Zhou Yanzi, Xie Daiqian, Zhang Yingkai
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.
Department of Chemistry, New York University , New York, New York 10003 United States.
J Phys Chem Lett. 2016 Apr 7;7(7):1138-42. doi: 10.1021/acs.jpclett.6b00373. Epub 2016 Mar 11.
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.
胱氨酸结肽对蛋白酶降解具有显著的稳定性，是基于肽的治疗和诊断试剂的有吸引力的支架。在这项工作中，通过从头算QM/MM分子动力学模拟研究胱氨酸结抑制剂MCTI-A及其变体的水解反应，我们阐明了一种抗蛋白水解的酰胺旋转阻碍机制：MCTI-A的蛋白水解由于在酰化四面体中间体处NH基团围绕可裂解肽键旋转时更高的自由能成本而受到阻碍，二硫键提供的共价约束是阻碍这种旋转的关键因素。在蛋白酶-肽米氏复合物状态下，肽水解反应的自由能垒与酰胺旋转自由能变化之间呈现出近乎线性的相关性。这表明酰胺旋转阻碍可能是估计肽蛋白水解稳定性的一个有用特征。
