Unfolding and folding internal friction of β-hairpins is smaller than that of α-helices.
By the forced unfolding of polyglutamine and polyalanine homopeptides in competing α-helix and β-hairpin secondary structures, we disentangle equilibrium free energetics from nonequilibrium dissipative effects. We find that α-helices are characterized by larger friction or dissipation upon unfolding, regardless of whether they are free energetically preferred over β-hairpins or not. Our analysis, based on MD simulations for atomistic peptide models with explicit water, suggests that this difference is related to the internal friction and mostly caused by the different number of intrapeptide hydrogen bonds in the α-helix and β-hairpin states.
Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany.
Julius C F
JC
Schulz
Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany.
Markus S
MS
Miettinen
Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany.
R R
RR
Netz
D001152:Arsenicals / Q000737:chemistry*; D004338:Drug Combinations; D017276:Friction; D057446:Hydrodynamics; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009355:Neomycin / Q000737:chemistry*; D009761:Nystatin / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011113:Polymyxins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D058767:Protein Unfolding; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D014783:Viscosity; D014867:Water / Q000737:chemistry
D001152:Arsenicals; D004338:Drug Combinations; D010455:Peptides; D011113:Polymyxins; D012997:Solvents; D014867:Water; D009761:Nystatin; C019529:polyalanine; C006119:acetarsol, dimethicone, neomycin, nystatin, polymyxin drug combination; D009355:Neomycin