Green function of correlated genes in a minimal mechanical model of protein evolution

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Title
Green function of correlated genes in a minimal mechanical model of protein evolution
Author(s)
Sandipan Dutta; Jean-Pierre Eckmann; Albert Libchaber; Tsvi Tlusty
Publication Date
2018-05
Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v.115, no.20, pp.E4559 - E4568
Publisher
NATL ACAD SCIENCES
Abstract
The function of proteins arises from cooperative interactions and rearrangements of their amino acids, which exhibit large-scale dynamical modes. Long-range correlations have also been revealed in protein sequences, and this has motivated the search for physical links between the observed genetic and dynamic cooperativity. We outline here a simplified theory of protein, which relates sequence correlations to physical interactions and to the emergence of mechanical function. Our protein is modeled as a strongly coupled amino acid network with interactions and motions that are captured by the mechanical propagator, the Green function. The propagator describes how the gene determines the connectivity of the amino acids and thereby, the transmission of forces. Mutations introduce localized perturbations to the propagator that scatter the force field. The emergence of function is manifested by a topological transition when a band of such perturbations divides the protein into subdomains. We find that epistasis-the interaction among mutations in the gene-is related to the nonlinearity of the Green function, which can be interpreted as a sum over multiple scattering paths. We apply this mechanical framework to simulations of protein evolution and observe long-range epistasis, which facilitates collective functional modes ⓒ 2018 National Academy of Sciences.
URI
https://pr.ibs.re.kr/handle/8788114/4989
ISSN
0027-8424
Appears in Collections:
Center for Soft and Living Matter(첨단연성물질 연구단) > Journal Papers (저널논문)
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