| TEM ?-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves activity against new drugs.The crystal structures of evolved mutant and wide type ?-lactamase are extremely similar,making functional changes are not easily explained according their differences.Based on a series of computational bioinformatics and molecular modeling methods,including Direct Coupling Analysis,coarse-grained and long time-scale all atom molecular dynamics and conformational frustration estimation,we explore the direct and indirect coupled residue pairs in the protein structures,and compare the occurred difference when the corresponding mutations of TEM-52 are introduced.We identify the strongest couplings within and between the domains of 238-loop and ?-loop,as well as among the locations of mutant residues E104 K,G238S and M182 T.The followed molecular conformational change simulation and frustration estimation proved that these couplings play important role of keeping the conformations of TEM.The mutations of TEM could disturb the stability of these couplings and result in obvious conformational change in TEM.This could improve the ability of recognition and hydrolysis of TEM to antibiotics,leading to drug resistance.Finally,by using a protein druggable binding site identification method Fd-DCA,we identify a novel druggable allosteric binding site which is also strongly coupled with ?-loop.This provides a new way for designing anti-resistance drugs against ?-lactamase.Meanwhile,by targeting against the identified potential allosteric binding site,virtual screening was used to predict the bioactive allosteric inhibitors from the SPECS database and detailed bioactive assays will be performed in the future. |
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