Structural variations within proteins can be as large as variations observed across their homologues

Vetrivel, Iyanar and de Brevern, Alexandre G and Cadet, Frederic and Srinivasan, Narayanaswamy and Offmann, Bernard (2019) Structural variations within proteins can be as large as variations observed across their homologues. In: BIOCHIMIE, 167 . pp. 162-170.

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Abstract

Understanding the structural plasticity of proteins is key to understanding the intricacies of their functions and mechanistic basis. In the current study, we analyzed the available multiple crystal structures of the same protein for the structural differences. For this purpose we used an abstraction of protein structures referred as Protein Blocks (PBs) that was previously established. We also characterized the nature of the structural variations for a few proteins using molecular dynamics simulations. In both the cases, the structural variations were summarized in the form of substitution matrices of PBs. We show that certain conformational states are preferably replaced by other specific conformational states. Interestingly, these structural variations are highly similar to those previously observed across structures of homologous proteins (r(2) = 0.923) or across the ensemble of conformations from NMR data (r(2) = 0.919). Thus our study quantitatively shows that overall trends of structural changes in a given protein are nearly identical to the trends of structural differences that occur in the topologically equivalent positions in homologous proteins. Specific case studies are used to illustrate the nature of these structural variations.

Item Type:	Journal Article
Publication:	BIOCHIMIE
Publisher:	ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER
Additional Information:	Copyright of this article belongs to ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER
Keywords:	Protein conformation; Protein structural variation; Structural alphabet; Molecular dynamics
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	18 Dec 2019 07:40
Last Modified:	18 Dec 2019 07:40
URI:	http://eprints.iisc.ac.in/id/eprint/64035

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