Disclosing Allostery Through Protein Contact Networks

Luisa Di Paola, Giampiero Mei, Almerinda Di Venere, Alessandro Giuliani

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Proteins are located in the twilight zone between chemistry and biology, where a peculiar kind of complexity starts. Proteins are the smallest ‘devices’ showing a sensible adaptation to their environment by the production of appropriate behavior when facing a specific stimulus. This fact qualifies (from the ‘effector’ side) proteins as nanomachines working as catalysts, motors, or switches. However (from the sensor side), the need to single out the ‘specific stimulus’ out of thermal noise qualifies proteins as information processing devices. Allostery corresponds to the modification of the configuration (in a broad sense) of the protein molecule in response to a specific stimulus in a non-strictly local way, thereby connecting the sensor and effector sides of the nanomachine. This is why the ‘disclosing’ of allostery phenomenon is at the very heart of protein function; in this chapter, we will demonstrate how a network-based representation of protein structure in terms of nodes (aminoacid residues) and edges (effective contacts between residues) is the natural language for getting rid of allosteric phenomena and, more in general, of protein structure/function relationships.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages7-20
Number of pages14
DOIs
Publication statusPublished - 2021

Publication series

NameMethods in Molecular Biology
Volume2253
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Network descriptors
  • Protein contact networks
  • Spectral clustering

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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