Relationship between Amino Acids Sequences and Protein Structures: Folding Patterns and Sequence Patterns

Abstract

Two crucial problems of protein folding are considered here. First, the hypothesis, that all proteins with an identical SSS, regardless of degree of sequence identity among sequences have common sequence pattern. To find conserved positions and create a sequences pattern a new algorithm of the structure-based multiple sequences alignment was developed. An essential feature of the algorithm is that the alignment is based on residues that form hydrogen bond contacts between strands in protein structures. It was shown that SSS-specific sequence patterns have very high sensitivity for identifying protein structure and can be used for SSS prediction without any prior structural information. Second, the rules by which secondary structure elements – beta strands come together into supersecondary structure (SSS) – folding patterns. Knowledge of these patterns that uncover the spatial arrangement of strands will likely prove useful in protein structure prediction.