Paper Citing NAMD - Abstract
Serrano, Arnaldo L.; Tucker, Matthew J.; Gai, Feng
Direct Assessment of the alpha-Helix Nucleation Time
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7472-7478, JUN 9 2011
The nucleation event in alpha-helix formation is a fundamental process in protein folding. However, determining how quickly it takes place based on measurements of the relaxation dynamics of helical peptides is difficult because such relaxations invariably contain contributions from various structural transitions such as from helical to nonhelic:al states and helical to partial-helical conformations. Herein, we measure the temperature-jump (T-jump) relaxation kinetics of three model peptides that fold into a single-turn alpha-helix, using time-resolved, infrared spectroscopy, aiming to provide a direct assessment of the helix nucleation rate. The alpha-helical structure of these peptides is stabilized by a covalent cross-linker formed between the side chains of two residues at the i and i + 4 positions. If we assume that this cross-linker mimics the structural constraint arising from a strong side chain-side chain interaction (e.g., a salt bridge) in proteins, these peptides would represent good models for studying the nucleation process of an alpha-helix in a protein environment. Indeed, we find that the T-jump induced relaxation rate of these peptides is approximately (0.6 mu s)(-1) at room temperature, which is slower than that of commonly studied alanine-based helical peptides but faster than that of a naturally occurring alpha-helix whose folded state is stabilized by a series of side chain-side chain interactions. Taken together, our results put an upper limit of about 1 mu s for the helix nucleation time at 20 degrees C and suggest that the subsequent propagation steps occur with a time constant of about 240 ns.
