COMPUTER SIMULATIONS OF ENZYMES AND DNA

来自实验的信息是必要的，但往往不足以描述酶和DNA中化学反应的机制和能量学。最近开发的赝键量子力学/分子力学方法将被应用于模拟酶和DNA中的反应；选择这些系统是因为它们固有的生物医学兴趣，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，他们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密度泛函理论的QM/MM模拟，作为研究酶和DNA中的结构和化学反应的实验的伙伴，并对生物系统中的化学反应机理提供洞察。本课题的具体工作如下：(1)4-氧代磷酸互变酶(4OT)是一类以其氨基末端的脯氨酸为总碱进行催化的酶。实验研究仅对4OT的反应机理提供了初步的了解。我们将使用赝键QM/MM自由能方法来探索4OT的机制细节，并提供对实验观测的理解。(2)环核苷酸磷酸二酯酶(PDE)是一个复杂的超家族，通过对最常见的第二信使3‘，5’-环腺苷一磷酸(CAMP)和3‘，5’-环鸟苷一磷酸(CGMP)的共同作用，在细胞信号转导中发挥重要作用。PDE的选择性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，以解决该机制是缔合的还是解离的，并为抑制剂的设计提供洞察力和指导。(3)腈水合酶(NHase)是一种细菌金属酶，催化氰化物水合反应，是工业上最成功的酶之一。关于这个活跃中心的重要结构和机制细节仍不清楚。用赝键QM/MM方法确定了其活性中心的结构，研究了Fe(III)中心这种独特的自旋择优的结构基础，并探讨了催化反应机理。(4)核酸的化学反应，特别是碱基氧化反应，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。用准分子键QM/MM方法研究了DNA中鸟嘌呤的氧化反应，定量描述了其反应机理和电子结构。(5)进一步的方法学发展将侧重于设计用于DNA计算的C-N单键中碳边界原子的有效核势。

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.