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外膜蛋白折叠和拓从计算转移自由能量尺度

Meishan Lin¹, Dennis Gessmann¹, Hammad Naveed¹

¹Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois 60607, United States.

Journal of the American Chemical Society

|February 11, 2016

概括

了解氨基酸转移自由能量是膜蛋白折叠和结构预测的关键. 本研究介绍了一种计算方法,用于计算外膜蛋白 (OMP) 的折叠自由能量,并对实验数据进行验证.

科学领域:

计算生物物理学
结构生物学
膜蛋白科学

背景情况:

对膜蛋白结构和折叠机制的准确预测需要对氨基酸在水和脂环境之间转移自由能量的知识.
外膜β-桶蛋白 (OMPs) 在格拉姆阴性细菌中起着至关重要的作用,但它们的折叠和结构决定因素仍然不完全理解.

研究的目的:

开发和验证一个计算方法来计算OMP的跨膜区域的折叠自由能量.
量化分析氨基酸在OmpLA的脂质双层内转移的自由能量,并将它们与实验性疏水性尺度相关联.
在不对称的细菌外膜的背景下研究影响OMP折叠,拓和功能结构的因素.

主要方法:

结合经验能量函数和减少离散状态空间模型来计算折叠的自由能量.
在OmpLA的跨膜 (TM) 区域内的不同位置对所有20个氨基酸残留物的量化转移自由能量.
根据实验推导的疏水性尺度验证了计算结果.

主要成果:

计算方法准确地预测了氨基酸转移的自由能量,与实验性疏水性尺度有很好的一致性.
发现细菌外膜的不对称性和特异性TM残留在体内决定了OMP的功能折叠.
证明OMP折叠是由面向脂质的残留物驱动的,NC-IN拓受差异膜稳定性的影响;脂质A和深度依赖的合作性进一步调节折叠.

结论:

开发的计算方法是一个快速,高效和广泛适用的工具,用于预测OMP折叠的自由能量和结构特征.
环境依赖的自由能量转移可以预测OMP中的功能重要区域和结构异常.
这项研究提供了细菌外膜独特环境中的OMP折叠和拓的驱动力和决定因素.

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