Velazquez Hector A, Hamelberg Donald
Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University , Atlanta, Georgia 30302-4098, United States.
J Phys Chem B. 2013 Oct 3;117(39):11509-17. doi: 10.1021/jp405271s. Epub 2013 Sep 17.
Human peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) is an essential enzyme in numerous phosphorylation-dependent regulatory pathways and has been implicated in many diseases, including cancer and Alzheimers. Pin1 specifically catalyzes cis-trans isomerization of prolyl-peptide bonds preceded by phosphorylated serine or phosphorylated threonine in its protein substrates. Yet, little is known about the catalytic mechanism of Pin1 in atomistic detail. Here, we present results from accelerated molecular dynamics simulations to show that catalysis occurs along a restricted path of the backbone configuration of the substrate, selecting out specific conformations of the substrate in the active site of Pin1. We show that the dynamics of Pin1 and the enzyme-substrate interactions are intricately coupled to isomerization during catalysis. The strength of the interactions between the phosphate binding pocket of Pin1 and the phosphate moiety of the substrate is dictated by the state of the substrate during catalysis. We also show that the transition-state configuration of the substrate binds better than the cis and trans states to the catalytic domain of Pin1, suggesting that Pin1 catalyzes its substrate by noncovalently stabilizing the transition state. These results suggest an atomistic detail understanding of the catalytic mechanism of Pin1 that is necessary for the design of novel inhibitors and the treatment of several diseases.
人肽基脯氨酰顺反异构酶NIMA相互作用蛋白1（Pin1）是众多磷酸化依赖性调节途径中的一种关键酶，并与包括癌症和阿尔茨海默病在内的多种疾病有关。Pin1特异性催化其蛋白质底物中磷酸化丝氨酸或磷酸化苏氨酸之前的脯氨酰肽键的顺反异构化。然而，关于Pin1催化机制的原子细节知之甚少。在此，我们展示了加速分子动力学模拟的结果，表明催化沿着底物主链构型的受限路径发生，在Pin1的活性位点选择出底物的特定构象。我们表明，Pin1的动力学和酶 - 底物相互作用在催化过程中与异构化复杂地耦合。Pin1的磷酸结合口袋与底物的磷酸部分之间相互作用的强度由催化过程中底物的状态决定。我们还表明，底物的过渡态构型比顺式和反式状态更好地结合到Pin1的催化结构域，这表明Pin1通过非共价稳定过渡态来催化其底物。这些结果表明对Pin1催化机制的原子细节理解对于新型抑制剂的设计和多种疾病的治疗是必要的。
