Protein flexibility prediction by an all-atom mean-field statistical theory

B. P. Pandey; Chi Zhang; Xianzhang Yuan; Jian Zi; Yaoqi Zhou

doi:10.1110/ps.041311005

Protein flexibility prediction by an all-atom mean-field statistical theory

B. P. Pandey, Chi Zhang, Xianzhang Yuan, Jian Zi, Yaoqi Zhou

Research output: Contribution to journal › Article › peer-review

18 Citations (Scopus)

Abstract

We extended a mean-field model to proteins with all atomic detail. The all-atom mean-field model was used to calculate the dynamic and thermodynamic properties of a three-helix bundle fragment of Staphylococcal protein A (Protein Data Bank [PDB] ID 1BDD) and alpha-spectrin SH3 domain protein (PDB ID 1SHG). We show that a model with all-atomic detail provides a significantly more accurate prediction of flexibility of residues in proteins than does a coarse-grained residue-level model. The accuracy of flexibility prediction is further confirmed by application of the method to 18 additional proteins with the largest size of 224 residues.

Original language	English
Pages (from-to)	1772-1777
Number of pages	6
Journal	Protein science : a publication of the Protein Society
Volume	14
Issue number	7
DOIs	https://doi.org/10.1110/ps.041311005
Publication status	Published - 2005
Externally published	Yes

Keywords

protein flexibility
mean-field statistical theory
protein thermodynamics
all-atom model

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10.1110/ps.041311005

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title = "Protein flexibility prediction by an all-atom mean-field statistical theory",

abstract = "We extended a mean-field model to proteins with all atomic detail. The all-atom mean-field model was used to calculate the dynamic and thermodynamic properties of a three-helix bundle fragment of Staphylococcal protein A (Protein Data Bank [PDB] ID 1BDD) and alpha-spectrin SH3 domain protein (PDB ID 1SHG). We show that a model with all-atomic detail provides a significantly more accurate prediction of flexibility of residues in proteins than does a coarse-grained residue-level model. The accuracy of flexibility prediction is further confirmed by application of the method to 18 additional proteins with the largest size of 224 residues.",

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year = "2005",

doi = "10.1110/ps.041311005",

language = "English",

volume = "14",

pages = "1772--1777",

journal = "Protein science : a publication of the Protein Society",

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TY - JOUR

T1 - Protein flexibility prediction by an all-atom mean-field statistical theory

AU - Pandey, B. P.

AU - Zhang, Chi

AU - Yuan, Xianzhang

AU - Zi, Jian

AU - Zhou, Yaoqi

PY - 2005

Y1 - 2005

N2 - We extended a mean-field model to proteins with all atomic detail. The all-atom mean-field model was used to calculate the dynamic and thermodynamic properties of a three-helix bundle fragment of Staphylococcal protein A (Protein Data Bank [PDB] ID 1BDD) and alpha-spectrin SH3 domain protein (PDB ID 1SHG). We show that a model with all-atomic detail provides a significantly more accurate prediction of flexibility of residues in proteins than does a coarse-grained residue-level model. The accuracy of flexibility prediction is further confirmed by application of the method to 18 additional proteins with the largest size of 224 residues.

AB - We extended a mean-field model to proteins with all atomic detail. The all-atom mean-field model was used to calculate the dynamic and thermodynamic properties of a three-helix bundle fragment of Staphylococcal protein A (Protein Data Bank [PDB] ID 1BDD) and alpha-spectrin SH3 domain protein (PDB ID 1SHG). We show that a model with all-atomic detail provides a significantly more accurate prediction of flexibility of residues in proteins than does a coarse-grained residue-level model. The accuracy of flexibility prediction is further confirmed by application of the method to 18 additional proteins with the largest size of 224 residues.

KW - protein flexibility

KW - mean-field statistical theory

KW - protein thermodynamics

KW - all-atom model

U2 - 10.1110/ps.041311005

DO - 10.1110/ps.041311005

M3 - Article

C2 - 15987905

SN - 0961-8368

VL - 14

SP - 1772

EP - 1777

JO - Protein science : a publication of the Protein Society

JF - Protein science : a publication of the Protein Society

IS - 7

ER -

Protein flexibility prediction by an all-atom mean-field statistical theory

Abstract

Keywords

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