title: Structural propensities and entropy effects in peptide helix-coil transitions.
abstract: The helix-coil transition in peptides is a critical structural transition leading to functioning proteins. Peptide chains have a large number of possible configurations that must be accounted for in statistical mechanical investigations. Using hydrogen bond and local helix propensity interaction terms, we develop a method for obtaining and incorporating the degeneracy factor that allows the exact calculation of the partition function for a peptide as a function of chain length. The partition function is used in calculations for engineered peptide chains of various lengths that allow comparison with a variety of different types of experimentally measured quantities, such as fraction of helicity as a function of both temperature and chain length, heat capacity, and denaturation studies. When experimental sensitivity in helicity measurements is properly accounted for in the calculations, the calculated curves fit well with the experimental curves. We determine values of interaction energies for comparison with known biochemical interactions, as well as quantify the difference in the number of configurations available to an amino acid in a random coil configuration compared to a helical configuration.
authors.affiliation: Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA.
authors.forename: Ilan E
authors.initials: IE
authors.lastname: Chemmama
authors.forename: Adam Colt
authors.initials: AC
authors.lastname: Pelea
authors.forename: Yuba R
authors.initials: YR
authors.lastname: Bhandari
authors.forename: Prem P
authors.initials: PP
authors.lastname: Chapagain
authors.forename: Bernard S
authors.initials: BS
authors.lastname: Gerstman
mesh_terms: D019277:Entropy; D006358:Hot Temperature; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011489:Protein Denaturation; D017433:Protein Structure, Secondary
chemical_list: D010455:Peptides