Enzymatic reactions of triosephosphate isomerase: A theoretical calibration study
Enzymatic reactions of triosephosphate isomerase: A theoretical calibration study
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磷酸三糖异构酶的酶促反应：理论校准研究
DOI：
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发表时间：
2002
期刊：
影响因子：
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通讯作者：
W. Thiel
中科院分区：
文献类型：
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作者：
C. Lennartz;A. Schäfer;Frank Terstegen;W. Thiel
结合量子力学（QM）和分子力学（MM）计算磷酸丙糖异构酶催化转化二羟丙酮磷酸甘油醛3-磷酸。相关质子转移反应的最小值和过渡态位于QM/MM势面上。这项工作的主要目标是研究优化的结构和相对能量对QM/MM模型中的变化的敏感性，包括QM方法的选择，QM区域的大小，优化的MM区域的大小，以及QM/MM边界的处理。已经应用的QM方法结合CHARMm力场范围从半经验（AM 1）到密度泛函（BP 86，B3 LYP）和从头算（MP2）方法，最广泛的QM计算涉及275个原子和2162个基函数在密度泛函水平。不同的选择QM/MM选项的能量分布的影响进行了讨论。从机械师…
Combined quantum mechanical (QM) and molecular mechanical (MM) calculations are reported for the triosephosphate isomerase-catalyzed conversion of dihydroxyacetone phosphate into glyceraldehyde 3-phosphate. The minima and transition states for the relevant proton-transfer reactions have been located on QM/MM potential surfaces. The primary objective of this work is to study the sensitivity of optimized structures and relative energies toward variations in the QM/MM model, including the choice of the QM method, the size of the QM region, the size of the optimized MM region, and the treatment of the QM/MM boundary. The QM methods that have been applied in combination with the CHARMm force field range from semiempirical (AM1) to density functional (BP86, B3LYP) and ab initio (MP2) methods, the most extensive QM calculations involving 275 atoms and 2162 basis functions at the density functional level. Implications of the different choices of QM/MM options on the energy profile are discussed. From a mechanisti...