Literature DB >> 12571353

Packing helices in proteins by global optimization of a potential energy function.

Marian Nanias1, Maurizio Chinchio, Jarosław Pillardy, Daniel R Ripoll, Harold A Scheraga.   

Abstract

An efficient method has been developed for packing alpha-helices in proteins. It treats alpha-helices as rigid bodies and uses a simplified Lennard-Jones potential with Miyazawa-Jernigan contact-energy parameters to describe the interactions between the alpha-helical elements in this coarse-grained system. Global conformational searches to generate packing arrangements rapidly are carried out with a Monte Carlo-with-minimization type of approach. The results for 42 proteins show that the approach reproduces native-like folds of alpha-helical proteins as low-energy local minima of this highly simplified potential function.

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Year:  2003        PMID： 12571353      PMCID： PMC149897          DOI： 10.1073/pnas.252760199

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


  14 in total

1.  Protein secondary structure prediction based on position-specific scoring matrices.

Authors:  D T Jones
Journal:  J Mol Biol       Date:  1999-09-17       Impact factor: 5.469

2.  Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions.

Authors:  E S Huang; R Samudrala; J W Ponder
Journal:  J Mol Biol       Date:  1999-07-02       Impact factor: 5.469

3.  A novel method for sampling alpha-helical protein backbones.

Authors:  B Fain; M Levitt
Journal:  J Mol Biol       Date:  2001-01-12       Impact factor: 5.469

4.  Environment-dependent residue contact energies for proteins.

Authors:  C Zhang; S H Kim
Journal:  Proc Natl Acad Sci U S A       Date:  2000-03-14       Impact factor: 11.205

5.  Application of multiple sequence alignment profiles to improve protein secondary structure prediction.

Authors:  J A Cuff; G J Barton
Journal:  Proteins       Date:  2000-08-15

6.  Fold prediction of helical proteins using torsion angle dynamics and predicted restraints.

Authors:  Chao Zhang; Jingtong Hou; Sung-Hou Kim
Journal:  Proc Natl Acad Sci U S A       Date:  2002-03-19       Impact factor: 11.205

7.  Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set.

Authors:  V A Eyrich; D M Standley; R A Friesner
Journal:  J Mol Biol       Date:  1999-05-14       Impact factor: 5.469

8.  Role of loop-helix interactions in stabilizing four-helix bundle proteins.

Authors:  K C Chou; G M Maggiora; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  1992-08-15       Impact factor: 11.205

9.  JPred: a consensus secondary structure prediction server.

Authors:  J A Cuff; M E Clamp; A S Siddiqui; M Finlay; G J Barton
Journal:  Bioinformatics       Date:  1998       Impact factor: 6.937

10.  Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors:  W Kabsch; C Sander
Journal:  Biopolymers       Date:  1983-12       Impact factor: 2.505
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  14 in total

1.  An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.

Authors:  Chi Zhang; Song Liu; Hongyi Zhou; Yaoqi Zhou
Journal:  Protein Sci       Date:  2004-02       Impact factor: 6.725

2.  Funnel sculpting for in silico assembly of secondary structure elements of proteins.

Authors:  Boris Fain; Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2003-08-18       Impact factor: 11.205

3.  A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling.

Authors:  Stefan Wallin; Hue Sun Chan
Journal:  Protein Sci       Date:  2005-06       Impact factor: 6.725

4.  An all-atom force field for tertiary structure prediction of helical proteins.

Authors:  T Herges; W Wenzel
Journal:  Biophys J       Date:  2004-11       Impact factor: 4.033

5.  Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field.

Authors:  Becky L Eggimann; Vitaly V Vostrikov; Gianluigi Veglia; J Ilja Siepmann
Journal:  Theor Chem Acc       Date:  2013-10-01       Impact factor: 1.702

6.  Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

Authors:  S Ołdziej; C Czaplewski; A Liwo; M Chinchio; M Nanias; J A Vila; M Khalili; Y A Arnautova; A Jagielska; M Makowski; H D Schafroth; R Kaźmierkiewicz; D R Ripoll; J Pillardy; J A Saunders; Y K Kang; K D Gibson; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2005-05-13       Impact factor: 11.205

7.  Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures.

Authors:  Weitao Sun; Jing He
Journal:  BMC Bioinformatics       Date:  2009-01-30       Impact factor: 3.169

8.  The HP-1 maquette: from an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange.

Authors:  Steve S Huang; Ronald L Koder; Mitchell Lewis; A Joshua Wand; P Leslie Dutton
Journal:  Proc Natl Acad Sci U S A       Date:  2004-03-31       Impact factor: 11.205

9.  Iterative assembly of helical proteins by optimal hydrophobic packing.

Authors:  G Albert Wu; Evangelos A Coutsias; Ken A Dill
Journal:  Structure       Date:  2008-08-06       Impact factor: 5.006

10.  Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

Authors:  Eshel Faraggi; Yuedong Yang; Shesheng Zhang; Yaoqi Zhou
Journal:  Structure       Date:  2009-11-11       Impact factor: 5.006
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