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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >The fragment molecular orbital method for geometry optimizations of polypeptides and proteins
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The fragment molecular orbital method for geometry optimizations of polypeptides and proteins

机译：片段分子轨道方法用于多肽和蛋白质的几何优化

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The fragment molecular orbital method (FMO) has been used with a large number of wave functions for single-point calculations, and its high accuracy in comparison to ab initio methods has been well established. We have developed the analytic derivative of the electrostatic interaction between far separated fragments and performed a number of restricted Hartree-Fock (RHF) geometry optimizations using FMO and ab initio methods. In particular, the alpha-helix, beta-turn, and extended conformers of a 10-residue polyalanine were studied and the good FMO accuracy was established (the rms deviations for the former two forms were about 0.2 A and for the latter structure about 0.001 A). Met-enkephalin dimer was used as a model for the polypeptide binding and computed at the 3-21G and 6-31G* levels with a similar accuracy achieved; the error in the binding energy predictions (FMO vs ab initio) was 1-3 kcal/mol. Chignolin (PDB: 1uao) and an agonist polypeptide of the erythropoietin receptor protein (emp1) were optimized at the 3-21(+)G level, with the rms deviation from ab initio of about 0.2 A, or 0.5 degrees in terms of bond angles. The effect of solvation on the structure optimization was studied in chignolin and the Trp-cage miniprotein construct (PDB:1l2y), by describing water with TIP3P. The computed structures in gas phase and solution are compared to each other and experiment.
机译：碎片分子轨道方法（FMO）已与大量波动函数一起用于单点计算，并且与从头算方法相比，它的准确性很高。我们已经开发了分离远的片段之间的静电相互作用的解析导数，并使用FMO和从头算方法进行了许多受限的Hartree-Fock（RHF）几何优化。特别是，研究了10个残基的聚丙氨酸的α-螺旋，β-转角和扩展构象异构体，并建立了良好的FMO精度（前两种形式的均方根偏差约为0.2 A，而后者结构的均方根偏差约为0.001。一种）。 Met-脑啡肽二聚体被用作多肽结合的模型，并以3-21G和6-31G *水平进行计算，获得了相似的准确度;结合能预测的误差（FMO与从头算）为1-3 kcal / mol。在3-21（+）G水平上优化了Chignolin（PDB：1uao）和促红细胞生成素受体蛋白的激动剂多肽（emp1），从头到尾的rms偏差约为0.2 A，即结合度为0.5度角度。通过用TIP3P描述水，在几丁质和Trp笼小蛋白构建体（PDB：1l2y）中研究了溶剂化对结构优化的影响。将气相和溶液中的计算结构相互比较并进行实验。

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