Role of Non-Covalent Interactions in Carbonic Anhydrase I-Topiramate Complex Based on QM/MM Approach.

ABSTRACT: Carbonic anhydrase (CA) I with a Topiramate (TPM) complex was investigated on the basis of a Quantum Mechanics/Molecular Mechanics (QM/MM) approach. The QM part was treated using Density Functional Theory (DFT) while the MM was simulated using Amberff14SB and GAFF force fields. In addition, the TIP3P model was applied to reproduce the polar environment influence on the studied complex. Next, three snapshots (after 5 ps, 10 ps, and 15 ps of the simulation time) were taken from the obtained trajectory to provide an insight into the non-covalent interactions present between the ligand and binding pocket of the protein. Our special attention was devoted to the binding site rearrangement, which is known in the literature concerning the complex. This part of the computations was performed using

SUBMITTER: Wojtkowiak K 

PROVIDER: S-EPMC10146004 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature