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

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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. | Turkish Journal of Biology http://journals.tubitak.gov.tr/biology/ Research Article Turk J Biol (2018) 42: 392-404 © TÜBİTAK doi:10.3906/biy-1802-77 Exploring allosteric communication in multiple states of the bacterial ribosome using residue network analysis Özge KÜRKÇÜOĞLU* Department of Chemical Engineering, Faculty of Chemical-Metallurgical Engineering, İstanbul Technical University, İstanbul, Turkey Received: 22.02.2018 Accepted/Published Online: 09.10.2018 Final Version: 25.10.2018 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. Key words: Allosteric communication, closeness centrality, betweenness centrality, drug-resistant bacteria, druggable sites 1. .