Neutron Frequency Windows and the Protein Dynamical Transition

Abstract

Proteins undergo an apparent dynamical transition on temperature variation that has been correlated with the onset of function. The transition in the mean-square displacement, AEDr 2 ae, that is observed using a spectrometer or computer simulation, depends on the relationship between the timescales of the relaxation processes activated and the timescale accessible to the instrument or simulation. Models are described of two extreme situations-an ''equilibrium'' model, in which the long-time dynamics changes with temperature and all motions are resolved by the instrument used; and a ''frequency window'' model, in which there is no change in the long-time dynamics but as the temperature increases, the relaxation frequencies move into the instrumental range. Here we demonstrate that the latter, frequency-window model can describe the temperature and timescale dependences of both the intermediate neutron scattering function and AEDr 2 ae derived from molecular dynamics simulations of a small protein in a cryosolution. The frequency-window model also describes the energy-resolution and temperature-dependences of AEDr 2 ae obtained from experimental neutron scattering on glutamate dehydrogenase in the same solvent. Although equilibrium effects should also contribute to dynamical transitions in proteins, the present results suggests that frequency-window effects can play a role in the simulations and experiments examined. Finally, misquotations of previous findings are discussed in the context of solvent activation of protein dynamics and the possible relationship of this to activity.

Mean-squared atomic displacements in hydrated lysozyme, native and denatured

“…For example, it has been reported that the transition is coupled to the onset of translational motions in hydration water [47][48][49]. In addition, it has been debated whether the transition is a real phenomenon, or merely a manifestation of the fact that the measurable atomic dynamics enter the experimentally accessible resolution window above certain temperatures [17,18,24,25,27]. In such a scenario, the dynamic motions of the biomolecules may increase without any discontinuity.…”

Proton Momentum Distribution in a Protein Hydration Shell

“…The dynamical properties of these water molecules, closely resembling that of a glassy system [1,2], and, in particular, the interplay with the slaved dynamical behavior of the protein itself, has likely implications for biological functionality [3][4][5][6], and as such is a subject of active research. The accurate study of the properties of water molecules hydrating proteins has seen a resurgence of interest in the past few years, possibly due to the availability of powerful simulation techniques along with the advent of new experimental approaches.…”

Long-time mean-square displacements in proteins

“…[33,38] The concept has also been incorporated into the formalism that describes the dynamics accompanying the glass transition in molecular systems. When the protein relaxation time decreases with temperature, as it usually does, it has been shown that measurement of r 2 R over a finite time window can introduce an apparent DT when there is no actual change in the elastic incoherent DSF, S(Q, ω = 0).…”

“…When the protein relaxation time decreases with temperature, as it usually does, it has been shown that measurement of r 2 R over a finite time window can introduce an apparent DT when there is no actual change in the elastic incoherent DSF, S(Q, ω = 0). [33,38] To avoid this issue, identification and use of an intrinsic, long time MSD r 2 would be helpful. Several MD studies have been performed aimed at understanding the origin of elastic neutron scattering from proteins.…”