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A method for integrative structure determination of protein-protein complexes

Dina Schneidman-Duhovny, Andrea Rossi, Agustin Avila-Sakar, Seung Joong Kim, Javier Velázquez-Muriel, Pavel Strop, Hong Liang, Kristin A. Krukenberg, Maofu Liao, Ho Min Kim, Solmaz Sobhanifar, Volker Dötsch (+5 others)
2012 Computer applications in the biosciences : CABIOS  
Results: Here, we present a combined approach that computationally integrates data from a variety of fast and accessible experimental techniques for rapid and accurate structure determination of protein-protein  ...  The method is tested on a docking benchmark consisting of 176 known complex structures and simulated experimental data.  ...  We are also grateful for computer hardware gifts from Ron Conway, Mike Homer, Intel, Hewlett-Packard, IBM and NetApp. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bts628 pmid:23093611 pmcid:PMC3519461 fatcat:ck4vkfpaezcgtef4nfhbnwcfgu

Mass spectrometry for semi-experimental protein structure determination and modeling [article]

Gerhard Mayer
2020 arXiv   pre-print
The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible.  ...  The structure of proteins is essential for its function.  ...  This constraint-based protein structure modeling method can not only used for predicting the tertiary structure of a single protein, but also for the quaternary structure of protein complexes.  ... 
arXiv:2003.00328v1 fatcat:er2hzplirjgenpwla6wresatce

Hybrid Mass Spectrometry: Towards Characterization of Protein Conformational States

Zainab Ahdash, Euan Pyle, Argyris Politis
2016 TIBS -Trends in Biochemical Sciences. Regular ed  
Hybrid approaches in structural biology integrate diverse methods to study the structure and dynamics of proteins and their complexes.  ...  Hybrid mass spectrometry (MS) has emerged as a key tool to study the structural dynamics of large protein complexes unattainable by traditional methods.  ... 
doi:10.1016/j.tibs.2016.04.008 pmid:27211036 fatcat:cosyvjvzdjcclgy2k7cnpnktw4

The Protein Structure Initiative: achievements and visions for the future

Gaetano Montelione
2012 F1000 Biology Reports  
Over the past 12 years, the PSI has evolved from a testing bed for new methods of sample and structure production to a core component of a wide range of biology programs.  ...  As advances in genomic sequencing, bioinformatics, homology modelling, and methods for rapid determination of 3D structures of proteins by X-ray crystallography and nuclear magnetic resonance (NMR) converged  ...  This work was supported by the National Institutes of General Medical Science Protein Structure Initiative (PSI:Biology) program, grant U54 GM094597.  ... 
doi:10.3410/b4-7 pmid:22500193 pmcid:PMC3318194 fatcat:3ououqfgmzha3jpwh3ftxukrqi

Integrating Diverse Data for Structure Determination of Macromolecular Assemblies

Frank Alber, Friedrich Förster, Dmitry Korkin, Maya Topf, Andrej Sali
2008 Annual Review of Biochemistry  
This approach is illustrated by determining the configuration of the 456 proteins in the nuclear pore complex (NPC) from baker's yeast.  ...  First, we review the varied experimental data that characterize the assemblies at several levels of resolution. We then describe computational methods for generating the structures using these data.  ...  In particular, we focus on advances in computational methods for comparative modeling of complexes and for docking atomic structures of proteins to other proteins.  ... 
doi:10.1146/annurev.biochem.77.060407.135530 pmid:18318657 fatcat:nwy2mqw4dfbangxrn7rpbixyz4

Interpretation of medium resolution cryoEM maps of multi-protein complexes

Ana Casañal, Shabih Shakeel, Lori A Passmore
2019 Current Opinion in Structural Biology  
Electron cryo-microscopy (cryoEM) is used to determine structures of biological molecules, including multi-protein complexes.  ...  Here, we review techniques for map interpretation and provide examples from recent studies of multi-protein complexes.  ...  Acknowledgements We thank Andrew Carter, Paul Emsley, Glenn Masson and Mark Skehel for comments on the manuscript.  ... 
doi:10.1016/j.sbi.2019.06.009 pmid:31362190 pmcid:PMC6863432 fatcat:ymg237ftpnbcbllppvsxk6guwq

From systems to structure — using genetic data to model protein structures

Hannes Braberg, Ignacia Echeverria, Robyn M. Kaake, Andrej Sali, Nevan J. Krogan
2022 Nature reviews genetics  
of individual proteins or protein complexes.  ...  Until recently, understanding the molecular mechanisms that underlie these interactions often required biophysical methods to determine the structures of the proteins involved.  ...  Babu for helpful discussion and comments on the manuscript.  ... 
doi:10.1038/s41576-021-00441-w pmid:35013567 pmcid:PMC8744059 fatcat:2gfcfglldzgofld7glzd2hqh6m

Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data

Keren Lasker, Jeremy L. Phillips, Daniel Russel, Javier Velázquez-Muriel, Dina Schneidman-Duhovny, Elina Tjioe, Ben Webb, Avner Schlessinger, Andrej Sali
2010 Molecular & Cellular Proteomics  
Correspondingly, integrative computational methods are being developed to provide descriptions of protein complexes at varying levels of accuracy and resolution, ranging from complex compositions to detailed  ...  Proteomics techniques have been used to generate comprehensive lists of protein interactions in a number of species.  ...  Recently, a number of macromolecular structures have been resolved by such integrative methods.  ... 
doi:10.1074/mcp.r110.000067 pmid:20507923 pmcid:PMC2938050 fatcat:dzipnnyfqzf2dem67ulmkvdwjm

