COMPUTER SIMULATIONS OF ENZYMES AND DNA

来自实验的信息是必要的，但往往不足以表征酶和DNA中化学反应的机制和能量学。最近发展的赝键量子力学/分子力学方法将应用于模拟酶和DNA中的反应；选择这些系统是因为它们内在的生物医学兴趣，作为起点的实验结构数据的可用性，以及与研究人员建立的合作关系，这些研究人员的实验室已经研究了这些系统并将继续这样做。该项目的长期目标是开发和建立基于dft的QM/MM模拟，作为酶和DNA结构和化学反应研究的实验伙伴，并为生物系统中的化学反应机制提供见解。本课题的具体任务如下：(1)4-草糖醛酸自变异构酶（4OT）是一类以其氨基末端脯氨酸作为总碱基进行催化的酶。实验研究仅提供了4OT反应机理的原始图像。伪键QM/MM自由能方法将用于探索4OT的机理细节，并提供对实验观察结果的理解。(2)环核苷酸磷酸二酯酶（Cyclic nucleotide phosphodi酯酶，PDE）是组成一个多样化的超家族的酶，通过水解最常见的第二信使3',5'-环腺苷单磷酸（cAMP）和3',5'-环鸟苷单磷酸（cGMP）的共同活性，在细胞信号传递中起着重要作用。选择性PDEs抑制剂具有潜在的治疗价值。我们建议研究PDE4水解cAMP的机制，以确定其是结合还是解离的机制，并为抑制剂的设计提供见解和指导。(3)腈水合酶（nase）是一种催化腈水合作用的细菌金属酶，是工业上最成功的酶之一。关于这个活动中心的重要结构和机械细节仍然不清楚。拟键QM/MM方法将确定其活性位点的结构，研究Fe （III）中心独特自旋偏好的结构基础，探索催化反应机理。(4)核酸的化学反应性，特别是核碱基氧化反应，对于理解DNA和RNA自然受损，导致衰老和癌症的机制具有内在的兴趣。伪键QM/MM方法将用于研究DNA中的鸟嘌呤氧化反应，从而定量描述其机理和电子结构。(5)进一步的方法开发将集中于设计用于DNA计算的碳氮单键碳边界原子的有效核心势。

Information from experiments is necessary, but often insufficient to characterize the mechanisms and energetics of chemical reactions in enzymes and DNA. The recently developed pseudobond quantum mechanical/molecular mechanical approach will be applied to simulate the reactions in enzymes and DNA; the systems are chosen because of their intrinsic biomedical interests, the availability of experimental structural data as starting point, and the collaborations established with investigators whose laboratories have investigated the systems and continue to do so. The long- term goal of this project is to develop and establish the DFT-based QM/MM simulation as a partner equal to experiments for the study of structure and chemical reactions in enzymes and DNA and to provide insight into the chemical reaction mechanisms in biological systems. The following are the specific tasks of this project: (1) 4-Oxalocrontonate tautomerase (4OT) belongs to a family of enzymes which use their amino-terminal proline as a general base in catalysis. Experimental studies have only provided a primitive picture of the reaction mechanism of 4OT. The pseudobond QM/MM free energy approach will be employed to explore the mechanistic details of 4OT and provide understanding of the experimental observations. (2) Cyclic nucleotide phosphodiesterases(PDE) are enzymes forming a diverse super family and play fundamental roles in cell signal transfer by their common activity of hydrolyzing the most common second messengers 3',5'-cyclic adenosine monophosphate(cAMP) and 3',5'-cyclic guanosine monophosphate (cGMP). Selective inhibitors of PDEs are of potential therapeutic values. We propose to study the mechanism by which PDE4 hydrolyze cAMP, to address whether the mechanism is associative or dissociative, and to provide insight and guide to inhibitor design. (3) Nitrile hydratase (NHase), a bacterial metalloenzyme catalyzing the hydration of nitriles, is well-known as one of the most industrially successful enzymes. Important structural and mechanistic details concerning this active center is still not clear. The pseudobond QM/MM method will be employed to determine the structure of its active site, study the structure basis for this unique spin-preference of Fe (III) center and explore the catalytic reaction mechanisms. (4) The chemical reactivity of nucleic acids, in particular, nucleobase oxidation reactions, is of intrinsic interest in understanding the mechanisms by which DNA and RNA is naturally damaged, leading to aging and cancer. The pesudobond QM/MM methods will be applied to investigate the guanine oxidation reactions in DNA, leading to a quantitative description of the mechanism and electronic structure. (5) Further methodology development will focus on the design of the effective core potential for the carbon boundary atom in the C-N single bond for DNA calculations.