Distance-constraint approach to higher-order structures of globular proteins with empirically determined distances between amino acid residues

Hiroshi Wako, Yasushi Kubota

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

An analysis of higher-order structures of globular proteins by means of a distance-constraint approach is presented. Conformations are generated for each of 21 test proteins of small and medium sizes by optimizing an objective function f=ΣΣwij(dij-〈dij〉)2, where dij is a distance between residues i and j in a calculated conformation, 〈dij〉 is an assigned distance to the (ij) pair of residues which is determined based on the statistics of known three-dimensional structures of 14 proteins in the earlier study, and wij is a weighting factor. 〈dij〉 involves information about hydrophobicity and hydrophilicity of each amino acid residue and about connectivity of a polypeptide chain. In these calculations, only the amino acid sequence is used as input data specific to a calculated protein. With respect to higher-order structures regenerated in the optimized conformations, the following properties are analyzed: (a) N14 of a residue, defined as the number of residues surrounding the residue located within a sphere of radius of 14 Å; (b) root-mean-square differences of the global and local conformations from the corresponding X-ray conformations; (c) distance profiles in the short and medium ranges; and (d) distance maps. The effects of supplementary information about locations of secondary structures and disulfide bonds are also examined to discuss the potential ability of this methodology to predict the three-dimensional structures of globular proteins.

Original languageEnglish
Pages (from-to)233-243
Number of pages11
JournalJournal of Protein Chemistry
Volume10
Issue number2
DOIs
Publication statusPublished - 1991 Apr

Fingerprint

Conformations
Amino acids
Proteins
Amino Acids
Hydrophobic and Hydrophilic Interactions
Polypeptides
Hydrophilicity
Hydrophobicity
Disulfides
Amino Acid Sequence
X-Rays
Statistics
X rays
Peptides

Keywords

  • Distance-constraint approach
  • higher-order structure of proteins
  • hydrophobicity of amino acids
  • prediction of protein conformation
  • protein folding

ASJC Scopus subject areas

  • Biochemistry

Cite this

@article{7d39b5c894e14947bdfa98c0d3fb55ca,
title = "Distance-constraint approach to higher-order structures of globular proteins with empirically determined distances between amino acid residues",
abstract = "An analysis of higher-order structures of globular proteins by means of a distance-constraint approach is presented. Conformations are generated for each of 21 test proteins of small and medium sizes by optimizing an objective function f=ΣΣwij(dij-〈dij〉)2, where dij is a distance between residues i and j in a calculated conformation, 〈dij〉 is an assigned distance to the (ij) pair of residues which is determined based on the statistics of known three-dimensional structures of 14 proteins in the earlier study, and wij is a weighting factor. 〈dij〉 involves information about hydrophobicity and hydrophilicity of each amino acid residue and about connectivity of a polypeptide chain. In these calculations, only the amino acid sequence is used as input data specific to a calculated protein. With respect to higher-order structures regenerated in the optimized conformations, the following properties are analyzed: (a) N14 of a residue, defined as the number of residues surrounding the residue located within a sphere of radius of 14 {\AA}; (b) root-mean-square differences of the global and local conformations from the corresponding X-ray conformations; (c) distance profiles in the short and medium ranges; and (d) distance maps. The effects of supplementary information about locations of secondary structures and disulfide bonds are also examined to discuss the potential ability of this methodology to predict the three-dimensional structures of globular proteins.",
keywords = "Distance-constraint approach, higher-order structure of proteins, hydrophobicity of amino acids, prediction of protein conformation, protein folding",
author = "Hiroshi Wako and Yasushi Kubota",
year = "1991",
month = "4",
doi = "10.1007/BF01024787",
language = "English",
volume = "10",
pages = "233--243",
journal = "Protein Journal",
issn = "1572-3887",
publisher = "Springer New York",
number = "2",

}

TY - JOUR

T1 - Distance-constraint approach to higher-order structures of globular proteins with empirically determined distances between amino acid residues

AU - Wako, Hiroshi

AU - Kubota, Yasushi

PY - 1991/4

Y1 - 1991/4

N2 - An analysis of higher-order structures of globular proteins by means of a distance-constraint approach is presented. Conformations are generated for each of 21 test proteins of small and medium sizes by optimizing an objective function f=ΣΣwij(dij-〈dij〉)2, where dij is a distance between residues i and j in a calculated conformation, 〈dij〉 is an assigned distance to the (ij) pair of residues which is determined based on the statistics of known three-dimensional structures of 14 proteins in the earlier study, and wij is a weighting factor. 〈dij〉 involves information about hydrophobicity and hydrophilicity of each amino acid residue and about connectivity of a polypeptide chain. In these calculations, only the amino acid sequence is used as input data specific to a calculated protein. With respect to higher-order structures regenerated in the optimized conformations, the following properties are analyzed: (a) N14 of a residue, defined as the number of residues surrounding the residue located within a sphere of radius of 14 Å; (b) root-mean-square differences of the global and local conformations from the corresponding X-ray conformations; (c) distance profiles in the short and medium ranges; and (d) distance maps. The effects of supplementary information about locations of secondary structures and disulfide bonds are also examined to discuss the potential ability of this methodology to predict the three-dimensional structures of globular proteins.

AB - An analysis of higher-order structures of globular proteins by means of a distance-constraint approach is presented. Conformations are generated for each of 21 test proteins of small and medium sizes by optimizing an objective function f=ΣΣwij(dij-〈dij〉)2, where dij is a distance between residues i and j in a calculated conformation, 〈dij〉 is an assigned distance to the (ij) pair of residues which is determined based on the statistics of known three-dimensional structures of 14 proteins in the earlier study, and wij is a weighting factor. 〈dij〉 involves information about hydrophobicity and hydrophilicity of each amino acid residue and about connectivity of a polypeptide chain. In these calculations, only the amino acid sequence is used as input data specific to a calculated protein. With respect to higher-order structures regenerated in the optimized conformations, the following properties are analyzed: (a) N14 of a residue, defined as the number of residues surrounding the residue located within a sphere of radius of 14 Å; (b) root-mean-square differences of the global and local conformations from the corresponding X-ray conformations; (c) distance profiles in the short and medium ranges; and (d) distance maps. The effects of supplementary information about locations of secondary structures and disulfide bonds are also examined to discuss the potential ability of this methodology to predict the three-dimensional structures of globular proteins.

KW - Distance-constraint approach

KW - higher-order structure of proteins

KW - hydrophobicity of amino acids

KW - prediction of protein conformation

KW - protein folding

UR - http://www.scopus.com/inward/record.url?scp=0025760191&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0025760191&partnerID=8YFLogxK

U2 - 10.1007/BF01024787

DO - 10.1007/BF01024787

M3 - Article

C2 - 1930636

AN - SCOPUS:0025760191

VL - 10

SP - 233

EP - 243

JO - Protein Journal

JF - Protein Journal

SN - 1572-3887

IS - 2

ER -