Literature DB >> 9079377

Modeling protein folding: the beauty and power of simplicity.

E I Shakhnovich1.   

Abstract

It is argued that simplified models capture key features of protein stability and folding, whereas more detailed models may be more appropriate for protein structure prediction. A brief overview of experimental and theoretical results is presented that corroborates these points. I argue that statistical models capture the key principle of protein stability-cooperativity- and therefore provide a reasonable estimate of protein free energy whereas more detailed but less physically transparent calculations fail to do so. I also explain that the previously published claim that simple models give predictions that are inconsistent with experiments on polypeptide block-copolymers is based on incomplete analysis of such experiment.

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Year:  1996        PMID: 9079377     DOI: 10.1016/s1359-0278(96)00027-2

Source DB:  PubMed          Journal:  Fold Des        ISSN: 1359-0278


  11 in total

1.  Sequence evolution and the mechanism of protein folding.

Authors:  A R Ortiz; J Skolnick
Journal:  Biophys J       Date:  2000-10       Impact factor: 4.033

2.  The calorimetric criterion for a two-state process revisited.

Authors:  Y Zhou; C K Hall; M Karplus
Journal:  Protein Sci       Date:  1999-05       Impact factor: 6.725

3.  Protein folding pathways and kinetics: molecular dynamics simulations of beta-strand motifs.

Authors:  Hyunbum Jang; Carol K Hall; Yaoqi Zhou
Journal:  Biophys J       Date:  2002-08       Impact factor: 4.033

4.  Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model.

Authors:  Feng Ding; Sergey V Buldyrev; Nikolay V Dokholyan
Journal:  Biophys J       Date:  2004-11-08       Impact factor: 4.033

5.  Comparing folding codes in simple heteropolymer models of protein evolutionary landscape: robustness of the superfunnel paradigm.

Authors:  Richard Wroe; Erich Bornberg-Bauer; Hue Sun Chan
Journal:  Biophys J       Date:  2004-10-22       Impact factor: 4.033

6.  Classifying proteinlike sequences in arbitrary lattice protein models using LatPack.

Authors:  Martin Mann; Daniel Maticzka; Rhodri Saunders; Rolf Backofen
Journal:  HFSP J       Date:  2008-11-26

7.  Shape-dependent designability studies of lattice proteins.

Authors:  Myron Peto; Andrzej Kloczkowski; Robert L Jernigan
Journal:  J Phys Condens Matter       Date:  2007-07-18       Impact factor: 2.333

8.  Initiation sites of protein folding by NMR analysis.

Authors:  S M Freund; K B Wong; A R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  1996-10-01       Impact factor: 11.205

9.  Is the molten globule a third phase of proteins?

Authors:  V S Pande; D S Rokhsar
Journal:  Proc Natl Acad Sci U S A       Date:  1998-02-17       Impact factor: 11.205

10.  Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models.

Authors:  Abhishek K Jha; Karl F Freed
Journal:  J Chem Phys       Date:  2008-01-21       Impact factor: 3.488

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