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Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints [chapter]

Frank Alber, Brian T. Chait, Michael P. Rout, Andrej Sali
2008 Computational Biology  
We propose such an approach, defined by its three main components: a hierarchical representation of the assembly, a scoring function consisting of spatial restraints derived from experimental data, and  ...  We illustrate the approach by determining the configuration of the 456 proteins in the nuclear pore complex from Baker's yeast.  ...  Madhusudan, Min-yi Shen, Keren Lasker, Daniel Russell, Friedrich Foerster, Drnitry Korkin, Maya Topf and Ben Webb for many discussions about structure characterization by satisfaction of spatial restraints  ... 
doi:10.1007/978-1-84800-125-1_6 fatcat:zvmi22oi2rgk3nd7wier2nzk5u

Structural Characterization of Assemblies from Overall Shape and Subcomplex Compositions

Frank Alber, Michael F. Kim, Andrej Sali
2005 Structure  
Function The most important aspect of structure characterization by satisfaction of spatial restraint is to accurately capture all available input information about the structure of the assembly.  ...  This goal is achieved by the satisfaction of spatial restraints that depends on a subunit rep-representation of each of the proteins (one sphere per protein), and a new symmetry restraint (see Approach  ... 
doi:10.1016/j.str.2005.01.013 pmid:15766545 fatcat:chpc2ubkyjb6tbkjupdzj2tptm

Integrating Diverse Data for Structure Determination of Macromolecular Assemblies

Frank Alber, Friedrich Förster, Dmitry Korkin, Maya Topf, Andrej Sali
2008 Annual Review of Biochemistry  
We propose such an approach, defined by its three main components: a hierarchical representation of the assembly, a scoring function consisting of spatial restraints derived from experimental data, and  ...  This approach is illustrated by determining the configuration of the 456 proteins in the nuclear pore complex (NPC) from baker's yeast.  ...  Calculation of the NPC bead structure by satisfaction of spatial restraints.  ... 
doi:10.1146/annurev.biochem.77.060407.135530 pmid:18318657 fatcat:nwy2mqw4dfbangxrn7rpbixyz4

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  
This gap can be bridged by combining data from proteomics experiments with data from established structure determination techniques.  ...  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  ...  Calculation of an Ensemble of Structures by Satisfaction of Spatial Restraints Next, all structural models that minimize the scoring function and therefore fit the original data must be found.  ... 
doi:10.1074/mcp.r110.000067 pmid:20507923 pmcid:PMC2938050 fatcat:dzipnnyfqzf2dem67ulmkvdwjm

Determining the architectures of macromolecular assemblies

Frank Alber, Svetlana Dokudovskaya, Liesbeth M. Veenhoff, Wenzhu Zhang, Julia Kipper, Damien Devos, Adisetyantari Suprapto, Orit Karni-Schmidt, Rosemary Williams, Brian T. Chait, Michael P. Rout, Andrej Sali
2007 Nature  
Overview of integrative structure determination Our approach to structure determination can be seen as an iterative series of four steps: data generation by experiment, translation of the data into spatial  ...  restraints, calculation of an ensemble of structures by satisfaction of these restraints, and an analysis of the ensemble to produce the final structure (Fig. 1) .  ...  the architecture of the NPC by integrating spatial restraints from proteomic data.  ... 
doi:10.1038/nature06404 pmid:18046405 fatcat:kdvotwkllne2zhilmi4rbfpsn4

Integration of Small-Angle X-Ray Scattering Data into Structural Modeling of Proteins and Their Assemblies

Friedrich Förster, Benjamin Webb, Kristin A. Krukenberg, Hiro Tsuruta, David A. Agard, Andrej Sali
2008 Journal of Molecular Biology  
Our integration of a SAXS profile into modeling by satisfaction of spatial restraints will facilitate further integration of different kinds of data for structure determination of proteins and their assemblies  ...  Thus, we integrated SAXS profiles into our software for modeling proteins and their assemblies by satisfaction of spatial restraints.  ...  Our integration of a SAXS profile into modeling by satisfaction of spatial restraints will facilitate further integration of different kinds of data for structure determination of proteins and their assemblies  ... 
doi:10.1016/j.jmb.2008.07.074 pmid:18694757 pmcid:PMC2745287 fatcat:ma3i7hrsgfg6fk4nn7wunwydlu

The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

Marco Faini, Florian Stengel, Ruedi Aebersold
2016 Journal of the American Society for Mass Spectrometry  
Protein complexes are key catalysts and regulators for the majority of cellular processes. Unveiling their assembly and structure is essential to understanding their function and mechanism of action.  ...  Recent applications have shown that a range of mass spectrometry (MS) techniques are able to generate interaction and spatial restraints (cross-linking MS) information on native complexes or to study the  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution  ... 
doi:10.1007/s13361-016-1382-4 pmid:27056566 pmcid:PMC4867889 fatcat:friaxmcf7vfhvpu6ww67sk55ua

Structure determination of genomic domains by satisfaction of spatial restraints

Davide Baù, Marc A. Marti-Renom
2010 Chromosome Research  
assemblies, could be used for integrating diverse experimental data towards the determination of the 3D architecture of genomic domains and entire genomes at unprecedented resolution.  ...  We illustrate our work by outlining the recent determination of the 3D architecture of the α-globin domain in the human genome.  ...  Acknowledgments We thank the Dekker group for their support during the development of our approach.  ... 
doi:10.1007/s10577-010-9167-2 pmid:21190133 fatcat:chucg2ctzneshakeyxh3cfmota

