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A method for integrative structure determination of protein-protein complexes
2012
Computer applications in the biosciences : CABIOS
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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]
2020
arXiv
pre-print
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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
2016
TIBS -Trends in Biochemical Sciences. Regular ed
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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
2012
F1000 Biology Reports
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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
2008
Annual Review of Biochemistry
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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
2019
Current Opinion in Structural Biology
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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
2022
Nature reviews genetics
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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
2010
Molecular & Cellular Proteomics
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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]
2017
Advances in Experimental Medicine and Biology
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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
2021
Protein Science
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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
2013
International Journal of Molecular Sciences
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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
2012
Biophysical Journal
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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
2016
Espert Review of Proteomics
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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
2012
Biophysical Journal
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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
2012
Proteomics
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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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