Structural characterization of overrepresented

Abstract: Background: Through the last decades vast amount of sequence information have been produced by various protein sequencing projects, which enables studies of sequential patterns. One of the bestknown efforts to chart short peptide sequences is the Prosite pattern data bank. While sequential patterns like those of Prosite have proved very useful for classifying protein families, functions etc. structural analysis may provide more information and possible crucial clues linked to protein folding. Today PDB, which is the main repository for protein structure, contains more than 50’000 entries which enables structural protein studies. Result: Strongly folded pentapeptides, defined as pentapeptides which retained a specific conformation in several significantly structurally different proteins, were studied out of PDB. Among these several groups were found. Possibly the most well defined is the “double Cys” pentapeptide group, with two amino acids in between (CXXCX|XCXXC) which were found to form backbone loops where the two Cysteine amino acids formed a possible Cys-Cys bridge. Other structural motifs were found both in helixes and in sheets like "ECSAM" and "TIKIW", respectively. Conclusion: There is much information to be extracted by structural analysis of pentapeptides and other oligopeptides. There is no doubt that some pentapeptides are more likely to obtain a specific fold than others and that there are many strongly folded pentapeptides. By combining the usage of such patterns in a protein folding model, such as the Hydrophobic-polar-model improvements in speed and accuracy can be obtained. Comparing structural conformations for important overrepresented pentapeptides can also help identify and refine both structural information data banks such as SCOP and sequential pattern data banks such as Prosite.