Literature DB >> 15148372

Geometry and symmetry presculpt the free-energy landscape of proteins.

Trinh Xuan Hoang1, Antonio Trovato, Flavio Seno, Jayanth R Banavar, Amos Maritan.   

Abstract

We present a simple physical model that demonstrates that the native-state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and hydrophobicity are sufficient to yield a free-energy landscape with broad minima even for a homopolymer. These minima correspond to marginally compact structures comprising the menu of folds that proteins choose from to house their native states in. Our results provide a general framework for understanding the common characteristics of globular proteins.

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Year:  2004        PMID: 15148372      PMCID: PMC419539          DOI: 10.1073/pnas.0402525101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  32 in total

1.  Protein folds: laws of form revisited.

Authors:  M Denton; C Marshall
Journal:  Nature       Date:  2001-03-22       Impact factor: 49.962

Review 2.  Is protein folding hierarchic? I. Local structure and peptide folding.

Authors:  R L Baldwin; G D Rose
Journal:  Trends Biochem Sci       Date:  1999-01       Impact factor: 13.807

3.  First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model.

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Journal:  Phys Rev Lett       Date:  1996-09-23       Impact factor: 9.161

4.  The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding.

Authors:  R V Pappu; R Srinivasan; G D Rose
Journal:  Proc Natl Acad Sci U S A       Date:  2000-11-07       Impact factor: 11.205

5.  The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins.

Authors:  David Eisenberg
Journal:  Proc Natl Acad Sci U S A       Date:  2003-09-09       Impact factor: 11.205

Review 6.  The classification and origins of protein folding patterns.

Authors:  C Chothia; A V Finkelstein
Journal:  Annu Rev Biochem       Date:  1990       Impact factor: 23.643

7.  Symmetry and the energy landscapes of biomolecules.

Authors:  P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  1996-12-10       Impact factor: 11.205

8.  Unusually stable helix formation in short alanine-based peptides.

Authors:  S Marqusee; V H Robbins; R L Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  1989-07       Impact factor: 11.205

9.  Origins of structure in globular proteins.

Authors:  H S Chan; K A Dill
Journal:  Proc Natl Acad Sci U S A       Date:  1990-08       Impact factor: 11.205

10.  Spin glasses and the statistical mechanics of protein folding.

Authors:  J D Bryngelson; P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  1987-11       Impact factor: 11.205

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  53 in total

1.  Improvement of structure-based potentials for protein folding by native and nonnative hydrogen bonds.

Authors:  Marta Enciso; Antonio Rey
Journal:  Biophys J       Date:  2011-09-20       Impact factor: 4.033

2.  Reducing the dimensionality of the protein-folding search problem.

Authors:  George D Chellapa; George D Rose
Journal:  Protein Sci       Date:  2012-07-06       Impact factor: 6.725

3.  Association thermodynamics and conformational stability of beta-sheet amyloid beta(17-42) oligomers: effects of E22Q (Dutch) mutation and charge neutralization.

Authors:  Nikolay Blinov; Lyudmyla Dorosh; David Wishart; Andriy Kovalenko
Journal:  Biophys J       Date:  2010-01-20       Impact factor: 4.033

4.  IDPs: Less Disordered and More Ordered than Expected.

Authors:  Robert Konrat
Journal:  Biophys J       Date:  2015-10-06       Impact factor: 4.033

5.  A glimpse at the organization of the protein universe.

Authors:  Michele Vendruscolo; Christopher M Dobson
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-12       Impact factor: 11.205

6.  A network representation of protein structures: implications for protein stability.

Authors:  K V Brinda; Saraswathi Vishveshwara
Journal:  Biophys J       Date:  2005-09-08       Impact factor: 4.033

7.  Secondary structure determines protein topology.

Authors:  Patrick J Fleming; Haipeng Gong; George D Rose
Journal:  Protein Sci       Date:  2006-07-05       Impact factor: 6.725

8.  Common attributes of native-state structures of proteins, disordered proteins, and amyloid.

Authors:  Trinh X Hoang; Luca Marsella; Antonio Trovato; Flavio Seno; Jayanth R Banavar; Amos Maritan
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-19       Impact factor: 11.205

Review 9.  Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.

Authors:  Eugene Shakhnovich
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

10.  Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels.

Authors:  Andriy Anishkin; Adina L Milac; H Robert Guy
Journal:  Proteins       Date:  2010-03
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