Mechanism of helix nucleation and propagation: microscopic view from microsecond time scale MD simulations.
Microsecond time scale molecular dynamics simulations of the 13-residue peptide RN24 were carried out to investigate the mechanism of helix nucleation and propagation. An extended and an ideal alpha-helical conformation were used as starting structures. NOE-derived interatomic distances were compared with distances calculated from the simulations, showing good agreement between experimental and simulation results. Based on almost 200 helix nucleation events observed, beta-turn and 3(10)-helix play an important role in helix nucleation; in most cases, helix nucleation is preceded by the formation of a short-lived beta-turn (60% probability) or 3(10)-helix (20% probability), and the conversion from beta-turn to alpha-turn involves bifurcated hydrogen bonds. Helix propagation in RN24 appears to occur preferentially from the N-terminus to the C-terminus, and helix unfolding preferentially in the opposite direction.
Monticelli
Luca
L
Centre for Biomolecular Interdisciplinary Studies and Industrial Applications, University of Milan, 20131 Milan, Italy. lmonti@ucalgary.ca
Tieleman
D Peter
DP
Colombo
Giorgio
G
D002096:C-Peptide / Q000737:chemistry*; D002942:Circular Dichroism; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary
D002096:C-Peptide