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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Conformational entropy of alanine versus glycine in protein denatured states
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Conformational entropy of alanine versus glycine in protein denatured states

机译：蛋白质变性状态下丙氨酸对甘氨酸的构象熵

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摘要

The presence of a solvent-exposed alanine residue stabilizes a helix by 0.4-2 kcal·mol~(-1) relative to glycine. Various factors have been suggested to account for the differences in helical propensity, from the higher conformational freedom of glycine sequences in the unfolded state to hydrophobic and van der Waals' stabilization of the alanine side chain in the helical state. We have performed all-atom molecular dynamics simulations with explicit solvent and exhaustive sampling of model peptides to address the backbone conformational entropy difference between Ala and Gly in the denatured state. The mutation of Ala to Gly leads to an increase in conformational entropy equivalent to ≈0.4 kcal·mol~(-1) in a fully flexible denatured, that is, unfolded, state. But, this energy is closely counterbalanced by the (measured) difference in free energy of transfer of the glycine and alanine side chains from the vapor phase to water so that the unfolded alanine-and glycine-containing peptides are approximately isoenergetic. The helix-stabilizing propensity of Ala relative to Gly thus mainly results from more favorable interactions of Ala in the folded helical structure. The small difference in energetics in the denatured states means that the Φ-values derived from Ala → Gly scanning of helices are a very good measure of the extent of formation of structure in proteins with little residual structure in the denatured state.
机译：溶剂暴露的丙氨酸残基的存在使螺旋相对于甘氨酸稳定了0.4-2 kcal·mol〜（-1）。已经提出了各种因素来解释螺旋倾向的差异，从未折叠状态的甘氨酸序列的较高构象自由性到螺旋状态的丙氨酸侧链的疏水性和范德华斯稳定化。我们用显式溶剂和模型肽的详尽取样进行了全原子分子动力学模拟，以解决变性状态下Ala和Gly之间的骨架构象熵差。 Ala突变为Gly导致构象熵的增加，在完全柔性的变性状态（即未折叠状态）下，相当于约0.4 kcal·mol〜（-1）。但是，该能量被甘氨酸和丙氨酸侧链从气相转移到水中的自由能的（测得的）差异所抵消（因此，未折叠的含丙氨酸和甘氨酸的肽大约是等能量的）。因此，Ala相对于Gly的螺旋稳定倾向主要是由于Ala在折叠的螺旋结构中更有利的相互作用所致。变性状态下的能量学差异很小，这意味着从螺旋的Ala→Gly扫描得出的Φ值非常好地衡量了变性状态下几乎没有残留结构的蛋白质中结构的形成程度。

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