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首页> 外文期刊>Journal of Molecular Structure. Theochem: Applications of Theoretical Chemistry to Organic, Inorganic and Biological Problems >Solvent effects on the φ-ψ potential surfaces of glycine and alanine dipeptides studied by PCM and I-PCM methods
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Solvent effects on the φ-ψ potential surfaces of glycine and alanine dipeptides studied by PCM and I-PCM methods

机译：PCM和I-PCM方法研究甘氨酸和丙氨酸二肽对φ-ψ势能表面的溶剂影响

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摘要

Two-dimensional φ-ψ potential surfaces of representative amino acid models, For-Gly-NH_2 (1) and For-Ala-NH_2 (2), were calculated at the HF/6-311++G(2d,2p)//HF/6-31G(d) level of theory in various solvents by applying the polarizable continuum model (PCM) and isodensity polarizable continuum model (I-PCM) methods. Three dielectric constants of medium (i.e. 4.335, 32.63, and 78.39) were selected corresponding to ether, methanol, and water, respectively. The PMC potential surfaces in the solvents were found to be significantly different from the corresponding I-PCM potential surfaces due presumably to the lower approximation level. However, the both methods commonly resulted in local energy minima at the α region for 1 and the α and β regions for 2. Thus, intrinsic conformational propensities of glycine and alanine residues to adopt folded secondary structures were suggested in the solvents. Comparison of the more reliable I-PCM potentials with the Ramachandran plots extracted from protein databank (PDB_SELECT) revealed that glycine and alanine residues in folded proteins roughly adopt random statistical structures in high energy ranges (ΔE>3 and 5 kcal/mol for 1 and 2, respectively). It was also proposed that the conformational space of a polypeptide molecule is significantly restricted in water compared with that in the gas phase.
机译：在HF / 6-311 ++ G（2d，2p）/下计算出代表性氨基酸模型For-Gly-NH_2（1）和For-Ala-NH_2（2）的二维φ-ψ势能面/ HF / 6-31G（d）通过应用可极化连续体模型（PCM）和等密度可极化连续体模型（I-PCM）方法在各种溶剂中的理论水平。选择三种介质的介电常数（即4.335、32.63和78.39），分别对应于醚，甲醇和水。发现溶剂中的PMC电位表面与相应的I-PCM电位表面明显不同，这可能是由于较低的近似水平所致。然而，这两种方法通常导致1的α区域和2的α和β区域具有局部最小能量。因此，建议在溶剂中甘氨酸和丙氨酸残基的固有构象倾向采用折叠的二级结构。比较更可靠的I-PCM电位与从蛋白质数据库（PDB_SELECT）提取的Ramachandran图，发现折叠蛋白质中的甘氨酸和丙氨酸残基在高能范围内（ΔE> 3和5 kcal / mol分别为1和2）大致采用随机统计结构。 2）。还提出了与气相相比，多肽分子的构象空间在水中显着受到限制。

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