Publication date: Available online 9 March 2016 Source:Journal of Structural Biology
Author(s): Luisa Calvanese, Gabriella D’Auria, Anna Vangone, Lucia Falcigno, Romina Oliva
NMR structures consist in ensembles of conformers, all satisfying the experimental restraints, which exhibit a certain degree of structural variability. We analyzed here the interface in NMR ensembles of protein-protein heterodimeric complexes and found it to span a wide range of different conservations. The different exhibited conservations do not simply correlate with the size of the systems/interfaces, and are most probably the result of an interplay between different factors, including the quality of experimental data and the intrinsic complex flexibility. In any case, this information is not to be missed when NMR structures of protein-protein complexes are analyzed; especially considering that, as we also show here, the first NMR conformer is usually not the one which best reflects the overall interface. To quantify the interface conservation and to analyze it, we used an approach originally conceived for the analysis and ranking of ensembles of docking models, which has now been extended to directly deal with NMR ensembles. We propose this approach, based on the conservation of the inter-residue contacts at the interface, both for the analysis of the interface in whole ensembles of NMR complexes and for the possible selection of a single conformer as the best representative of the overall interface. In order to make the analyses automatic and fast, we made the protocol available as a web tool at: https://www.molnac.unisa.it/BioTools...srank-nmr.html.
[NMR paper] Accounting for Conformational Variability in Protein-Ligand Docking with NMR-Guided Rescoring.
Accounting for Conformational Variability in Protein-Ligand Docking with NMR-Guided Rescoring.
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J Am Chem Soc. 2013 Apr 8;
Authors: Skjærven L, Codutti L, Angelini A, Grimaldi M, Latek D, Monecke P, Dreyer MK, Carlomagno T
Abstract
A key component to success in structure-based drug design is reliable information on protein-ligand interactions. Recent development in NMR techniques has accelerated this process by overcoming some of...
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Accounting for Conformational Variability in Protein–Ligand Docking with NMR-Guided Rescoring
Accounting for Conformational Variability in Protein–Ligand Docking with NMR-Guided Rescoring
Lars Skjærven, Luca Codutti, Andrea Angelini, Manuela Grimaldi, Dorota Latek, Peter Monecke, Matthias K. Dreyer and Teresa Carlomagno
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja4007468/aop/images/medium/ja-2013-007468_0009.gif
Journal of the American Chemical Society
DOI: 10.1021/ja4007468
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/39zhOcXGgnI
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Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes.
Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes.
Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes.
Amino Acids. 2011 Apr 9;
Authors: Hu M, Li Y, Yang G, Li G, Li M, Wen Z
Internal motions and flexibility are essential for biological functions in proteins. To assess the internal fluctuations and conformational flexibility of proteins, reliable computational methods are needed. In this study, wavelet transformation was used to filter out the noise and...
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04-12-2011 11:08 AM
[NMR paper] Rapid analysis of large protein-protein complexes using NMR-derived orientational con
Rapid analysis of large protein-protein complexes using NMR-derived orientational constraints: the 95 kDa complex of LpxA with acyl carrier protein.
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J Mol Biol. 2004 Nov 5;343(5):1379-89
Authors: Jain NU, Wyckoff TJ, Raetz CR, Prestegard JH
Characterization of protein-protein interactions that are critical to the specific function of many biological systems has become a primary...
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11-24-2010 10:03 PM
[NMR paper] Principal components analysis of protein structure ensembles calculated using NMR dat
Principal components analysis of protein structure ensembles calculated using NMR data.
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J Biomol NMR. 2001 May;20(1):61-70
Authors: Howe PW
One important problem when calculating structures of biomolecules from NMR data is distinguishing converged structures from outlier structures. This paper describes how Principal Components Analysis (PCA) has the potential to classify calculated structures automatically, according to correlated...
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11-19-2010 08:32 PM
[NMR paper] Structure prediction of protein complexes by an NMR-based protein docking algorithm.
Structure prediction of protein complexes by an NMR-based protein docking algorithm.
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J Biomol NMR. 2001 May;20(1):15-21
Authors: Kohlbache O, Burchardt A, Moll A, Hildebrandt A, Bayer P, Lenhof HP
Protein docking algorithms can be used to study the driving forces and reaction mechanisms of docking processes. They are also able to speed up the lengthy process of experimental structure elucidation of protein complexes by proposing potential...
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[NMR paper] 31P NMR analysis of the DNA conformation induced by protein binding SRY/DNA complexes
31P NMR analysis of the DNA conformation induced by protein binding SRY/DNA complexes.
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Eur J Biochem. 2000 Feb;267(4):1223-9
Authors: Castagné C, Murphy EC, Gronenborn AM, Delepierre M
Complexes of the HMG box protein SRY with two duplexes of 8 and 14 base pairs have been studied by 31P NMR and complete assignment of all phosphorus signals of the bound DNA duplexes are presented. While for the free DNA, all 31P signals display limited...
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Structure-based protein NMR assignments using native structural ensembles
Structure-based protein NMR assignments using native structural ensembles
Mehmet Serkan Apaydın, Vincent Conitzer and Bruce Randall Donald
Journal of Biomolecular NMR; 2008; 40(4); pp 263-276
Abstract:
An important step in NMR protein structure determination is the assignment of resonances and NOEs to corresponding nuclei. Structure-based assignment (SBA) uses a model structure (“template”) for the target protein to expedite this process. Nuclear vector replacement (NVR) is an SBA framework that combines multiple sources of NMR data (chemical shifts, RDCs, sparse NOEs, amide exchange...
Analysis of the interface variability in NMR structure ensembles of protein-protein complexes
Linear Mode
