Network Re-Wiring During Allostery and Protein-Protein Interactions: A Graph Spectral Approach

Gadiyaram, V and Dighe, A and Ghosh, S and Vishveshwara, S (2021) Network Re-Wiring During Allostery and Protein-Protein Interactions: A Graph Spectral Approach. [Book Chapter]

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Abstract

The process of allostery is often guided by subtle changes in the non-covalent interactions between residues of a protein. These changes may be brought about by minor perturbations by natural processes like binding of a ligand or protein-protein interaction. The challenge lies in capturing minute changes at the residue interaction level and following their propagation at local as well as global distances. While macromolecular effects of the phenomenon of allostery are inferred from experiments, a computational microscope can elucidate atomistic-level details leading to such macromolecular effects. Network formalism has served as an attractive means to follow this path and has been pursued further for the past couple of decades. In this chapter some concepts and methods are summarized, and recent advances are discussed. Specifically, the changes in strength of interactions (edge weight) and their repercussion on the overall protein organization (residue clustering) are highlighted. In this review, we adopt a graph spectral method to probe these subtle changes in a quantitative manner. Further, the power of this method is demonstrated for capturing re-ordering of side-chain interactions in response to ligand binding, which culminates into formation of a protein-protein complex in β2-adrenergic receptors. © 2021, Springer Science+Business Media, LLC, part of Springer Nature.

Item Type:	Book Chapter
Publication:	Methods in Molecular Biology
Series.:	Methods in Molecular Biology
Publisher:	Springer Protocols
Additional Information:	Copyright to this article belongs to Humana Press Inc
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit Division of Physical & Mathematical Sciences > Mathematics
Date Deposited:	12 Feb 2021 11:07
Last Modified:	25 Jan 2023 12:01
URI:	https://eprints.iisc.ac.in/id/eprint/67518

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