对话

Origin Of Scaling Behavior Of Protein Packing Density: A Sequential Monte Carlo Study Of Compact Long Chain Polymers

JOURNAL OF CHEMICAL PHYSICS(2003)

引用 72|浏览53
摘要
Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find that the radius of gyration provides a poor description of protein packing but the alpha contact number we introduce here characterize proteins well. We further demonstrate that protein-like scaling relationship between packing density and chain length is observed in off-lattice self-avoiding walks. A key problem in studying compact chain polymers is the attrition problem: It is difficult to generate independent samples of compact long self-avoiding walks. We develop an algorithm based on the framework of sequential Monte Carlo and succeed in generating populations of compact long chain off-lattice polymers up to length N = 2000. Results based on analysis of these chain polymers suggest that maintaining high packing density is only characteristic of short chain proteins. We found that the scaling behavior of packing density with chain length of proteins is a generic feature of random polymers satisfying loose constraint in compactness. We conclude that proteins are not optimized by evolution to eliminate packing voids. (C) 2003 American Institute of Physics.
更多
查看译文
关键词
packing defects,sequential monte carlo.,protein packing,protein voids,physical properties,satisfiability,self avoiding walk,radius of gyration,single domain,sequential monte carlo
AI 理解论文
溯源树
样例
生成溯源树,研究论文发展脉络
0
您的评分 :

暂无评分

数据免责声明
页面数据均来自互联网公开来源、合作出版商和通过AI技术自动分析结果,我们不对页面数据的有效性、准确性、正确性、可靠性、完整性和及时性做出任何承诺和保证。若有疑问,可以通过电子邮件方式联系我们:report@aminer.cn