Coarse-Grained Multitorsional Potentials for Along-Chain Coupling of Local Conformational States in Proteins with...

The multitorsional potentials that account for the coupling between the conformational states of amino-acid residues at the coarse-grained level developed and implemented in the UNRES force field in our earlier work have been revised to cover proteins containing d-amino-acid residues by expressing the phase shifts of the consecutive Cα···Cα···Cα···Cα backbone virtual-bond dihedral angles as sums of single-residue-type contributions. Initial multitorsional-potential parameters were determined by the maximum-likelihood method, based on the statistics from the Protein Data Bank. Subsequently, UNRES with the new multitorsional potentials was calibrated by using a set of nine proteins with different secondary and tertiary structures. The UNRES force field with the revised multitorsional potentials showed improved performance in modeling the structures of α and α + β proteins and produced good models of proteins containing both l- and d-amino-acid residues. The results suggest that the along-chain coupling of local conformational states at the coarse-grained level extends to polypeptide chains composed of heterochiral amino-acid residues.