Designing Well-Structured Cyclic Pentapeptides Based on Sequence-Structure Relationships.

ABSTRACT: Cyclic peptides are a promising class of molecules for unique applications. Unfortunately, cyclic peptide design is severely limited by the difficulty in predicting the conformations they will adopt in solution. In this work, we use explicit-solvent molecular dynamics simulations to design well-structured cyclic peptides by studying their sequence-structure relationships. Critical to our approach is an enhanced sampling method that exploits the essential transitional motions of cyclic peptides to efficiently sample their conformational space. We simulated a range of cyclic pentapeptides from all-glycine to a library of cyclo-(X1X2AAA) peptides to map their conformational space and determine cooperative effects of neighboring residues. By combining the results from all cyclo-(X1X2AAA) pepti

SUBMITTER: Slough DP 

PROVIDER: S-EPMC6071411 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature