Details

Autor(en) / Beteiligte

• Davis, Caitlin M
• Zanetti-Polzi, Laura
• Gruebele, Martin
• Amadei, Andrea
• Dyer, R. Brian
• Daidone, Isabella

Titel

A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopyElectronic supplementary information (ESI) available: Temperature-dependent circular dichroism and FTIR, SVD analysis of the FTIR data, global fitting of thermal melts, Arrhenius plots of observed kinetics, expanded computational methods, the computational distribution of IR intensities, and complete tables of relaxation kinetics of 1619 cm−1, 1634 cm−1, 1661 cm−1 and 1680 cm−1. See DOI: 10.1039

Erscheinungsjahr

2018-12

Quelle

EZB Electronic Journals Library

Beschreibungen/Notizen

• For small molecule reaction kinetics, computed reaction coordinates often mimic experimentally measured observables quite accurately. Although nowadays simulated and measured biomolecule kinetics can be compared on the same time scale, a gap between computed and experimental observables remains. Here we directly compared temperature-jump experiments and molecular dynamics simulations of protein folding dynamics using the same observable: the time-dependent infrared spectrum. We first measured the stability and folding kinetics of the fastest-folding β-protein, the GTT35 WW domain, using its structurally specific infrared spectrum. The relaxation dynamics of the peptide backbone, β-sheets, turn, and random coil were measured independently by probing the amide I′ region at different frequencies. Next, the amide I′ spectra along folding/unfolding molecular dynamics trajectories were simulated by accurate mixed quantum/classical calculations. The simulated time dependence and spectral amplitudes at the exact experimental probe frequencies provided relaxation and folding rates in agreement with experimental observations. The calculations validated by experiment yield direct structural evidence for a rate-limiting reaction step where an intermediate state with either the first or second hairpin is formed. We show how folding switches from a more homogeneous (apparent two-state) process at high temperature to a more heterogeneous process at low temperature, where different parts of the WW domain fold at different rates. We break the barrier between simulation and experiment by comparing identical computed and experimental infrared observables.