Physical model of the genotype-to-phenotype map of proteins

Citation data:

Physical Review X, ISSN: 2160-3308, Vol: 7, Issue: 2

Publication Year:
2017
Usage 1
Clicks 1
Captures 38
Readers 38
Social Media 21
Tweets 15
Shares, Likes & Comments 6
Citations 7
Citation Indexes 7
Repository URL:
http://arxiv.org/abs/1608.03145; http://scholarworks.unist.ac.kr/handle/201301/22247
DOI:
10.1103/physrevx.7.021037
Author(s):
Tlusty, Tsvi; Libchaber, Albert; Eckmann, Jean-Pierre
Publisher(s):
American Physical Society (APS); American Physical Society
Tags:
Physics and Astronomy; Physics - Biological Physics; Nonlinear Sciences - Adaptation and Self-Organizing Systems; Quantitative Biology - Biomolecules
Most Recent Tweet View All Tweets
review description
How DNA is mapped to functional proteins is a basic question of living matter.We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to function. We therefore treat protein as learning amorphous matter that evolves towards such a mechanical function: Genes are binary sequences that encode the connectivity of the amino acid network that makes a protein. The gene is evolved until the network forms a shear band across the protein, which allows for long-range, soft modes required for protein function. The evolution reduces the high-dimensional sequence space to a low-dimensional space of mechanical modes, in accord with the observed dimensional reduction between genotype and phenotype of proteins. Spectral analysis of the space of 106 solutions shows a strong correspondence between localization around the shear band of both mechanical modes and the sequence structure. Specifically, our model shows how mutations are correlated among amino acids whose interactions determine the functional mode.