• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Journal of Molecular Biology >Prudent modeling of core polar residues in computational protein design.
【24h】

Prudent modeling of core polar residues in computational protein design.

机译：计算蛋白质设计中核心极性残基的审慎建模。

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

Hydrogen bond interactions were surveyed in a set of protein structures. Compared to surface positions, polar side-chains at core positions form a greater number of intra-molecular hydrogen bonds. Furthermore, the majority of polar side-chains at core positions form at least one hydrogen bond to main-chain atoms that are not involved in hydrogen bonds to other main-chain atoms. Based on this structural survey, hydrogen bond rules were generated for each polar amino acid for use in protein core design. In the context of protein core design, these prudent polar rules were used to eliminate from consideration polar amino acid rotamers that do not form a minimum number of hydrogen bonds. As an initial test, the core of Escherichia coli thioredoxin was selected as a design target. For this target, the prudent polar strategy resulted in a minor increase in computational complexity compared to a strategy that did not allow polar residues. Dead-end elimination was used to identify global minimum energy conformations for the prudent polar and no polar strategies. The prudent polar strategy identified a protein sequence that was thermodynamically stabilized by 2.5kcal/mol relative to wild-type thioredoxin and 2.2kcal/mol relative to a thioredoxin variant whose core was designed without polar residues.
机译：在一组蛋白质结构中调查了氢键相互作用。与表面位置相比，在核心位置的极性侧链形成大量的分子内氢键。此外，在核心位置的大多数极性侧链形成与主链原子的至少一个氢键，而该氢键不参与与其他主链原子的氢键。基于此结构调查，为蛋白质核心设计中使用的每个极性氨基酸生成了氢键规则。在蛋白质核心设计的背景下，这些审慎的极性规则被用于从考虑中消除没有形成最小数目氢键的极性氨基酸旋转异构体。作为初始测试，选择了大肠杆菌硫氧还蛋白的核心作为设计目标。对于该目标，与不允许极性残基的策略相比，谨慎的极性策略导致计算复杂性的小幅增加。死角消除用于确定谨慎极性策略和非极性策略的全局最小能量构象。谨慎的极性策略确定了一种蛋白质序列，相对于野生型硫氧还蛋白而言，该蛋白质序列具有2.5kcal / mol的热力学稳定性，相对于其核心没有极性残基的硫氧还蛋白变体而言，其具有2.2kcal / mol的热力学稳定性。

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