Secondary Structure in Protein Analysis

Abstract

Proteins are linear, unbranched polymers of the 20 naturally occurring amino acid residues. Under physiological conditions, most proteins self-assemble into a unique, biologically relevant structure: the native fold. This structure can be dissected into chemically recognizable, topologically simple elements of secondary structure: alpha-helix, 310-helix, beta-strand, polyproline II helix, turns, andV-loops. Together, these six familiar motifs account for ,95% of the total protein structure, and they are utilized repeatedly in mix-and-match patterns, giving rise to the repertoire of known folds. In principle, a protein’s three- dimensional structure is predictable from its amino acid sequence, but this problem remains unsolved. A related, but ostensibly simpler, problem is to predict a protein’s secondary structure elements from its sequence.