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Abriata LA, Dal Peraro M. Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction? J Chem Inf Model 2020; 60:2443-2447. [PMID: 32134661 DOI: 10.1021/acs.jcim.0c00177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein dynamics is undoubtedly a pervasive ingredient in all biological functions. However, structural biology has been strongly driven by a static-centered view of protein architecture. We argue that the recent advances of cryo-electron microscopy (EM) have the potential to more broadly explore the conformational landscapes of protein complexes and therefore will enhance our ability to predict the diverse conformations of tertiary and quaternary protein structures that are functionally relevant in physiological conditions.
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Affiliation(s)
- Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
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2
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Yang Y, Gao J, Wang J, Heffernan R, Hanson J, Paliwal K, Zhou Y. Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Brief Bioinform 2018; 19:482-494. [PMID: 28040746 PMCID: PMC5952956 DOI: 10.1093/bib/bbw129] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/15/2016] [Indexed: 11/13/2022] Open
Abstract
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new methods breathe new life into this field. The highest three-state accuracy without relying on structure templates is now at 82-84%, a number unthinkable just a few years ago. These improvements came from increasingly larger databases of protein sequences and structures for training, the use of template secondary structure information and more powerful deep learning techniques. As we are approaching to the theoretical limit of three-state prediction (88-90%), alternative to secondary structure prediction (prediction of backbone torsion angles and Cα-atom-based angles and torsion angles) not only has more room for further improvement but also allows direct prediction of three-dimensional fragment structures with constantly improved accuracy. About 20% of all 40-residue fragments in a database of 1199 non-redundant proteins have <6 Å root-mean-squared distance from the native conformations by SPIDER2. More powerful deep learning methods with improved capability of capturing long-range interactions begin to emerge as the next generation of techniques for secondary structure prediction. The time has come to finish off the final stretch of the long march towards protein secondary structure prediction.
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Affiliation(s)
- Yuedong Yang
- Insitute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Drive, Southport, QLD, Australia
| | - Jianzhao Gao
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Rhys Heffernan
- Signal Processing Laboratory, Griffith University, Brisbane, Australia
| | - Jack Hanson
- Signal Processing Laboratory, Griffith University, Brisbane, Australia
| | - Kuldip Paliwal
- Signal Processing Laboratory, Griffith University, Brisbane, Australia
| | - Yaoqi Zhou
- Insitute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Drive, Southport, QLD, Australia
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
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3
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Mir S, Alhroub Y, Anyango S, Armstrong DR, Berrisford JM, Clark AR, Conroy MJ, Dana JM, Deshpande M, Gupta D, Gutmanas A, Haslam P, Mak L, Mukhopadhyay A, Nadzirin N, Paysan-Lafosse T, Sehnal D, Sen S, Smart OS, Varadi M, Kleywegt GJ, Velankar S. PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. Nucleic Acids Res 2018; 46:D486-D492. [PMID: 29126160 PMCID: PMC5753225 DOI: 10.1093/nar/gkx1070] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/14/2017] [Accepted: 10/26/2017] [Indexed: 01/12/2023] Open
Abstract
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.
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Affiliation(s)
- Saqib Mir
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Younes Alhroub
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen Anyango
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David R Armstrong
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John M Berrisford
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alice R Clark
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew J Conroy
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose M Dana
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mandar Deshpande
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Deepti Gupta
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pauline Haslam
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lora Mak
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abhik Mukhopadhyay
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nurul Nadzirin
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Typhaine Paysan-Lafosse
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- InterPro, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Sehnal
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
| | - Sanchayita Sen
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Oliver S Smart
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mihaly Varadi
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Frappier V, Duran M, Keating AE. PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode. Protein Sci 2017; 27:276-285. [PMID: 29024246 DOI: 10.1002/pro.3320] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/09/2017] [Accepted: 10/09/2017] [Indexed: 11/08/2022]
Abstract
PixelDB, the Peptide Exosite Location Database, compiles 1966 non-redundant, high-resolution structures of protein-peptide complexes filtered to minimize the impact of crystal packing on peptide conformation. The database is organized to facilitate study of structurally conserved versus non-conserved elements of protein-peptide engagement. PixelDB clusters complexes based on the structural similarity of the peptide-binding protein, and by comparing complexes within a cluster highlights examples of domains that engage peptides using more than one binding mode. PixelDB also identifies conserved peptide core structural motifs characteristic of each binding mode. Peptide regions that flank core motifs often make non-structurally conserved interactions with the protein surface in regions we call exosites. Many examples establish that exosite contacts can be important for enhancing protein binding and interaction specificity. PixelDB provides a resource for computational and structural biologists to study, model, and predict core-motif and exosite-contacting peptide interactions. PixelDB is available to the community without restriction in a convenient flat-file format with accompanying visualization tools.
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Affiliation(s)
- Vincent Frappier
- MIT Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Madeleine Duran
- MIT Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Amy E Keating
- MIT Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
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