Literature DB >> 9336831

Ideal architecture of residue packing and its observation in protein structures.

G Raghunathan1, R L Jernigan.   

Abstract

A simple model of sphere packing has been investigated as an ideal model for long-range interactions for the packing of non-bonded residues in protein structures. By superposing all residues, the geometry of packing around a central residue is investigated. It is found that all residues conform almost perfectly to this lattice model for sphere packing when a radius of 6.5 A is used to define non-bonded (virtual) interacting residues. Side-chain positions with respect to sequential backbone segments are relatively regular as well. This lattice can readily be used in conformation simulations to reduce the conformational space.

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Year:  1997        PMID： 9336831      PMCID： PMC2143567          DOI： 10.1002/pro.5560061003

Source DB:  PubMed          Journal:  Protein Sci        ISSN： 0961-8368            Impact factor:   6.725


  28 in total

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Journal:  Adv Protein Chem       Date:  1959

Review 2.  Knowledge-based potentials for proteins.

Authors:  M J Sippl
Journal:  Curr Opin Struct Biol       Date:  1995-04       Impact factor: 6.809

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Authors:  B A Reva; D S Rykunov; A J Olson; A V Finkelstein
Journal:  J Comput Biol       Date:  1995       Impact factor: 1.479

4.  What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties.

Authors:  M Munson; S Balasubramanian; K G Fleming; A D Nagi; R O'Brien; J M Sturtevant; L Regan
Journal:  Protein Sci       Date:  1996-08       Impact factor: 6.725

5.  Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation.

Authors:  I Bahar; R L Jernigan
Journal:  J Mol Biol       Date:  1997-02-14       Impact factor: 5.469

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Authors:  P K Ponnuswamy; V Sasisekharan
Journal:  Int J Protein Res       Date:  1971

7.  The complexity and accuracy of discrete state models of protein structure.

Authors:  B H Park; M Levitt
Journal:  J Mol Biol       Date:  1995-06-02       Impact factor: 5.469

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Authors:  S Miyazawa; R L Jernigan
Journal:  J Mol Biol       Date:  1996-03-01       Impact factor: 5.469

9.  Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets.

Authors:  A Godzik; A Koliński; J Skolnick
Journal:  Protein Sci       Date:  1995-10       Impact factor: 6.725

10.  Mobile unnatural amino acid side chains in the core of staphylococcal nuclease.

Authors:  R Wynn; P C Harkins; F M Richards; R O Fox
Journal:  Protein Sci       Date:  1996-06       Impact factor: 6.725
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  9 in total

1.  Measures of residue density in protein structures.

Authors:  F Baud; S Karlin
Journal:  Proc Natl Acad Sci U S A       Date:  1999-10-26       Impact factor: 11.205

2.  Folding simulation of protein models on the structure-based cubo-octahedral lattice with the Contact Interactions algorithm.

Authors:  L Toma; S Toma
Journal:  Protein Sci       Date:  1999-01       Impact factor: 6.725

3.  Small-world communication of residues and significance for protein dynamics.

Authors:  Ali Rana Atilgan; Pelin Akan; Canan Baysal
Journal:  Biophys J       Date:  2004-01       Impact factor: 4.033

4.  Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication.

Authors:  Ali Rana Atilgan; Deniz Turgut; Canan Atilgan
Journal:  Biophys J       Date:  2007-02-09       Impact factor: 4.033

5.  Structure fluctuations and conformational changes in protein binding.

Authors:  Anatoly M Ruvinsky; Tatsiana Kirys; Alexander V Tuzikov; Ilya A Vakser
Journal:  J Bioinform Comput Biol       Date:  2012-04       Impact factor: 1.122

6.  Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron.

Authors:  Yaping Feng; Robert L Jernigan; Andrzej Kloczkowski
Journal:  Proteins       Date:  2008-11-15

7.  An effective evolutionary algorithm for protein folding on 3D FCC HP model by lattice rotation and generalized move sets.

Authors:  Jyh-Jong Tsay; Shih-Chieh Su
Journal:  Proteome Sci       Date:  2013-11-07       Impact factor: 2.480

8.  Optimized null model for protein structure networks.

Authors:  Tijana Milenković; Ioannis Filippis; Michael Lappe; Natasa Przulj
Journal:  PLoS One       Date:  2009-06-26       Impact factor: 3.240

9.  Constraint Logic Programming approach to protein structure prediction.

Authors:  Alessandro Dal Palù; Agostino Dovier; Federico Fogolari
Journal:  BMC Bioinformatics       Date:  2004-11-30       Impact factor: 3.169
  9 in total

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