Intramolecular disulphide bond arrangements in nonhomologous proteins

Hartig, Gerald R. S., Tran, Tran T. and Smythe, Mark L. (2005) Intramolecular disulphide bond arrangements in nonhomologous proteins. Protein Science, 14 2: 474-482. doi:10.1110/ps.04923305


Author Hartig, Gerald R. S.
Tran, Tran T.
Smythe, Mark L.
Title Intramolecular disulphide bond arrangements in nonhomologous proteins
Journal name Protein Science   Check publisher's open access policy
ISSN 0961-8368
Publication date 2005-01-01
Sub-type Article (original research)
DOI 10.1110/ps.04923305
Volume 14
Issue 2
Start page 474
End page 482
Total pages 9
Place of publication Woodbury
Publisher Cold Spring Harbor Lab Press, Publications Dept
Collection year 2005
Language eng
Subject C1
239901 Biological Mathematics
780103 Chemical sciences
Abstract The presence and location of intramolecular disulphide bonds are a key determinant of the structure and function of proteins. Intramolecular disulphide bonds in proteins have previously been analyzed under the assumption that there is no clear relationship between disulphide arrangement and disulphide concentration. To investigate this, a set of sequence nonhomologous protein chains containing one or more intramolecular disulphide bonds was extracted from the Protein Data Bank, and the arrangements of the bonds, Protein Data Bank header, and Structural Characterization of Proteins fold were analyzed as a function of intramolecular, containing proteins were disulphide bond concentration. Two populations of intramolecular disulphide bond-containing identified, with a naturally occurring partition at 25 residues per bond. These populations were named intramolecular disulphide bond-rich and -poor. Benefits of partitioning were illustrated by three results: (1) rich chains most frequently contained three disulphides, explaining the plateaux in extant disulphide frequency distributions; (2) a positive relationship between median chain length and the number of disulphides, only seen when the data were partitioned-, and (3) the most common bonding pattern for chains with three disulphide bonds was based on the most common for two, only when the data were partitioned. The two populations had different headers, folds, bond arrangements, and chain lengths. Associations between IDSB concentration, IDSB bonding pattern, loop sizes, SCOP fold, and PDB header were also found. From this, we found that intramolecular disulphide bond-rich and -poor proteins follow different bonding rules, and must be considered separately to generate meaningful models of bond formation.
Keyword Disulphide
Disulfide
Nonhomologous
Pdb
Pdbselect
Arrangement
Pattern
Biochemistry & Molecular Biology
Globular-proteins
Classification
Stability
Connectivity
Sequences
Cysteines
Database
Cross
State
Q-Index Code C1

 
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Created: Wed, 15 Aug 2007, 16:25:46 EST