COMPUTER SIMULATIONS OF ENZYMES AND DNA

酶和 DNA 的计算机模拟

• 批准号: 6190792
• 负责人: Weitao Yang
• 金额: $ 19.04万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-07-01 至 2004-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6190792
• 关键词: DNA; active sites; chemical hydration; chemical kinetics; chemical models; chemical reaction; computer simulation; cyclic AMP; cyclic GMP; enzyme activity; enzyme inhibitors; enzyme mechanism; hydro lyase; hydrolase; isomerase; metalloenzyme; method development; model design /development; nucleic acids; oxalates; oxidation; phosphodiesterases; protein structure function; quantum chemistry; structural biology

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.

实验信息是必要的，但通常不足以表征酶和 DNA 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、实验结构数据的可用性作为起点，以及与实验室已经研究并继续研究这些系统的研究人员建立的合作。该项目的长期目标是开发和建立基于 DFT 的 QM/MM 模拟，作为研究酶和 DNA 的结构和化学反应的实验伙伴，并提供对生物系统中化学反应机制的深入了解。本项目的具体任务如下：（1）4-草酸醛酸互变异构酶（4OT）属于以氨基末端脯氨酸作为催化通用碱基的酶家族。实验研究仅提供了4OT反应机理的原始图景。将采用赝键 QM/MM 自由能方法来探索 4OT 的机制细节并提供对实验观察结果的理解。 (2) 环核苷酸磷酸二酯酶 (PDE) 是形成多样化超家族的酶，通过水解最常见的第二信使 3',5'-环单磷酸腺苷 (cAMP) 和 3',5'-环单磷酸鸟苷 (cGMP) 的共同活性，在细胞信号传递中发挥重要作用。 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，以确定该机制是缔合还是解离，并为抑制剂设计提供见解和指导。 (3)腈水合酶(NHase)是一种催化腈水合的细菌金属酶，是众所周知的工业上最成功的酶之一。有关这个活动中心的重要结构和机械细节仍不清楚。采用赝键QM/MM方法确定其活性位点的结构，研究Fe(III)中心这种独特的自旋偏好的结构基础，并探索催化反应机制。 (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 自然损伤、导致衰老和癌症的机制具有内在意义。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C-N单键中碳边界原子的有效核心势。