A Practical Guide to iSPOT Modeling: An Integrative Structural Biology Platform [chapter]

An Hsieh, Lanyuan Lu, Mark R. Chance, Sichun Yang
2017 Advances in Experimental Medicine and Biology  
Integrative structure modeling is an emerging method for structural determination of protein-protein complexes that are challenging for conventional structural techniques.  ...  Despite decades of effort, however, structure determination of protein-protein complexes is still a daunting task for conventional techniques due to size, stability, and/or complexity of protein complexes  ...  The content is solely the responsibility of the authors and does not necessarily reflect the official views of the National Institute of General Medical Sciences or the National Institutes of Health.  ... 
doi:10.1007/978-981-10-6038-0_14 pmid:29218563 fatcat:tsyxabmcdrhjbdq7u7nfrl6mt4

Improving integrative 3D modeling into low- to medium- resolution EM structures with evolutionary couplings

Caitlyn L McCafferty, David W Taylor, Edward M Marcotte
2021 Protein Science  
Electron microscopy (EM) continues to provide near-atomic resolution structures for well-behaved proteins and protein complexes.  ...  A method that employs co-evolutionary information obtained solely from sequence data could prove invaluable for quick, confident localization of subunits within these structures.  ...  ACKNOWLEDGMENTS All code and sample files are available at https://github. com/marcottelab/CoEVxIMP, along with our final integrative model of the bacterial holo-translocon.  ... 
doi:10.1002/pro.4067 pmid:33759266 pmcid:PMC8040867 fatcat:6tbl55yax5h5bk4tzd2nujtqyy

Mass Spectrometry Coupled Experiments and Protein Structure Modeling Methods

Jaewoo Pi, Lee Sael
2013 International Journal of Molecular Sciences  
Furthermore, the dynamics of the protein is being identified as a critical factor in its function.  ...  Although accuracy of protein structure prediction methods is high, provided there are structural templates, most methods are still insensitive to amino-acid differences at critical points that may change  ...  [42] propose an integrative modeling method for identifying the subunit architecture for intact protein complexes using MS and homology modeling.  ... 
doi:10.3390/ijms141020635 pmid:24132151 pmcid:PMC3821635 fatcat:epuudrvnnrhgrda6or5lh5qwoi

Novel Integrative Protocol for Reconstructing Large Macromolecules using Atomic Force Microscopy Data and Computational Docking

Jean-Luc Pellequer, Minh-Hieu Trinh, Michael Odorico, Michael E. Pique, Jean-Marie Teulon, Victoria A. Roberts, Lynn F. Ten Eyck, Elizabeth D. Getzoff, Pierre Parot, Shu-wen W. Chen
2012 Biophysical Journal  
The tertiary structures of protein complexes provide a crucial insight about the molecular mechanisms that regulate their functions and assembly.  ...  However, solving protein complex structures by experimental methods is often more difficult than single protein structures.  ...  Considering a substantial number of multimeric complexes of diverse kinds exist in a cell, there is an urgent need for the development of a multiple protein docking prediction method that does not target  ... 
doi:10.1016/j.bpj.2011.11.1433 fatcat:2wwy3upezvc75o7agi7hfcvg5q

The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology

Nurcan Tuncbag, Attila Gursoy, Ozlem Keskin, Ruth Nussinov
2016 Espert Review of Proteomics  
Keywords integrative modeling; structural bioinformatics; assembly modeling; protein interactions In the cell, proteins are not isolated entities.  ...  The strength of the non-covalent interactions and the life times of the assemblies vary in the cell and the spatial organization of their so-called 'interactomes' reflects a temporal and dynamic behavior  ...  This research was supported (in part) by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.  ... 
doi:10.1080/14789450.2016.1182023 pmid:27104235 pmcid:PMC4938151 fatcat:l7n5kjtpnje4pcx7zmhxqkv75m

Computational Methods for Multiple Protein Docking for Asymmetric Complexes

Juan Esquivel-Rodriguez, Daisuke Kihara
2012 Biophysical Journal  
The tertiary structures of protein complexes provide a crucial insight about the molecular mechanisms that regulate their functions and assembly.  ...  However, solving protein complex structures by experimental methods is often more difficult than single protein structures.  ...  Considering a substantial number of multimeric complexes of diverse kinds exist in a cell, there is an urgent need for the development of a multiple protein docking prediction method that does not target  ... 
doi:10.1016/j.bpj.2011.11.1431 fatcat:urcgj3wgsfahrl34nqkrneeusy

Integrating mass spectrometry of intact protein complexes into structural proteomics

Suk-Joon Hyung, Brandon T. Ruotolo
2012 Proteomics  
As this technology continues to move forward, one of the main challenges is to integrate the information content of such intact protein complex measurements with other MS approaches in structural biology  ...  MS analysis of intact protein complexes has emerged as an established technology for assessing the composition and connectivity within dynamic, heterogeneous multiprotein complexes at low concentrations  ...  An important development in the AP-MS method involves quantitative stoichiometry determinations of isolated protein complexes.  ... 
doi:10.1002/pmic.201100520 pmid:22611037 pmcid:PMC3895494 fatcat:5uala2nfird3vgmxzyknrq4bgu
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