...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>The Journal of Chemical Physics >Statistical geometry of lattice chain polymers with voids of defined shapes: Sampling with strong constraints
【24h】

Statistical geometry of lattice chain polymers with voids of defined shapes: Sampling with strong constraints

机译：具有确定形状的空隙的晶格链聚合物的统计几何：有严格约束的采样

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

Proteins contain many voids, which are unfilled spaces enclosed in the interior. A few of them have shapes compatible to ligands and substrates and are important for protein functions. An important general question is how the need for maintaining functional voids is influenced by, and affects other aspects of proteins structures and properties (e.g., protein folding stability, kinetic accessibility, and evolution selection pressure). In this paper, we examine in detail the effects of maintaining voids of different shapes and sizes using two-dimensional lattice models. We study the propensity for. conformations to form a void of specific shape, which is related to the entropic cost of void maintenance. We also study the location that voids of a specific shape and size tend to form, and the influence of compactness on the formation of such voids. As enumeration is infeasible for long chain polymer, a key development in this work is the design of a novel sequential Monte Carlo strategy for generating large number of sample conformations under very constraining restrictions. Our method is validated by comparing results obtained from sampling and from enumeration for short polymer chains. We succeeded in accurate estimation of entropic cost of void maintenance, with and without an increasing number of restrictive conditions, such as loops forming the wall of void with fixed length, with additionally fixed starting position in the sequence. Additionally, we have identified the key structural properties of voids that are important in determining the entropic cost of void formation. We have further developed a parametric model to predict quantitatively void entropy. Our model is highly effective, and these results indicate that voids representing functional sites can be used as an improved model for studying the evolution of protein functions and how protein function relates to protein stability. (C) 2008 American Institute of Physics.
机译：蛋白质包含许多空隙，这些空隙是封闭在内部的未填充空间。它们中的一些具有与配体和底物相容的形状，并且对于蛋白质功能很重要。一个重要的一般性问题是，维持功能性空隙的需求如何受到蛋白质结构和特性的其他方面的影响，并影响其他方面（例如，蛋白质折叠稳定性，动力学可及性和进化选择压力）。在本文中，我们详细研究了使用二维晶格模型保持不同形状和大小的空隙的效果。我们研究的倾向。形成特定形状的空隙，这与空隙维护的熵成本有关。我们还研究了特定形状和大小的空洞倾向于形成的位置，以及紧密度对此类空洞形成的影响。由于枚举对于长链聚合物是不可行的，因此这项工作的关键进展是设计了一种新颖的顺序蒙特卡洛策略，该策略可以在非常严格的限制下生成大量样品构象。通过比较从短聚合物链的采样和枚举获得的结果来验证我们的方法。我们成功地准确估计了空洞维护的熵成本，无论是否增加限制条件的数量，例如形成具有固定长度的空洞壁的环，以及依次固定的起始位置。此外，我们已经确定了空隙的关键结构特性，这些特性对确定空隙形成的熵成本很重要。我们进一步开发了一个参数模型来预测定量的空隙熵。我们的模型非常有效，这些结果表明，代表功能位点的空位可以用作研究蛋白质功能进化以及蛋白质功能与蛋白质稳定性之间关系的改进模型。 （C）2008美国物理研究所。

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