title: Like-charged residues at the ends of oligoalanine sequences might induce a chain reversal.
abstract: We have examined the effect of like-charged residues on the conformation of an oligoalanine sequence. This was facilitated by circular dichroism (CD) and NMR spectroscopic and differential scanning calorimetric (DSC) measurements, and molecular dynamics calculations of the following three alanine-based peptides: Ac-K-(A)(5) -K-NH(2) (KAK5), Ac-K-(A)(4) -K-NH(2) (KAK4), Ac-K-(A)(3) -K-NH(2) (KAK3), where A and K denote alanine and lysine residues, respectively. Our earlier studies suggested that the presence of like-charged residues at the end of a short polypeptide chain composed of nonpolar residues can induce a chain reversal. For all three peptides, canonical molecular dynamics simulations with NMR-derived restraints demonstrate the presence of ensembles of structures with a tendency to form a chain reversal. The KAK3 peptide exhibits a bent shape with its ends close to each other, while KAK4 and KAK5 are more extended. In the KAK5 peptide, the lysine residues do not have any influence on each other and are very mobile. Nevertheless, the tendency to form a more or less pronounced chain reversal is observed and it seems to be stable in all three peptides. This chain reversal seems to be caused by screening of the nonpolar core from the solvent by the hydrated charged residues.
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland. royek@chem.univ.gda.pl
authors.forename: Joanna
authors.initials: J
authors.lastname: Makowska
authors.forename: Adam
authors.initials: A
authors.lastname: Liwo
authors.forename: Wioletta
authors.initials: W
authors.lastname: Zmudzińska
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Lewandowska
authors.forename: Lech
authors.initials: L
authors.lastname: Chmurzyński
authors.forename: Harold A
authors.initials: HA
authors.lastname: Scheraga
mesh_terms: D000409:Alanine / Q000737:chemistry* / Q000378:metabolism; D002152:Calorimetry, Differential Scanning; D002627:Chemistry, Physical; D002942:Circular Dichroism; D008239:Lysine / Q000737:chemistry* / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides; D012997:Solvents; D008239:Lysine; D000409:Alanine