Conformation equilibria of valine studies by dynamics simulation
Conformation equilibria of valine studies by dynamics simulation
复制标题
通过动力学模拟研究缬氨酸的构象平衡
DOI：
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发表时间：
1991
期刊：
影响因子：
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通讯作者：
J. Hermans
中科院分区：
文献类型：
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作者：
R. H. Yun;J. Hermans
通过分子动力学模拟明确水合系统：二肽、四肽和10-、14-和18-残基寡聚丙氨酸螺旋，计算了缬氨酸二肽中缬氨酸残基和α-螺旋中缬氨酸侧链的构象概率分布，以及用缬氨酸取代丙氨酸时螺旋稳定性的变化。所有计算出的自由能差异是来自至少八个单独的缓慢生长模拟的平均值，每个方向四个，并报告其均方根偏差。折叠自由能的变化（Δ-Δ G度）的不同值已计算与使用力场具有全原子和中心原子表示的甲基等。与全原子力场得到的值与新的实验值（3千焦/摩尔= 0.7千卡/摩尔）吻合良好。此外，螺旋中最稳定的缬氨酸侧链旋转异构体对于这两种表示是不同的。全原子构象的最稳定的旋转异构体与已知构象的蛋白质中α-螺旋中缬氨酸占优势的旋转异构体相同。较低的构象自由度的螺旋中的缬氨酸侧链贡献1千焦/摩尔的差异计算的稳定性与所有原子的潜力;不利的相互作用的侧链与螺旋，即使在最稳定的构象，进一步增加Δ Δ G度。
: The conformational probability distribution of a valine residue in the valine dipeptide and of the valine side chain in an alpha-helix, as well as the change in helix stability for replacing alanine with valine, has been calculated by molecular dynamics simulations of explicitly hydrated systems: dipeptide, tetrapeptide and 10-, 14- and 18-residue oligoalanine helices. All computed free-energy differences are means from at least eight separate slow-growth simulations, four in each direction and are reported with their root-mean-square deviations. Different values for the change in free energy of folding (delta delta G degrees) have been calculated with the use of forcefields having an all-atom and a central-atom representation of methyl groups, etc. The value obtained with the all-atom forcefield agrees well with new experimental values (3 kJ/mol = 0.7 kcal/mol). Furthermore, the most stable valine side-chain rotamer in the helix is different for these two representations. The most stable rotamer for the all atom conformation is the same one that predominates for valines in alpha-helices in proteins of known conformation. The lower conformational freedom of the valine side chain in the helix contributes 1 kJ/mol to the difference in stability computed with the all-atom potential; unfavorable interactions of the side chain with helix, even in the most stable conformation, further increase delta delta G degrees.