Computer Simulation of Enzymatic Reactions

描述（由申请人提供）：酶催化生物化学反应，并在执行和控制大多数生命过程中发挥重要作用。因此，对生物系统的详细了解需要了解相应酶的作用。许多疾病可以通过开发药物来控制，这些药物可以阻断导致这些疾病的病原体的关键生物途径中的酶的作用，这一事实突出了这种理解的重要性。至少在原则上，我们也有可能开发出药物来恢复与毁灭性疾病有关的有缺陷的酶的活性。另一个重要的发展是酶设计领域的出现，在定向进化和计算机辅助设计方面取得了可喜的进展。然而，这一进展尚未导致设计酶可以与天然酶竞争。因此，这一重要领域的潜力可以通过计算方法来提高，这些方法实际上确定了被催化反应的活化势垒。在以前的资助期间，我们开发了改进和应用强大的方法来模拟酶的反应，并检查了它们的性能。使用这些方法帮助我们量化了关键的催化因子，并使我们进入了一个阶段，在这个阶段，我们可以为酶设计的新前沿和催化景观的探索做出重大贡献。在此，我们提出以下计划：（i）我们将主要致力于计算机辅助酶设计：（a）推进EVB作为酶设计最后阶段的定量工具的使用;（B）为不同的筛选阶段开发粗粒度的方法，以及（c）在实际的酶设计项目中使用我们的方法，包括改变混杂酶的作用，改进可用的设计酶并帮助设计新的酶。(ii)我们将继续发展从头算自由能微扰方法，使其能够有效地用于酶促反应的研究。这将包括：（a）改进QM（ai）/MM自由能模拟中EV B参考势的使用;（B）发展和改进我们的具有平均势和基于Langevin动力学的平均力势的加速QM/MM方法;（c）改进CDFT方法在金属酶研究和自由能映射中的使用。(iii)我们将通过推进以下项目来量化折叠和稳定性之间的关系：（a）探索活性位点的预组织与蛋白质的局部稳定性之间的关系;（B）探索热稳定性与催化之间的关系;以及（c）使用简化模型来评估总稳定性和相应的化学活化自由能。(iv)我们将对几类重要的酶促反应进行研究。(v)我们将继续对不同的非静电催化方案进行系统的研究。

DESCRIPTION (provided by applicant): Enzymes catalyze biochemical reactions and play a major role in performing and controlling most life processes. Therefore, a detailed understanding of biological systems requires an understanding of the action of the corresponding enzymes. The importance of such an understanding is highlighted by the fact that many diseases can be controlled by developing drugs that block the action of enzymes in the crucial biological pathways of the pathogens that cause these diseases. It is also possible, at least in principle, to develop drugs that restore the activity of defective enzymes that are involved in devastating diseases. Another important development has been the emergence of the field of enzyme design, with promising advances in directed evolution and in computer aided design. However, this progress has not yet led to designer enzymes that can rival native enzymes. Thus, the potential of this important field can be enhanced in a major way by computational approaches that actually determine the activation barriers of the reactions that are being catalyzed. During previous grant periods, we developed refined and applied powerful methods for simulating reactions in enzymes and examined their performance. Using these methods helped us to quantify key catalytic factors and brought us to a stage where we can make significant contributions to the new frontiers of enzyme design and the exploration of catalytic landscapes. Here, we propose the following projects: (i) We will invest major effort into computer-aided enzyme design by: (a) advancing the use of the EVB as a quantitative tool in the final stage of enzyme design; (b) developing coarse grained approaches for the different screening stages, and (c) using our approaches in actual enzyme design projects, including changing the action of promiscuous enzymes, improving available designer enzymes and helping in the design of new enzymes. (ii) We will continue to develop ab initio-free energy perturbation approaches to a level where they can be used effectively in studies of enzymatic reactions. This will include: (a) improving the use of EVB reference potentials for QM(ai)/MM free energy simulations; (b) developing and refining our accelerated QM/MM approach with average potentials and a Langevin dynamics based potential of mean force, and (c) refining the use of the CDFT method in studies of metalloenzymes and in free energy mapping. (iii) We will quantify the relationship between folding and stability by advancing the following projects: (a) exploring the relationship between the pre-organization of the active sites and the local stability of the protein; (b) exploring the relationship between thermostability and catalysis, and (c) using a simplified model to evaluate the total stability and the corresponding chemical activation free energy. (iv) We will conduct studies of several important classes of enzymatic reactions. (v) We will continue with the systematic examination of different non-electrostatic catalytic proposals.