Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure

Abstract

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 β-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.

Key words:

• protein blocks
• protein structures
• conformational changes
• structurally equivalent positions
• loop regions

Acknowledgments

SM is supported by PhD scholarship grant from Fonds Européen de Dévelopment Régional and Conseil Regional de La Réunion [20100079, Tiers: 144645]. This research is also supported by Indo-French collaborative grant (CEFIPRA/IFCPAR 3903-E) to NS and AdB. This work was supported by grants from the Ministry of Research (France), University of Paris Diderot, Sorbonne Paris Cité (France), National Institute for Blood Transfusion (INTS, France), Institute for Health and Medical Research (INSERM, France) to AdB; University of Nantes (France) and Conseil Régional Pays de La Loire (France) to BO and Department of Biotechnology (India) to NS.