English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Single domain proteins are thought to be tightly packed. The introduction ofvoids by mutations is often regarded as destabilizing. In this study we showthat packing density for single domain proteins decreases with chain length. Wefind that the radius of gyration provides poor description of protein packingbut the alpha contact number we introduce here characterize proteins well. Wefurther demonstrate that protein-like scaling relationship between packingdensity and chain length is observed in off-lattice self-avoiding walks. A keyproblem in studying compact chain polymer is the attrition problem: It isdifficult to generate independent samples of compact long self-avoiding walks.We develop an algorithm based on the framework of sequential Monte Carlo andsucceed in generating populations of compact long chain off-lattice polymers upto length $N=2,000$. Results based on analysis of these chain polymers suggestthat maintaining high packing density is only characteristic of short chainproteins. We found that the scaling behavior of packing density with chainlength of proteins is a generic feature of random polymers satisfying looseconstraint in compactness. We conclude that proteins are not optimized byevolution to eliminate packing voids.Comment: 9 pages, 10 figures. Accepted by J. Chem. Phy

Origin of scaling behavior of protein packing density: A sequential Monte Carlo study of compact long chain polymers