Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence

Explaining the helical behaviour of amino acid sequences without tertiary interactions, in aqueous solution, could be considered one of the first steps to solve the protein folding problem in a rational way. In the accompanying paper the information about the conformational behaviour of helical peptides in solution, as well as the studies on alpha-helix stability in proteins has been utilised to derive a database of energy interactions. This database, when implemented in an algorithm based on the helix-coil transition theory (AGADIR), correctly calculates the average helical behaviour in solution of 423 peptides analysed by circular dichroism. The majority of these peptides have been studied at low temperatures (0 to 10 degrees C), and neutral pH. However, in vivo, proteins fold at higher temperatures and in some cases low or high pH values. To understand protein folding it is necessary to calculate the helical behaviour of linear peptides under very different temperature and pH experimental conditions. We have included the temperature and pH effects on the helical behaviour of peptides by means of generally accepted assumptions and simplifications. The inclusion of these terms allow us to calculate the helical behaviour of polyalanine-based peptides, as well as of complex natural sequences, under different experimental conditions.