, and de novo modeling methods. It is also observed that machine learning (ML) techniques have been increasingly applied following the rapid progress of the ML field. Here, we review these different categories of macromolecule structure modeling methods and discuss their advances over time.
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Affiliation(s)
- Eman Alnabati
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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Kim DN, Sanbonmatsu KY. Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model. Biosci Rep 2017; 37:BSR20170072. [PMID: 28963369 PMCID: PMC5715128 DOI: 10.1042/bsr20170072] [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: 07/04/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 12/16/2022] Open
Abstract
As cryo-electron microscopy (cryo-EM) enters mainstream structural biology, the demand for fitting methods is high. Here, we review existing flexible fitting methods for cryo-EM. We discuss their importance, potential concerns and assessment strategies. We aim to give readers concrete descriptions of cryo-EM flexible fitting methods with corresponding examples.
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Affiliation(s)
- Doo Nam Kim
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, U.S.A
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, U.S.A.
- New Mexico Consortium, Los Alamos, U.S.A
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Burnley T, Palmer CM, Winn M. Recent developments in the CCP-EM software suite. Acta Crystallogr D Struct Biol 2017; 73:469-477. [PMID: 28580908 PMCID: PMC5458488 DOI: 10.1107/s2059798317007859] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 05/26/2017] [Indexed: 11/13/2023] Open
Abstract
As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessible via a user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The current CCP-EM suite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail.
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Affiliation(s)
- Tom Burnley
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, England
| | - Colin M Palmer
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, England
| | - Martyn Winn
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, England
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Simkovic F, Ovchinnikov S, Baker D, Rigden DJ. Applications of contact predictions to structural biology. IUCRJ 2017; 4:291-300. [PMID: 28512576 PMCID: PMC5414403 DOI: 10.1107/s2052252517005115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallo-graphy, cryo-EM or NMR. Integrative structural bioinformatics packages such as Rosetta can already exploit contact predictions in a variety of ways. The contribution of contact predictions begins at construct design, where structural domains may need to be expressed separately and contact predictions can help to predict domain limits. Structure solution by molecular replacement (MR) benefits from contact predictions in diverse ways: in difficult cases, more accurate search models can be constructed using ab initio modelling when predictions are available, while intermolecular contact predictions can allow the construction of larger, oligomeric search models. Furthermore, MR using supersecondary motifs or large-scale screens against the PDB can exploit information, such as the parallel or antiparallel nature of any β-strand pairing in the target, that can be inferred from contact predictions. Contact information will be particularly valuable in the determination of lower resolution structures by helping to assign sequence register. In large complexes, contact information may allow the identity of a protein responsible for a certain region of density to be determined and then assist in the orientation of an available model within that density. In NMR, predicted contacts can provide long-range information to extend the upper size limit of the technique in a manner analogous but complementary to experimental methods. Finally, predicted contacts can distinguish between biologically relevant interfaces and mere lattice contacts in a final crystal structure, and have potential in the identification of functionally important regions and in foreseeing the consequences of mutations.
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Affiliation(s)
- Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Sergey Ovchinnikov
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Box 357370, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Box 357370, Seattle, WA 98195, USA
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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Vishwanath S, Sukhwal A, Sowdhamini R, Srinivasan N. Specificity and stability of transient protein-protein interactions. Curr Opin Struct Biol 2017; 44:77-86. [PMID: 28088083 DOI: 10.1016/j.sbi.2016.12.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 11/03/2016] [Accepted: 12/19/2016] [Indexed: 11/18/2022]
Abstract
Remarkable features that are achieved in a protein-protein complex to precise levels are stability and specificity. Deviation from the normal levels of specificity and stability, which is often caused by mutations, could result in disease conditions. Chemical nature, 3-D arrangement and dynamics of interface residues code for both specificity and stability. This article reviews roles of interfacial residues in transient protein-protein complexes. It is proposed that aside from hotspot residues conferring stability to the complex, a small set of 'rigid' residues at the interface that maintain conformation between complexed and uncomplexed forms, play a major role in conferring specificity. Exceptionally, 'super hotspot' residues, which confer both stability and specificity, are attractive sites for interaction with small molecule inhibitors.
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Affiliation(s)
- Sneha Vishwanath
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Anshul Sukhwal
- National Centre for Biological Sciences, TIFR, UAS-GKVK Campus, Bellary road, Bangalore 560065, India; SASTRA Deemed University, Tirumalai Samudram, Thanjavur 613402, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, TIFR, UAS-GKVK Campus, Bellary road, Bangalore 560065, India
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