通过分子动力学模拟和蛋白质数据库搜索,研究在模型酸乙-Phe-Gly-Gly-N-甲基胺中的芳香骨胺相互作用
1Department of Biomedical Sciences, School of Medicine, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, USA.
Journal of the American Chemical Society
|November 22, 2001
概括
芳香环-脊柱胺基相互作用 (Ar-HN) 稳定特定的形状. 分子动力学模拟显示,这些相互作用降低了溶剂可访问性和结,影响了蛋白质结构.
科学领域:
- 生物物理学的生物物理.
- 计算化学计算化学
- 蛋白质结构 蛋白质结构
背景情况:
- 弱极相互作用,特别是芳香环与脊柱胺基 (Ar-HN) 相互作用,在独特的形状状态中观察到.
- 了解这些相互作用对于表征形状和控制它们的因素至关重要.
研究的目的:
- 描述与Ar-HN相互作用相关的形状区域.
- 阐明决定中Ar-HN相互作用的构造的因素.
主要方法:
- 利用了四个4-n分子动力学模拟与一个模型三 (Ac-Phe-Gly-Gly-NH-CH(3)).
- 采用模拟回火来获得低能耗的起始形状,并分析了一个扩展的形状.
- 基于扭转角度和计算的Ar-HN吸引能量的集群结构.
主要成果:
- Ar(i) -HN(i+1) 相互作用的频率是Ar(i) -HN(i+2) 相互作用的四倍.
- 与Ar-HN相互作用的对称性显示出涉及的残留物和减少的溶剂结的溶剂接入表面面积明显较小.
- 对于Ar-HN相互作用的计算吸引能从-1.98到-9.24kJmol{-1}不等.
结论:
- Ar-HN 相互作用在稳定特定形状方面发挥着重要作用.
- 这些相互作用与减少溶剂暴露和改变结模式有关.
- 模拟的形状与蛋白质数据库中的蛋白质结构中发现的形状非常相似.
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