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Molecular dynamics simulations identify the regions of compromised thermostability in SazCA
Author(s) -
Kumar Shashi,
Seth Deepak,
Deshpande Parag Arvind
Publication year - 2021
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.26022
Subject(s) - thermostability , molecular dynamics , chemistry , root mean square , salt bridge , thermal stability , molecular model , opls , computational chemistry , stereochemistry , physics , water model , biochemistry , enzyme , organic chemistry , mutant , gene , quantum mechanics
The present study examined the structure and dynamics of the most active and thermostable carbonic anhydrase, SazCA, probed using molecular dynamics simulations. The molecular system was described by widely used biological force‐fields (AMBER, CHARMM22, CHARMM36, and OPLS‐AA) in conjunction with TIP3P water model. The comparison of molecular dynamics simulation results suggested AMBER to be a suitable choice to describe the structure and dynamics of SazCA. In addition to this, we also addressed the effect of temperature on the stability of SazCA. We performed molecular dynamics simulations at 313, 333, 353, 373, and 393 K to study the relationship between thermostability and flexibility in SazCA. The amino acid residues VAL98, ASN99, GLY100, LYS101, GLU145, and HIS207 were identified as the most flexible residues from root‐mean‐square fluctuations. The salt bridge analysis showed that ion‐pairs ASP113‐LYS81, ASP115‐LYS81, ASP115‐LYS114, GLU144‐LYS143, and GLU144‐LYS206, were responsible for the compromised thermal stability of SazCA.