Alexandre G. de Brevern's publications
Year 2014
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Mahajan S., de Brevern A.G., , Offmann B., Srinivasan N.#
Correlation between local structural dynamics of proteins inferred from NMR ensembles
and evolutionary dynamics of homologues of known structure
J Biol Struct Dyn (2014) in press.
Conformational changes in proteins are extremely important for their biochemical functions. Correlation between inherent conformational variations in a protein and conformational differences in its homologues of known structure is still unclear. In this study, we have used a structural alphabet called Protein Blocks (PBs). PBs are used to perform abstraction of protein 3-D structures into a 1-D strings of 16 alphabets (a–p) based on dihedral angles of overlapping pentapeptides. We have analyzed the variations in local conformations in terms of PBs represented in the ensembles of 801 protein structures determined using NMR spectroscopy. In the analysis of concatenated data over all the residues in all the NMR ensembles, we observe that the overall nature of inherent local structural variations in NMR ensembles is similar to the nature of local structural differences in homologous proteins with a high correlation coefficient of .94. High correlation at the alignment positions corresponding to helical and ß-sheet regions is only expected. However, the correlation coefficient by considering only the loop regions is also quite high (.91). Surprisingly, segregated position-wise analysis shows that this high correlation does not hold true to loop regions at the structurally equivalent positions in NMR ensembles and their homologues of known structure. This suggests that the general nature of local structural changes is unique; however most of the local structural variations in loop regions of NMR ensembles do not correlate to their local structural differences at structurally equivalent positions in homologues.
preprint
.
collaboration with Pr. N. Srinivasan of Molecular Biophysics Unit (IISc, India) and Pr. B. Offmann of University of Nantes (France). Funding:- Indo-French collaborative grant (CEFIPRA/IFCPAR 3903-E) [link to the project]
- The Ministry of Research (France)
- The University Paris Diderot, Sorbonne Paris Cite (France)
- The National Institute of Blood Transfusion (INTS, France)
- The National Institute of Health and Medical Research (INSERM, France)
- The Laboratories of Excellence, GR-Ex (France)
- The University of Nantes (France)
- Conseil Régional Pays de La Loire (France)
- Fonds Européen de Dévelopment Régional and Conseil Regional de La Réunion [20100079, Tiers: 144645]
- Department of Biotechnology (India)
Alexandre G. de Brevern
Last Modification : January 2014
