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Exploring allosteric communication in multiple states of the bacterial ribosome using residue network analysis

Authors
  • KÜRKÇÜOĞLU, Özge1
  • 1 Department of Chemical Engineering, Faculty of Chemical-Metallurgical Engineering, İstanbul Technical University, İstanbul , (Turkey)
Type
Published Article
Journal
Turkish Journal of Biology
Publisher
The Scientific and Technological Research Council of Turkey
Publication Date
Oct 25, 2018
Volume
42
Issue
5
Pages
392–404
Identifiers
DOI: 10.3906/biy-1802-77
PMID: 30930623
PMCID: PMC6438126
Source
PubMed Central
Keywords
License
Green

Abstract

Antibiotic resistance is one of the most important problems of our era and hence the discovery of new effective therapeutics is urgent. At this point, studying the allosteric communication pathways in the bacterial ribosome and revealing allosteric sites/residues is critical for designing new inhibitors or repurposing readily approved drugs for this enormous machine. To shed light onto molecular details of the allosteric mechanisms, here we construct residue networks of the bacterial ribosomal complex at four different states of translation by using an effective description of the intermolecular interactions. Centrality analysis of these networks highlights the functional roles of structural components and critical residues on the ribosomal complex. High betweenness scores reveal pathways of residues connecting numerous sites on the structure. Interestingly, these pathways assemble highly conserved residues, drug binding sites, and known allosterically linked regions on the same structure. This study proposes a new residue-level model to test how distant sites on the molecular machine may be linked through hub residues that are critically located on the contact topology to inherently form communication pathways. Findings also indicate intersubunit bridges B1b, B3, B5, B7, and B8 as critical targets to design novel antibiotics.

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