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通过Gly-to-d-Ala替代蛋白质稳定性的实验和计算分析:原始状态和展开状态效应的卷积

Junjie Zou¹, Benben Song¹, Carlos Simmerling¹

¹Department of Chemistry and ‡Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794-3400, United States.

Journal of the American Chemical Society

|December 10, 2016

概括

用d-氨基酸取代甘氨酸可以通过减少未折叠状态来增强蛋白质的稳定性. 这种策略,特别是对于特定的甘氨酸位置,为蛋白质设计提供了可预测的方法.

科学领域:

蛋白质工程
生物化学
计算生物学

背景情况:

蛋白质的稳定性对于蛋白质的设计至关重要,努力往往集中在折叠状态上.
蛋白质稳定性是由折叠和展开状态之间的自由能量差异定义的,这使得这两个目标都是可行的.
针对未折叠状态的策略旨在减少链,例如通过替换甘氨酸残留物.

研究的目的:

批判性地研究甘氨酸与d-alanine (甘氨酸与d-Ala) 替代对蛋白质稳定性的影响.
通过氨基酸替代进行可预测的蛋白质稳定,研究向未折叠状态的潜力.
确定适合Gly-to-d-Ala替代的位置,并了解稳定或不稳定的潜在机制.

主要方法:

评估蛋白质稳定的实验方法.
分子动力学模拟以建模蛋白质的行为.
计算自由能量以量化稳定性的变化.
检测高分辨率的蛋白质结构以确定替代部位.

主要成果:

绝大多数蛋白质可以通过用d-alanine替换特定的甘氨酸 (例如C-capping甘氨酸) 来稳定.
通过序列对齐可以确定合适的替代位点,成功率很高.
在原生状态下很少观察到体冲突,并且可能是少数非稳定性替代的原因.

结论:

通过减少未折叠状态来增强蛋白质稳定性的可行且经常有效的策略是gly-to-d-Ala替代.
这种方法为蛋白质设计提供了可预测的方法,可通过快速算法识别有利的候选者.
了解甘氨酸残留物的结构背景是成功实施这种稳定策略的关键.

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