All-atom molecular dynamics simulations of beta-hairpins stabilized by a tight turn: pronounced heterogeneous folding pathways.
Formation of beta-hairpins for a series of peptides having the same general sequence, RYVEV-XG-KKILQ-NH(2), where the i + 1th residue, X, at the beta-turn is varied (Aib or B in BG12, (D)Pro or (D)P in (D)PG12, (L)Pro or P in PG12, and Asn or N in NG12) was studied by means of all-atom Molecular Dynamics (MD) simulations. Trajectories of the tryptophan zipper beta-hairpin peptide, TZ2 (SWTWE-NG-KWTWK), were also run under similar conditions to provide a comparison with results for a like-sized peptide with a different characteristic folding mechanism. Four-residue peptides with a sequence, X-BG-K-NH(2) (where X is a V or (D)V) were further simulated, particularly focusing on the mirror turn propensity in these hairpins. Microscopic bases for several previous experimental observations are clearly indicated in our MD trajectories. Our results suggest that the two Gellman hairpins, BG12 and (D)PG12, have stabilities with a pronounced contribution from the tight turn and a moderate contribution from the cross-strand interactions, resulting in a complicated interplay between turn and strand, while TZ2 appears to undergo simpler (un)folding, dominated by cross-strand interactions. Such an interplay between the turn and the strand observed with BG12 and (D)PG12 may underlie their heterogeneous folding dynamics and the absence of a sigmoidal transition in their thermal unfolding profiles determined with IR spectra, as has been shown in previous experimental studies.
Kim
Joohyun
J
Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (M/C 111), Chicago, Illinois 60607-7061, USA.
Keiderling
Timothy A
TA
D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D014364:Tryptophan / Q000737:chemistry
D010455:Peptides; D014364:Tryptophan