Dynamics of a protein and its surrounding environment: A quasielastic neutron scattering study of myoglobin in water and glycerol mixtures

Abstract

In this quasielastic neutron scattering (QENS) study we have investigated the relation between protein and solvent dynamics. Myoglobin in different water:glycerol mixtures has been studied in the temperature range of 260-320 K. In order to distinguish between solvent and protein dynamics we have measured protonated as well as partly deuterated samples. As commonly observed for bulk as well as for confined water, the dynamics of the surrounding solvent is well described by a jump diffusion model. The intermediate scattering function I(Q,t) from the protein (partly deuterated samples) was analyzed by fitting a single Kohlrausch-Williams-Watts (KWW) stretched exponential function to the data. However, due to the limited experimental time window, two different curve fitting approaches were used. The first one was performed with the assumption that I(Q,t) decays to zero at long times, i.e., it was assumed that all protein relaxations that are observed on the experimental time scale, as well as would be observed on longer time scales, can be described by a single KWW function. In the second approach we instead assumed that both the protein relaxation time tau(p) and the stretching parameter beta(KWW) were Q-independent, i.e., we assumed that the protein dynamics is dominated by more local motions. Advantages and disadvantages of both approaches are discussed. The first approach appears to work best at higher Q-values, indicating a power law relation of the Q-dependent protein dynamics for all samples and temperatures, whereas the second approach seems to work at lower Q-values, where the expected confined diffusion of hydrogen atoms in the protein gives the assumed Q-independent relaxation time. Independent of the chosen approach we find a significant correlation between the average relaxation time of the protein and the diffusion constant (or in this case the related relaxation time) of the solvent. However, the correlation is not perfect since the average relaxation time of the protein is more strongly dependent on the total amount of solvent than the diffusion constant of the solvent itself. Thus, the average relaxation time of the protein decreases not only with increasing solvent mobility, but also with increasing solvent content.

Hydration dynamics as an intrinsic ruler for refining protein structure at lipid membrane interfaces

“…The results show that the ρ t value exhibits a small dispersion between 2.4 and 4.0, suggesting that hydration water is relatively freely, and roughly evenly, diffusing near the protein surface in the unbound state. This result displays typical characteristics of hydration water around solvent-exposed protein surfaces with ρ t values found between 2 and 5 (32,(47)(48)(49), confirming that αS in solution is in an overall unstructured state, where each residue is significantly exposed to bulk water.…”

“…As illustrated in Fig. 1, the coupling between the electron spin and water proton is shown to be sensitively modulated within the dynamic range of hydration water at solvent-exposed surfaces of proteins (ρ t = 2-5) (32,(47)(48)(49), as well as on the surfaces or within cores of lipid bilayers (ρ t = 5-11) (21-23), affording the use of ODNP to probe conformational changes or interactions between proteins and lipid membranes by monitoring the changes in the local hydration dynamics at molecular interfaces. Crucially, biological samples at dilute concentrations (approximately tens of micromolars), of minute volumes (approximately a few microliters), and in an environment of excess water, lipids and other biological constituents at physiological temperature are experimentally accessible.…”

Correlation of the dynamics of native human acetylcholinesterase and its inhibited huperzine A counterpart from sub-picoseconds to nanoseconds

“…The relaxation times are indeed much longer than the instrumental resolution times. Typical values of b found in the literature are between ¼ 0.6 and 0.8 for polymers [45], 0.3 and 0.5 for proteins [46] and 0.4 and 0.7 for glasses [47], and Kneller found values around 0.5 analysing measured and simulated data of lysozyme and myoglobin [21]. A physical interpretation of this value is, however, not straightforward.…”

The protein glass transition as measured by dielectric spectroscopy and differential scanning calorimetry

“…3A) hydration level, respectively. This relaxation process arises above the crossover temperature of the main water relaxation and it is most likely due to the relaxation of polar side groups based on earlier interpretations from measurements of hydrated proteins by time-domain reflectometry [35] and recent observations by quasielastic neutron scattering [36]. Whether these side chains move together with the possible secondary solvent relaxation (process III, Fig.…”