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 language | English |
|---|---|
| Pages (from-to) | 233-243 |
| Number of pages | 11 |
| Journal | Journal of Protein Chemistry |
| Volume | 10 |
| Issue number | 2 |
| DOIs | |
| Publication status | Published - 1991 Apr |
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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
Distance-constraint approach to higher-order structures of globular proteins with empirically determined distances between amino acid residues. / Wako, Hiroshi; Kubota, Yasushi.
In: Journal of Protein Chemistry, Vol. 10, No. 2, 04.1991, p. 233-243.Research output: Contribution to journal › Article
}
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 -