title: Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds.
abstract: We study atomic models of the thermodynamics of the structural transition of peptides that form alpha-helices. The effect of sequence variation on alpha-helix formation for alanine-rich peptides, Ac-Ala21-methyl amide (A21) and Ac-A5 (AAARA)3A-methyl amide (Fs peptide), is investigated by atomic simulation studies of the thermodynamics of the helix-coil transition in explicit water. The simulations show that the guanidinium group in the Arg side chains in the Fs peptide interacts with the carbonyl group four amino acids upstream in the chain and desolvates backbone hydrogen bonds. This desolvation can be directly correlated with a higher probability of hydrogen bond formation. We find that Fs has higher helical content than A21 at all temperatures. A small modification in the amber force field reproduces the experimental helical content and helix-coil transition temperatures for the Fs peptide.
authors.affiliation: Theoretical Division, T10 MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. angel@t10.land.gov
authors.forename: Angel E
authors.initials: AE
authors.lastname: García
authors.forename: Kevin Y
authors.initials: KY
authors.lastname: Sanbonmatsu
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D010455:Peptides