Fast internal dynamics in alcohol dehydrogenase

Abstract

Large-scale domain motions in alcohol dehydrogenase (ADH) have been observed previously by neutron spin-echo spectroscopy (NSE). We have extended the investigation on the dynamics of ADH in solution by using high-resolution neutron time-of-flight (TOF) and neutron backscattering (BS) spectroscopy in the incoherent scattering range. The observed hydrogen dynamics were interpreted in terms of three mobility classes, which allowed a simultaneous description of the measured TOF and BS spectra. In addition to the slow global protein diffusion and domain motions observed by NSE, a fast internal process could be identified. Around one third of the protons in ADH participate in the fast localized diffusive motion. The diffusion coefficient of the fast internal motions is around two third of the value of the surrounding D2O solvent. It is tempting to associate the fast internal process with solvent exposed amino acid residues with dangling side chains.

Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding

“…The observed slow dynamic process could be, for example, attributed to the reorientational motions of buried groups in the protein or the slow rotational motions of side-chains. The slow relaxation time of apo-and holo-Mb determined is similar to the previous results on the dynamics of alcohol dehydrogenase (t = 160 ps), 39 the LOV photoreceptor protein SB1 in the dark-and light-adapted states (t = 170 and 150 ps, respectively), 40 but appears to be larger than that of the structurally related haemoglobin in red blood cells (t = 121 ps), 33 or also of the membrane protein bacteriorhodopsin (t = 120 ps). 41 The G 2 recorded on IRIS and IN5 of the apo-Mb states showed a q-dependent behaviour and could be described analytically by a jump-diffusion mechanism.…”

“…45 More recently, we have attributed the observed dynamics to the jumps of aminoacid side-chains mostly located on the surface of the protein. 39,46 We find no significant variations of the jump-diffusion coefficients of apo-Mb between the different folded states. The diffusivity of internal protein motions on the picosecond time-scale agrees well with the values of H 2 O bulk solvent.…”

Dynamics of proteins in solution

“…Although incapable of distinguishing heterogeneous dynamics on the same timescale, as the authors noted (Ameseder et al, 2018b), the Brownian oscillator model yielded reasonably similar results with D fast int = 95.8 + 1.8 Å 2 ns −1 and D slow int = 24.5 + 1.5 Å 2 ns −1 in the native protein and diffusion coefficients between 14 and 21 Å 2 ns −1 in denatured BSA. As remarked by Ameseder and collaborators, D fast int and D slow int obtained with this model are on the same order of magnitude as the diffusion coefficients obtained from the switching model applied before on BSA at the same temperature (Grimaldo et al, 2015a) and D fast int is in good agreement with a 'slow' dynamics of amino acid side-chains in folded proteins observed by Monkenbusch et al (2015) and characterized by effective diffusion coefficients of around 70-80 Å 2 ns −1 (Ameseder et al, 2018b) (see also section 'Combination of neutron spectroscopy techniques: alcohol dehydrogenase'). The apparent disappearance of the fast dynamics upon denaturation is to be interpreted together with the drastic increase of the fraction of atoms moving on both the timescales accessible by TOF and NSE, respectively, as obtained from the Brownian oscillator model.…”

“…Both the internal and center-of-mass dynamics of ADH, a protein responsible for the interconversion between alcohol and ketones, were investigated with NSE, TOF and NBS, on a broad range of timescales (Biehl et al, 2008;Stadler et al, 2013a;Monkenbusch et al, 2015). Biehl et al (2008) determined the main domain motions of ADH by employing NSE.…”

Microscopic diffusion processes measured in living planarians

“…The width of the measured signal dominated by hydration water, which is expected to be system-specific, exceeds the values for hydration water in prokaryotes Thermococcus barophilus and Thermococcus kodakarensis 15 , but shows good agreement with the values for eukaryotic human cells of invasive breast carcinoma 8 .While the broad QENS component measured at all Q values largely originates from various water populations, it may also have contribution from the internal dynamics of other cell components, such as cell proteome, the signal from which is comparable in width to the signal from water 15 . In other relevant example, the internal dynamics of alcohol dehydrogenase was measured at about two-thirds of the solvent diffusivity 19 . Besides the too large width of the signal from bulk water, which makes it indistinguishable from the background, the dominance of the hydration water and hydration water-driven proteome dynamics 19 in the broad QENS signal measured at high Q could be due to the spatially confined character of such dynamics, which thus gives rise to the relatively stronger QENS signal at high Q.…”