Classification of protein disulphide-bridge topologies

Citation
Jm. Mas et al., Classification of protein disulphide-bridge topologies, J COMPUT A, 15(5), 2001, pp. 477-487
Citations number
65
Categorie Soggetti
Chemistry & Analysis
Journal title
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
ISSN journal
0920654X → ACNP
Volume
15
Issue
5
Year of publication
2001
Pages
477 - 487
Database
ISI
SICI code
0920-654X(200105)15:5<477:COPDT>2.0.ZU;2-B
Abstract
The preferential occurrence of certain disulphide-bridge topologies in prot eins has prompted us to design a method and a program, KNOT-MATCH, for thei r classification. The program has been applied to a database of proteins wi th less than 65% homology and more than two disulphide bridges. We have inv estigated whether there are topological preferences that can be used to gro up proteins and if these can be applied to gain insight into the structural or functional relationships among them. The classification has been perfor med by Density Search and Hierarchical Clustering Techniques, yielding thir teen main protein classes from the superimposition and clustering process. It is noteworthy that besides the disulphide bridges, regular secondary str uctures and loops frequently become correctly aligned. Although the lack of significant sequence similarity among some clustered proteins precludes th e easy establishment of evolutionary relationships, the program permits us to find out important structural or functional residues upon the superimpos ition of two protein structures apparently unrelated. The derived classific ation can be very useful for finding relationships among proteins which wou ld escape detection by current sequence or topology-based analytical algori thms.