...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
【24h】

Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

机译：在计算机中折叠蛋白质：蛋白质A折叠/展开的原子描述

获取原文
获取原文并翻译 | 示例
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

We study the folding mechanism of a three-helix bundle protein at atomic resolution, including effects of explicit water. Using replica exchange molecular dynamics we perform enough sampling over a wide range of temperatures to obtain the free energy, entropy, and enthalpy surfaces as a function of structural reaction coordinates. Simulations were started from different configurations covering the folded and unfolded states. Because many transitions between all minima at the free energy surface are observed, a quantitative determination of the free energy barriers and the ensemble of configurations associated with them is now possible. The kinetic bottlenecks for folding can be determined from the thermal ensembles of structures on the free energy barriers, provided the kinetically determined transition-state ensembles are similar to those determined from free energy barriers. A mechanism incorporating the interplay among backbone ordering, side-chain packing, and desolvation arises from these calculations. Large Φ values arise not only from native contacts, which mostly form at the transition state, but also from contacts already present in the unfolded state that are partially destroyed at the transition.
机译：我们研究了一种三螺旋束蛋白在原子分辨率下的折叠机制，包括显性水的作用。使用复制体交换分子动力学，我们可以在很宽的温度范围内进行足够的采样，以获得自由能，熵和焓表面，它们是结构反应坐标的函数。从覆盖折叠和展开状态的不同配置开始进行仿真。因为在自由能表面的所有极小值之间都观察到许多过渡，所以现在可以定量确定自由能垒和与之相关的构型集合。可以从自由能垒上的结构的热集合确定折叠的动力学瓶颈，条件是动力学确定的过渡态集合与从自由能垒确定的那些相似。从这些计算中得出了一种机制，其结合了主链排序，侧链堆积和去溶剂化之间的相互作用。较大的Φ值不仅来自主要在过渡状态下形成的本机触点，而且还来自已经存在于展开状态的，在过渡状态下部分破坏的触点。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号