Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra

Abstract

Terahertz time-domain spectra (THz-TDS) were investigated using the results of molecular dynamics (MD) simulations of Staphylococcal nuclease at two hydration states in the temperature range between 100 and 300 K. The temperature dependence of THz-TDS was found to differ significantly from that of the incoherent neutron scattering spectra (INSS) calculated from the same MD simulation results. We further examined contributions of the mutual and auto-correlations of the atomic fluctuations to THz-TDS and found that the negative value of the former contribution nearly canceled out the positive value of the latter, resulting in a monotonic increase of the reduced absorption cross section. Because of this cancellation, no distinct broad peak was observed in the absorption lineshape function of THz-TDS, whereas the protein boson peak was observed in INSS. The contribution of water molecules to THz-TDS was extremely large for the hydrated protein at temperatures above 200 K, in which large-amplitude motions of water were excited. The combination of THz-TDS, INSS and MD simulations has the potential to extract function-relevant protein dynamics occurring on the picosecond to nanosecond timescale.Conformational dynamics plays an important role in protein function. Collective motions in proteins slower than pico-seconds in timescale are of particular interest. Incoherent neutron scattering experiments are among the successful methods to study protein dynamics on the picosecond to nanosecond timescale. The protein boson peak is a broad peak found in the low-frequency region (16-32 cm −1 , corresponding to 1-2 ps) of the incoherent neutron scattering spectra (INSS) [1][2][3][4]. Frequencies of the protein boson peak shift higher upon hydration, indicating that solvent molecules are associated with the origin of the peak [2,4]. As the temperature increases, the boson peak for a hydrated protein shifts to lower frequency and becomes buried in the quasi-elastic contribution [1]. Another temperature-dependent phenomenon with regard to protein dynamics is a dynamical The temperature dependence of terahertz time-domain spectra (THz-TDS) is shown to differ significantly from that of incoherent neutron scattering spectra (INSS) using molecular dynamics simulations of Staphylococcal nuclease at two hydration states in the temperature range between 100 and 300 K. The mutual correlation between distinct atomic fluctuations and water dynamics to THz-TDS, which are negligible in INSS, contributes to this difference. This work provides the first theoretical and computational analysis of the dynamical components that contribute to THz-TDS.

Incoherent Neutron Scattering and Terahertz Time-Domain Spectroscopy on Protein and Hydration Water

“…In contrast, THz-TDS is derived from the fluctuation of the dipole moment. Recently, terahertz spectra have been calculated via MD simulation [ 22 ], but so far, the direct comparison of THz-TDS and MD simulations is difficult. A simulation model that includes dipole effects needs to be developed before it can be directly compared to the experimental data.…”

“…Recently, the hysteresis of hydrated protein dynamics was identified by terahertz spectroscopy and neutron scattering as the freezing of hydration water [ 18 , 19 ]. Although molecular dynamics simulations can easily calculate the INS spectrum quantitatively [ 20 , 21 ], it is not as easy to calculate the THz spectrum [ 22 ]. A major advantage of THz-TDS over INS is that the experiment can be performed on a lab scale.…”

Terahertz absorption characteristics of ammonium salt solution based on self-sampling microfluidic chip

“…The basic parameters are related to the amount of hydrogen in the sample and change significantly as the water state changes. Joti Y et al 6 used THz-TDS system to study and analyze the offsetting phenomenon between autocorrelation and cross-correlation contributions of protein and water in dynamics. Wang et al 7 experimentally studied the THz spectra of DNA nuclease crystals using a THz-TDS system, and analyzed the vibration spectra of solid-state DNA nuclease by generalized energy fragmentation method (PBC-GEBF) under periodic boundary conditions, and assigned the corresponding vibration modes to the main peaks in the experimental spectrum.…”