title: Stabilizing helical polyalanine peptides with negative polarity or charge: capping with cysteine.
abstract: Alanine-based peptides are widely known for their propensity to form helices, whether in the gas phase or in aqueous solution. Interactions of substituent groups or peptides with the helical macrodipole may either encourage or discourage the formation or stability of a helix, depending upon the placement of these groups. We report the first study of the inductive stabilization of a number of peptides through electronegative or anionic N-terminal residue capping. Using Charmm27/CMAP equilibrium and replica-exchange (REX) molecular dynamics (MD) simulations with Generalized Born implicit solvation methods, we find that the N-terminal cysteine capping of alanine peptides strongly enhances the helicity, even allowing the helical moiety to remain at temperatures beyond the denaturing temperature. Though the overall number of hydrogen bonds is enhanced, this stabilization seems to occur indirectly through interaction with the helical macrodipole rather than as a direct result of hydrogen bonding involving the cysteine, though the nature of the hydrogen bonding changes.
authors.affiliation: Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, California 95211, USA.
authors.forename: Silvya
authors.initials: S
authors.lastname: Oommachen
authors.forename: Jianhua
authors.initials: J
authors.lastname: Ren
authors.forename: C Michael
authors.initials: CM
authors.lastname: McCallum
mesh_terms: D003198:Computer Simulation; D003545:Cysteine / Q000737:chemistry; D006860:Hydrogen Bonding; D007477:Ions / Q000737:chemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013438:Sulfhydryl Compounds / Q000737:chemistry
chemical_list: D007477:Ions; D010455:Peptides; D013438:Sulfhydryl Compounds; C019529:polyalanine; D003545:Cysteine