Molecular dynamics-derived rotamer libraries for d-amino acids within homochiral and heterochiral polypeptides.

ABSTRACT: Computational resources have contributed to the design and engineering of novel proteins by integrating genomic, structural and dynamic aspects of proteins. Non-canonical amino acids, such as d-amino acids, expand the available sequence space for designing and engineering proteins; however, the rotamer libraries for d-amino acids are usually constructed as the mirror images of l-amino acid rotamer libraries, an assumption that has not been tested. To this end, we have performed molecular dynamics (MD) simulations of model host-guest peptide systems containing d-amino acids. Our simulations systematically address the applicability of the mirror image convention as well as the effects of neighboring residue chirality. Rotamer libraries derived from these systems provide realistic rotamer dis

SUBMITTER: Childers MC 

PROVIDER: S-EPMC6205366 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature