Origin of Scaling Behavior of Protein Packing Density A Sequential Monte Carlo Study of Com.pdf

Origin of Scaling Behavior of Protein Packing Density: A Sequential Monte Carlo Study of Compact Long Chain Polymers 3 0 1 1,2 3 1,∗ Jinfeng Zhang , Rong Chen , Chao Tang , and Jie Liang 0 1Departments of Bioengineering and 2Information Decision Science 2 University of Illinois at Chicago, 845 S. Morgan St, Chicago, IL 60607 n 3 a NEC Research Institute, 4 Independence Way, Princeton, NJ 08540 J (Dated: February 2, 2008) 8 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 ] t proteins decreases with chain length. We find that the radius of gyration provides poor description f o of protein packing but the alpha contact number we introduce here characterize proteins well. We s further demonstrate that protein-like scaling relationsh ip between packing density and chain length t. is observed in off-lattice self-avoiding walks. A key problem in studying compact chain polymer is a the attrition problem: It is difficult to generate independent samples of compact long self-avoiding m walks. We develop an algorithm based on the framework of sequential Monte Carlo and succeed in - generating popula