Secondary Structure and Neighbor Preferences of Amino Acids

Abstract

The mystery of the relation between amino acid sequences and folding of the proteins started to fascinate researchers starting from 1960’ies. When three-dimensional structures of globular proteins were first obtained by X-ray crystallography, there was no obvious relation foundbetween amino acid sequence and conformation. The ability of globular proteins refold from their denatured, time-random coils in the absence of other biological material, led some scientists to believe in that all the information for the native, biologically active conformation is contained within the amino acid sequence. In 1970’ies Anfinsen postulated that the native structure of a protein depends only on the amino acid sequence and on the conditions of solution, and not on the kinetic folding pathway. During that decade protein folding code was seen as a sum of many small interactions. But the key idea was that the primary sequence encoded secondary structures, which then encoded tertiary structures. In this article the claim that primary sequence encodes the secondary structure will be tested by the propensity of amino acids to helix-sheet-coil conformations.