Computational Study of Catalytic Mechanisms and Specificities of Serine-Carboxyl Peptidases

本项目的目的是应用分子动力学和自由能模拟，结合混合量子力学和分子力学势函数，结合实验研究来了解丝氨酸-羧基肽酶（sedolisins），这是最近发现的一种蛋白质水解酶家族。与传统丝氨酸肽酶相比，Sedolisins改变了催化三联体和氧阴离子孔。它们存在于各种各样的生物体中，包括古细菌、细菌、霉菌、黏菌、阿米巴原虫、鱼类和哺乳动物，并在酸性环境和高温下活跃。关于sedolisins的催化过程和底物特异性的起源存在相当大的不确定性，因此通过综合计算和实验方法对这些酶进行详细研究是相当重要的。从酶催化机制的角度来看，这个家族也特别有趣，因为它似乎表现出一种结合了经典丝氨酸和天冬氨酸肽酶特征的新机制。将进行晶体学、诱变和其他实验研究，以证实从计算机模拟中得到的预测。该项目所研究的新的机理原理和催化机理将有利于生物化学领域的研究，并可能对酶的理解产生根本性的影响。这个项目的广泛影响是多方面的。PI将把研究活动与不同层次的教育结合起来。参与这个项目的研究生和本科生，包括那些来自代表性不足的群体的学生，将接受培训，他们将被邀请到国家主要的国家实验室之一与实验人员互动。与丝氨酸羧基肽酶领域的杰出日本专家合作的机会将增加国际层面，并为研究和教育活动提供额外的好处。PI将与当地高中的学生密切互动。高中学生将有机会通过各种项目在pi实验室做研究。这项活动将增强高中生的学习经验，并鼓励他们以科学为职业。PI将开发一个网站来了解酶的机制和蛋白质的构象变化，这将使教学和学习过程更加容易。

The objective of this project is to apply molecular dynamics and free energy simulations along with hybrid quantum mechanical and molecular mechanical potential function in combination with experimental studies to understand serine-carboxyl peptidases (sedolisins), a recently characterized and poorly understood family of proteolytic enzymes. Sedolisins have altered catalytic triad and oxyanion hole compared to those from classical serine peptidases. They are present in a wide variety of organisms, including archaea, bacteria, molds, slime molds, amoebas, fishes and mammals and are active under acidic environments and often at high temperature. There are considerable uncertainties concerning the catalytic processes and origins of substrate specificities for sedolisins, and detailed investigations of these enzymes through integrated computational and experimental approaches are therefore of considerable importance. This family is also of particular interest from the point of view of enzyme catalytic mechanism, because it seems to exhibit a novel mechanism that combines the features of classical serine and aspartic peptidases. Crystallographic, mutagenesis and other experimental studies will be performed to confirm the predictions obtained from computer simulations. The new mechanistic principles and catalytic mechanism studied from this project will benefit the general biochemistry community and may have a fundamental impact on understanding enzymes. The broader impacts of this project are diverse. The PI will integrate the research activities with education at different levels. Graduate and undergraduate students, including those from underrepresented groups, involved in this project will receive training and they will be invited to go to one of the nations premier national laboratories to interact with experimentalists. The opportunity to collaborate with the outstanding Japanese experts in the field of serine-carboxyl peptidases will add an international dimension and provide additional benefits to the research and educational activities. The PI will interact closely with the students at local high schools. High school students will have the opportunity to do research in the PIs lab through a variety of programs. This activity will enhance the learning experience of high school students and encourage them to pursue science as their careers. The PI will develop a website for understanding enzyme mechanisms and protein conformational changes, and this will make the teaching and learning processes much easier.