Modeling of reaction mechanisms and site specificity in the human 20S proteasome system

人体通过一系列相互关联的循环来运作。蛋白质是通过一系列敏感而细致的调控过程来创造和破坏的，我们只是在过去的几十年里才开始掌握这些过程。蛋白酶体是这个循环中的关键参与者之一，它是一种负责降解不需要或受损蛋白质的酶复合物。如果后者不能有效地从细胞中去除，则会发生细胞凋亡。因此，20 S蛋白酶体的抑制成为治疗多种疾病的有效途径，包括癌症和病毒infections.In本项目中，我们的目标是确定在人类20 S蛋白酶体复合物中位点和底物选择性背后的因素。这一目标将通过应用多尺度建模工具来实现，从分子动力学到高级相关波函数方法。将根据其pH敏感性、位点残基所跨越的构象空间以及与抑制剂和模型底物的特异性相互作用，对6个单独的活性位点进行表征。将探讨抑制剂力场参数化的自动化模型。这些研究的结果将与最近的晶体数据和比较晶体浸泡实验进行比较。蛋白酶体抑制的反应途径将通过量子力学/分子力学方法建模。重点将放在胰凝乳蛋白酶，半胱天冬酶和胰蛋白酶的网站之间的差异。该项目的分层结构，从自由蛋白酶位点的建模，抑制剂的对接和随后的化学步骤不硬塞该项目与特异性可能发生的先验概念。本研究的结果将为未来的光束线实验提供一个框架。此外，这种基本步骤的原子模型应提供改进的描述符的选择性（非）共价结合和动力学的产品释放的高通量筛选/药物设计中的应用。

The human body operates through a series of interconnected cycles. Proteins are created and destroyed by a sensitive and meticulous chain of regulation processes which we only have come to grasp in the last few decades. One of the key players in this cycle is the proteasome, an enzymatic complex responsible for the degradation of unneeded or damaged proteins. In case the latter are not efficiently removed from the cell, apoptosis will occur. Thereby, the inhibition of the 20S proteasome emerges as an effective road to treatment of several ailments, including cancer and viral infections.In this project, we aim to determine the factors behind site and substrate selectivity in the human 20S proteasome complex. This goal will be achieved by the application of multiscale modelling tools, from molecular dynamics down to high-level correlated wave function methods. The six individual active sites will be characterized on the basis of their pH sensitivity, conformational space spanned by site residues and specific interactions to inhibitors as well as model substrates. Automated models for the parameterization of inhibitor force fields will be explored. The results of these studies will be compared to recent crystal data and comparative crystal soaking experiments.The reaction pathways for the proteasome inhibition are to be modelled by quantum mechanics/molecular mechanics methods. Emphasis will be placed in the differences between chymotryptic, caspase and trypsin sites. The layered structure of the project, from the modelling of the free protease sites, the docking of inhibitors and the subsequent chemical steps does not shoehorn the project with an a priori conception of where the specificity may occur. It provides a well needed breadth into the atomistic modeling of this complex system.The results of this research are expected to establish a framework for future beamline experiments. Furthermore, the atomistic modelling of such fundamental steps should provide improved descriptors for the selectivity in (non-)covalent binding and the kinetics of product release for application in high-throughput screening/drug design.