TITLE

CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data

AUTHOR(S)
Ángyán, Annamária F; Szappanos, Balázs; Perczel, András; Gáspári, Zoltán
PUB. DATE
January 2010
SOURCE
BMC Structural Biology;2010, Vol. 10, p39
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. These ensembles are usually substantially more diverse than conventional NMR ensembles and eliminate the expectation that a single conformer should fulfill all NMR parameters originating from 1016 - 1017 molecules in the sample tube. Thus, the accuracy of dynamic conformational ensembles should be evaluated differently to that of single conformers. Results: We constructed the web application CoNSEnsX (Consistency of NMR-derived Structural Ensembles with eXperimental data) allowing fast, simple and convenient assessment of the correspondence of the ensemble as a whole with diverse independent NMR parameters available. We have chosen different ensembles of three proteins, human ubiquitin, a small protease inhibitor and a disordered subunit of cGMP phosphodiesterase 5/6 for detailed evaluation and demonstration of the capabilities of the CoNSEnsX approach. Conclusions: Our results present a new conceptual method for the evaluation of dynamic conformational ensembles resulting from NMR structure determination. The designed CoNSEnsX approach gives a complete evaluation of these ensembles and is freely available as a web service at http://consensx.chem.elte.hu.
ACCESSION #
55571145

 

Related Articles

  • NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data. Mao, Wusong; Cong, Peisheng; Wang, Zhiheng; Lu, Longjian; Zhu, Zhongliang; Li, Tonghua // PLoS ONE;Dec2013, Vol. 8 Issue 12, p1 

    Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with...

  • Mining electron density for functionally relevant protein polysterism in crystal structures. Fraser, James; Jackson, Colin // Cellular & Molecular Life Sciences;Jun2011, Vol. 68 Issue 11, p1829 

    This review focuses on conceptual and methodological advances in our understanding and characterization of the conformational heterogeneity of proteins. Focusing on X-ray crystallography, we describe how polysterism, the interconversion of pre-existing conformational substates, has traditionally...

  • Comparison of parallel multi-objective approaches to protein structure prediction. Calvo, J.; Ortega, J.; Anguita, M. // Journal of Supercomputing;Nov2011, Vol. 58 Issue 2, p253 

    Protein structure prediction (PSP) is an open problem with many useful applications in disciplines such as medicine, biology and biochemistry. As this problem presents a vast search space and the analysis of each protein structure requires a significant amount of computing time, it is necessary...

  • CABS-flex predictions of protein flexibility compared with NMR ensembles. Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian // Bioinformatics;Aug2014, Vol. 30 Issue 15, p2150 

    Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an...

  • Helical membrane protein conformations and their environment. Cross, Timothy; Murray, Dylan; Watts, Anthony // European Biophysics Journal;Oct2013, Vol. 42 Issue 10, p731 

    Evidence that membrane proteins respond conformationally and functionally to their environment is growing. Structural models, by necessity, have been characterized in preparations where the protein has been removed from its native environment. Different structural methods have used various...

  • An alternative flexible conformation of the E. coli HUβ protein: structural, dynamics, and functional aspects. Garnier, Norbert; Loth, Karine; Coste, Franck; Augustyniak, Rafal; Nadan, Virginie; Damblon, Christian; Castaing, Bertrand // European Biophysics Journal;Feb2011, Vol. 40 Issue 2, p117 

    The histone-like HU protein is the major nucleoid-associated protein involved in the dynamics and structure of the bacterial chromosome. Under physiological conditions, the three possible dimeric forms of the E. coli HU protein (EcHUα, EcHUβ, and EcHUαβ) are in thermal equilibrium...

  • Structure and Calcium Binding Properties of a Neuronal Calcium-Myristoyl Switch Protein, Visinin-Like Protein 3. Li, Congmin; Lim, Sunghyuk; Braunewell, Karl H.; Ames, James B. // PLoS ONE;11/7/2016, Vol. 11 Issue 11, p1 

    Visinin-like protein 3 (VILIP-3) belongs to a family of Ca2+-myristoyl switch proteins that regulate signal transduction in the brain and retina. Here we analyze Ca2+ binding, characterize Ca2+-induced conformational changes, and determine the NMR structure of myristoylated VILIP-3. Three Ca2+...

  • Sculpting a domain by splicing. Davletov, Bazbek; Jimenez, Jose L. // Nature Structural & Molecular Biology;Jan2004, Vol. 11 Issue 1, p4 

    Comments on a study which demonstrates that a short insert from alternative splicing in a neuronal protein domain leads to rearrangements of surface loops and domain fold. Structural basis for the change of functional properties associated with alternative splicing; Functional regulation of...

  • Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles. Fenwick, R.; Esteban-Martín, Santi; Salvatella, Xavier // European Biophysics Journal;Dec2011, Vol. 40 Issue 12, p1339 

    We review the role conformational ensembles can play in the analysis of biomolecular dynamics, molecular recognition, and allostery. We introduce currently available methods for generating ensembles of biomolecules and illustrate their application with relevant examples from the literature. We...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics