THREE-DIMENSIONAL STRUCTURAL FEATURE SEARCH OF PROTEINS

This paper describes a three-dimensional (3D) structural feature search, or motif search, of proteins using SS3D-P. Our present approach is based upon the use of a substructure searching program for small organic molecules, SS3D, reported in our previous work. In SS3D-P, the 3D structure of a protein is approximated with the coordinates of α-carbon atoms of the main chain, and treated as a molecular graph that is represented using a distance matrix. The program allows us to specify the tolerance value of the inter-residual distances to be compared. Several characterization schemes are also available for the different amino acid residues that can be distinguished. The program we have developed was validated by search trials with 3D query patterns of known protein motif structures: the P-loop, the EF-hand, and the Zinc finger motif using Protein Data Bank (PDB) structure files.

[1]  Julian R. Ullmann,et al.  An Algorithm for Subgraph Isomorphism , 1976, J. ACM.

[2]  Xiaodong Cheng,et al.  The structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[3]  S J Remington,et al.  A systematic approach to the comparison of protein structures. , 1980, Journal of molecular biology.

[4]  J. Walker,et al.  Distantly related sequences in the alpha‐ and beta‐subunits of ATP synthase, myosin, kinases and other ATP‐requiring enzymes and a common nucleotide binding fold. , 1982, The EMBO journal.

[5]  P Willett,et al.  Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. , 1993, Journal of molecular biology.

[6]  P. R. Sibbald,et al.  The P-loop--a common motif in ATP- and GTP-binding proteins. , 1990, Trends in biochemical sciences.

[7]  K. Mizuguchi,et al.  Comparison of spatial arrangements of secondary structural elements in proteins. , 1995, Protein engineering.

[8]  P Willett,et al.  Use of techniques derived from graph theory to compare secondary structure motifs in proteins. , 1990, Journal of molecular biology.

[9]  I. von Zabern,et al.  The amino-acid sequence of sarcine adenylate kinase from skeletal muscle. , 1974, European journal of biochemistry.

[10]  Aaron Klug,et al.  ‘Zinc fingers’: a novel protein motif for nucleic acid recognition , 1987 .

[11]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[12]  Yoshimasa Takahashi,et al.  Development of a Three-Dimensional Substructure Search Program for Organic Molecules , 1997 .

[13]  W R Taylor,et al.  Protein structure alignment. , 1989, Journal of molecular biology.

[14]  Peter Willett,et al.  Rapid geometric searching in protein structures , 1989 .

[15]  U. Hobohm,et al.  Selection of representative protein data sets , 1992, Protein science : a publication of the Protein Society.

[16]  Arthur M. Lesk,et al.  Detection of three-dimensional patterns of atoms in chemical structures , 1979, CACM.

[17]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.