title: Conformational analysis of long spacers in PROSITE patterns.
abstract: To determine if variable sequences (spacers) between conserved positions in a sequence motif or pattern share a consensus structure, three-dimensional structures containing PROSITE patterns with spacers of fixed length greater than three residues were analyzed. Structural similarities of a given pattern were evaluated by computing the backbone phi, psi and side-chain chi1 dihedral order parameters. The exact bias information in analyzing the conformational variability of the patterns was taken into account by introducing a new parameter, the bias coefficient, which describes the number and distribution of residue types found at each position of a pattern in the structures. The results of the analyses show that backbone conformational heterogeneity at a given position in a sequence motif does not necessarily correlate with the residue-type variability at that position, and the long spacer region can adopt a well-defined backbone conformation, in addition to the conserved residues. Furthermore, a PROSITE pattern may be redefined to yield two or more "refined" regular expressions, each corresponding to a distinct backbone conformation. A way in which the observed structural consensus in a pattern may be employed to improve the accuracy of function prediction from sequence is suggested.
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, 11529.
authors.forename: K Y
authors.initials: KY
authors.lastname: Lin
authors.forename: J
authors.initials: J
authors.lastname: Wright
authors.forename: C
authors.initials: C
authors.lastname: Lim
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D015982:Bias; D001665:Binding Sites; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods*; D016384:Consensus Sequence; D017124:Conserved Sequence; D016208:Databases, Factual; D008024:Ligands; D010363:Pattern Recognition, Automated; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012680:Sensitivity and Specificity; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D008024:Ligands; D011506:Proteins