From integrative structural biology to cell biology

Andrej Sali
2021 Journal of Biological Chemistry  
Second, the scope of structural biology is expanded by linking the wwPDB resource for integrative structures with archives of data that have not been generally used for structure determination but are  ...  First, the impact of integrative structures is maximized by PDB-Development, a prototype wwPDB repository for archiving, validating, visualizing, and disseminating integrative structures.  ...  The sampling explores both the conformations of the components and/or their configuration, searching for those assembly structures that satisfy the spatial restraints as well as possible.  ... 
doi:10.1016/j.jbc.2021.100743 pmid:33957123 fatcat:jqhrfsu5k5ehpk3aiq6udibgca

A mass spectrometry–based hybrid method for structural modeling of protein complexes

Argyris Politis, Florian Stengel, Zoe Hall, Helena Hernández, Alexander Leitner, Thomas Walzthoeni, Carol V Robinson, Ruedi Aebersold
2014 Nature Methods  
We describe a method that integrates data derived from different mass spectrometry (MS)-based techniques with a modeling strategy for structural characterization of protein assemblies.  ...  We encoded structural data derived from native MS, bottom-up proteomics, ion mobility-MS and chemical cross-linking MS into modeling restraints to compute the most likely structure of a protein assembly  ...  With the data encoded into spatial restraints in hand, we applied our computational strategy for structure determination of protein complexes.  ... 
doi:10.1038/nmeth.2841 pmid:24509631 pmcid:PMC3972104 fatcat:n4yemwyofvbovccg7yuqevg6ae

Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images

J. Velazquez-Muriel, K. Lasker, D. Russel, J. Phillips, B. M. Webb, D. Schneidman-Duhovny, A. Sali
2012 Proceedings of the National Academy of Sciences of the United States of America  
Thus, integrative structural biology can now benefit from the relative ease with which the EM class averages are determined. integrative modeling | structural determination | computational biology E M  ...  To obtain a structural model of a macromolecular assembly by single-particle EM, a large number of particle images need to be collected, aligned, clustered, averaged, and finally assembled via reconstruction  ...  This work was supported by National Institutes of Health National Institute of General Medical Sciences Grants R01 (GM083960) and U54 (RR022220).  ... 
doi:10.1073/pnas.1216549109 pmid:23112201 pmcid:PMC3503186 fatcat:qpbx3a7mz5dwtglnunfkmmzy7q

Spc110 N-Terminal Domains Act Independently to Mediate Stable γ-Tubulin Small Complex Binding and γ-Tubulin Ring Complex Assembly [article]

Andrew S. Lyon, Alex Zelter, Shruthi Viswanath, Alison Maxwell, Richard Johnson, King Clyde B. Yabut, Michael MacCoss, Trisha N. Davis, Eric Muller, Andrej Sali, David A. Agard
2018 bioRxiv   pre-print
We determined the structure of this coiled-coil segment by X-ray crystallography and used it in combination with our XL-MS dataset to generate an integrative structural model of the γTuSC-Spc110 complex  ...  This assembly process requires higher-order oligomers of the coiled-coil protein Spc110 to bind multiple γTuSCs, thereby stabilizing the otherwise low-affinity interface between γTuSCs.  ...  Acknowledgements We gratefully acknowledge many helpful discussions with members of the Agard and  ... 
doi:10.1101/311027 fatcat:dkxmoouy3rbi3kpgki4xbwblhi

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex

Yi Shi, Javier Fernandez-Martinez, Elina Tjioe, Riccardo Pellarin, Seung Joong Kim, Rosemary Williams, Dina Schneidman-Duhovny, Andrej Sali, Michael P. Rout, Brian T. Chait
2014 Molecular & Cellular Proteomics  
We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (ϳ600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear  ...  We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray  ...  We are also grateful to Daniel Russel, Charles Greenberg, and Benjamin Webb at UCSF for their help with and support of the PMI library and the Integrative Modeling Platform (IMP) package.  ... 
doi:10.1074/mcp.m114.041673 pmid:25161197 pmcid:PMC4223482 fatcat:lq66g3kfmbhy3k3hueft4vigta

Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies

Giorgio Tamò, Andrea Maesani, Sylvain Träger, Matteo T. Degiacomi, Dario Floreano, Matteo Dal Peraro
2017 Scientific Reports  
Citation for published item: m oD qF nd wesniD eF nd r¤ gerD F nd hegiomiD wFF nd plorenoD hF nd hl erroD wtteo @PHIUA 9hisentngling onstrints using viility evolution priniples in integrtive modeling of  ...  made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of  ...  G.T. was supported by the Swiss National Science Foundation (200021_157217).  ... 
doi:10.1038/s41598-017-00266-w pmid:28331186 pmcid:PMC5427971 fatcat:dxxqea6dybgy7c2ql6zz6d7tay

Computational modeling of RNA 3D structures, with the aid of experimental restraints

Marcin Magnus, Dorota Matelska, Grzegorz Łach, Grzegorz Chojnowski, Michal J Boniecki, Elzbieta Purta, Wayne Dawson, Stanislaw Dunin-Horkawicz, Janusz M Bujnicki
2014 RNA Biology  
Boniecki M and in general the development and application of RNA folding methods that use distance restraints from FRET experiments have been supported by the German Science Foundation (DFG) within SPP  ...  Acknowledgments The research on the development of methods for RNA 3D structure modeling in the Bujnicki laboratory has been funded from several sources.  ...  Constraint satisfaction problem Fragment assembly RNA Composer A method that can assemble large RNA structures from fragments taken from RNA FRABASe, using user-defined restraints, based on  ... 
doi:10.4161/rna.28826 pmid:24785264 pmcid:PMC4152360 fatcat:2q34pag7mrg6zbrmo7rxfk3qlq
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