title: Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides.
abstract: Cystine-knot peptides have remarkable stability against protease degradation and are attractive scaffolds for peptide-based therapeutic and diagnostic agents. In this work, by studying the hydrolysis reaction of a cystine-knot inhibitor MCTI-A and its variants with ab initio QM/MM molecular dynamics simulations, we have elucidated an amide rotation hindrance mechanism for proteolysis resistance: The proteolysis of MCTI-A is retarded due to the higher free energy cost during the rotation of NH group around scissile peptide bond at the tetrahedral intermediate of acylation, and covalent constraint provided by disulfide bonds is the key factor to hinder this rotation. A nearly linear correlation has been revealed between free energy barriers of the peptide hydrolysis reaction and the amide rotation free energy changes at the protease-peptide Michaelis complex state. This suggests that amide rotation hindrance could be one useful feature to estimate peptide proteolysis stability.
authors.affiliation: Laboratory of Mesoscopic Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China.
authors.forename: Yanzi
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Laboratory of Mesoscopic Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China.
authors.forename: Daiqian
authors.initials: D
authors.lastname: Xie
authors.affiliation: Department of Chemistry, New York University , New York, New York 10003 United States.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.
authors.forename: Yingkai
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D000215:Acylation; D000595:Amino Acid Sequence; D000818:Animals; D003553:Cystine / Q000737:chemistry* / Q000378:metabolism*; D004220:Disulfides / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D059748:Proteolysis; D013552:Swine; D013816:Thermodynamics; D014357:Trypsin / Q000378:metabolism*
chemical_list: D004220:Disulfides; D010455:Peptides; D003553:Cystine; D014357:Trypsin