FEASIBILITY OF MODELING REACTIONS IN ENZYME ACTIVE SITES

氯代烃是EPA超级基金中最大的一类有毒化学物质。将氯化碳氢化合物转化为毒性较小的化学物质的一种有趣的方法是生物修复，在这种方法中，生物体利用或分离有毒化学物质作为其生物功能的一部分。我们广泛的，长期的目标是使用计算方法来指导更有效的酶的工程负责生物修复。我们将首先研究模型系统中描述反应的计算方法，然后探索使用这些方法来描述酶活性部位发生的反应。我们将重点介绍1,2-二氯乙烷转化为2-氯乙醇催化的卤代烷烃脱卤酶。该反应的机理和中间结构是已知的。我们将使用两个模型系统：氯离子与氯甲烷在水中的反应，以及氢氧根离子与1,2-二氯乙烷在四氯化碳中的反应。从头计算量子力学能量，并将其用于参数化势能函数。平均力势将用蒙特卡罗方法计算。模型系统的结果将用于探索二氯乙烷在脱卤酶活性位点的反应。利用从头算方法对反应路径上各点上活性位点的几何形状进行优化。然后将优化后的结构放回酶中，用自由能摄动法计算整个酶-底物复合物的反应谱。

Chlorinated hydrocarbons constitute the largest class of toxic chemicals in EPA Superfund sites. One intriguing method of converting chlorinated hydrocarbons into less toxic chemicals is bioremediation, in which living organisms use or isolate the toxic chemicals as part of their biological function. Our broad, long-term objective is to use computational methods to guide the engineering of more efficient enzymes responsible for bioremediation. We will study first computational methods for describing reactions in model systems, then explore the use of these methods to describe reactions occurring in the active site of enzymes. We will focus on the conversion of 1,2-dichloroethane to 2-chloroethanol catalyzed the haloalkane dehalogenase. The mechanism and intermediate structures of this reaction are known. We will use two model systems: the reaction of chloride ion with methyl chloride in water, and the reaction of hydroxide ion with 1,2-dichloroethane in carbon tetrachloride. Ab initio quantum mechanical energies will be calculated and use to parameterize a potential energy function. Potentials of mean force will be calculated by Monte Carlo methods. The results from the model systems will be used to explore the reaction of dichloroethane in the active site of dehalogenase. The geometry of the active site at various points along the reaction pathway will be optimized using ab initio methods. The optimized structures will then be put back into the enzyme, and the reaction profile for the entire enzyme- substrate complex calculated with a free energy perturbation method.