Environment as Well as Sequence Determines the Secondary Structure of Proteins

Abstract

The effect of solvent environment can overwhelm the propensity of an amino acid sequence for a particular secondary structure. Equivocal sequences that are predicted to be α-helical from amino acid preference but are found to be ß-strand from x-ray diffraction of their respective proteins, and equivocal sequences that are predicted to be ß-strand but found to be a-helical, are shown by circular dichroism (CD) to be α-helical in alcohol solvents and B-strand in hydrophobic solvents. Some sequences have a strong enough propensity to overcome environmental factors, but most sequences with a propensity for a particular secondary structure assume the structure dictated by the environment These results are experimental proof that environment as well as sequence is important in determining secondary structure. This implies that the microsolvent (environment) seen by a secondary structure due to nonlocal interactions of amino acids from the tertiary structure of a protein may be an important factor in determining secondary structure. Therefore environment should be considered to correctly predict the secondary structure of an amino acid sequence in proteins.