Implementation of Replica-Averaged Restraints from Nuclear Magnetic Resonance Measurement with UNRES Coarse Grained Model of Polypeptide Chains.

ABSTRACT: We report the implementation of replica-averaged molecular dynamics in the UNRES coarse-grained model of polypeptide chains, with application to the restraints determined by nuclear magnetic resonance. The analytical ESCASA algorithm is used to estimate interproton distances from coarse-grained geometry. With synthetic restraints derived from two selected conformations of the L129-L153 loop of the Slr1183 protein from Synechocystis sp. (2KW5), the replica-averaged extension of UNRES retrieved the ensemble of conformations close to the parent structures, with residual content of those not similar to any of them, and comparable populations of both families. Tests with a small putatively multistate protein (PDB: 2LWA) and two proteins with disordered regions (2KW5 and 2KZN, respectivel

SUBMITTER: Shirkov L 

PROVIDER: S-EPMC12654794 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature