Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy.
We studied the microsecond folding dynamics of three beta hairpins (Trp zippers 1-3, TZ1-TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLS(aa)) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1-TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLS(aa) TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations.
Snow
Christopher D
CD
Department of Chemistry and Biophysics Program, Stanford University, Stanford, CA 94305-5080, USA.
Qiu
Linlin
L
Du
Deguo
D
Gai
Feng
F
Hagen
Stephen J
SJ
Pande
Vijay S
VS
D003198:Computer Simulation; D006358:Hot Temperature; D010455:Peptides / Q000378:metabolism*; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D013057:Spectrum Analysis; D013997:Time Factors; D014364:Tryptophan / Q000378:metabolism*
D010455:Peptides; D014364:Tryptophan