Monitoring the Folding Kinetics of a β-Hairpin by Time-Resolved IR Spectroscopy in Silico

Abstract

Protein folding is one of the most fundamental problems in modern biochemistry. Time-resolved infrared (IR) spectroscopy in the amide I region is commonly used to monitor folding kinetics. However, associated atomic detail information on the folding mechanism requires simulations. In atomistic simulations structural order parameters are typically used to follow the folding process along the simulated trajectories. However, a rigorous test of the reliability of the mechanisms found in the simulations requires calculation of the time-dependent experimental observable, i.e., in the present case the IR signal in the amide I region. Here, we combine molecular dynamics simulation with a mixed quantum mechanics/molecular mechanics theoretical methodology, the Perturbed Matrix Method, in order to characterize the folding of a β-hairpin peptide, through modeling the time-dependence of the amide I IR signal. The kinetic and thermodynamic data (folding and unfolding rate constants, and equilibrium folded- and unfolded-state probabilities) obtained from the fit of the calculated signal are in good agreement with the available experimental data [Xu et al. J. Am. Chem. Soc. 2003, 125, 15388-15394]. To the best of our knowledge, this is the first report of the simulation of the time-resolved IR signal of a complex process occurring on a long (microsecond) time scale.

A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy

“…This enables statistically relevant sampling of the quantum-center and environment configurations, which is required for accurate IR spectra calculations of proteins. This method has been calibrated recently with static IR spectra of amyloids,21 unfolded protein states,22,23 and equilibrium protein folding,24,25 as well as by calculating reduction potentials26,27 and electron transfer processes28,29 in proteins.…”

Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α -Helical Stability and Folding Kinetics

“…1). Temporal resolution and structural sensitivity were achieved using transient-infrared (IR) measurements after a laser-induced temperature-jump (T-jump) (23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33) in the amide I 0 spectral region, which is a sensitive probe of the backbone conformation (34)(35)(36)(37). Combined analysis of our steady-state ultraviolet circular dichroism (UV CD) and T-jump transient-IR measurements allows a detailed study of the folding and unfolding kinetics.…”

Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation

“…Here, we apply the perturbed matrix method (PMM) to calculate the amide I′ IR spectra of a fast‐folding β‐hairpin peptide, the Fip35 WW domain, in different conformational states. The MD‐PMM approach is based on the joint use of extended MD simulations and a mixed quantum/classical theoretical computational methodology (PMM) , and has been successfully used to model several relevant experimental observables such as absorption spectra , redox potentials , kinetic rates and the amide I′ spectra of helical and β‐sheet peptides as well as amyloids and unfolded states .…”