Literature DB >> 28282198

Graph's Topology and Free Energy of a Spin Model on the Graph.

Jeong-Mo Choi1, Amy I Gilson1, Eugene I Shakhnovich1.   

Abstract

In this Letter we investigate a direct relationship between a graph's topology and the free energy of a spin system on the graph. We develop a method of separating topological and energetic contributions to the free energy, and find that considering the topology is sufficient to qualitatively compare the free energies of different graph systems at high temperature, even when the energetics are not fully known. This method was applied to the metal lattice system with defects, and we found that it partially explains why point defects are more stable than high-dimensional defects. Given the energetics, we can even quantitatively compare free energies of different graph structures via a closed form of linear graph contributions. The closed form is applied to predict the sequence-space free energy of lattice proteins, which is a key factor determining the designability of a protein structure.

Entities:  

Year:  2017        PMID: 28282198      PMCID: PMC5668130          DOI: 10.1103/PhysRevLett.118.088302

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  7 in total

1.  Structural determinant of protein designability.

Authors:  Jeremy L England; Eugene I Shakhnovich
Journal:  Phys Rev Lett       Date:  2003-05-29       Impact factor: 9.161

2.  Collective dynamics of 'small-world' networks.

Authors:  D J Watts; S H Strogatz
Journal:  Nature       Date:  1998-06-04       Impact factor: 49.962

3.  Structural properties of Si1-xGex alloys: A Monte Carlo simulation with the Stillinger-Weber potential.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1995-02-15

4.  Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions.

Authors:  Muyoung Heo; Sergei Maslov; Eugene Shakhnovich
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-22       Impact factor: 11.205

5.  A new approach to the design of stable proteins.

Authors:  E I Shakhnovich; A M Gutin
Journal:  Protein Eng       Date:  1993-11

6.  Gene expression analysis on biochemical networks using the Potts spin model.

Authors:  Rainer König; Roland Eils
Journal:  Bioinformatics       Date:  2004-07-10       Impact factor: 6.937

7.  Reconstruction of a Real World Social Network using the Potts Model and Loopy Belief Propagation.

Authors:  Cristian Bisconti; Angelo Corallo; Laura Fortunato; Antonio A Gentile; Andrea Massafra; Piergiuseppe Pellè
Journal:  Front Psychol       Date:  2015-11-09
  7 in total
  3 in total

1.  Protein Melting Temperature Cannot Fully Assess Whether Protein Folding Free Energy Underlies the Universal Abundance-Evolutionary Rate Correlation Seen in Proteins.

Authors:  Rostam M Razban
Journal:  Mol Biol Evol       Date:  2019-09-01       Impact factor: 16.240

2.  ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.

Authors:  Rostam M Razban; Amy I Gilson; Niamh Durfee; Hendrik Strobelt; Kasper Dinkla; Jeong-Mo Choi; Hanspeter Pfister; Eugene I Shakhnovich
Journal:  Bioinformatics       Date:  2018-10-15       Impact factor: 6.937

Review 3.  The Protein Folding Problem: The Role of Theory.

Authors:  Roy Nassar; Gregory L Dignon; Rostam M Razban; Ken A Dill
Journal:  J Mol Biol       Date:  2021-07-03       Impact factor: 6.151

  3 in total

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