Homogeneous and heterogeneous dynamics in native and denatured bovine serum albumin

Abstract

A characteristic property of unfolded and disordered proteins is their high molecular flexibility, which enables the exploration of a large conformational space. We present neutron scattering experiments on the dynamics of denatured and native folded bovine serum albumin (BSA) in solution. Global protein diffusion and internal macromolecular dynamics were measured using quasielastic neutron time-of-flight and backscattering spectroscopy on the picosecond to nanosecond time- and Ångstrom length-scale. Internal protein dynamics were analysed in a first approach using stretched exponential functions. In denatured BSA predominantly slow heterogeneous dynamics dominates the observed macromolecular motions. Reduction of disulphide bridges in denatured BSA does not significantly alter the visible motions. In native folded BSA fast homogeneous dynamics and slow heterogeneous dynamics were observed. In an alternative data analysis approach, internal protein dynamics was interpreted using the analytical model of the overdamped Brownian oscillator, which allowed us to extract mean square displacements of protein internal dynamics and the fraction of hydrogen atoms participating in the observed motions. Our results demonstrate that denaturation modifies the physical nature of internal protein dynamics significantly as compared to the native folded structure.

Effect of red blood cell shape changes on haemoglobin interactions and dynamics: a neutron scattering study

“…By considering the short-time range probed by QENS, our results indicated that hydrodynamic interactions of Hb in concentrated solutions were stronger than predicted from the theory for simple colloidal hard-sphere suspensions; this predicted a value of H = 1 − 1.831ϕ = 0.63 for a volume fraction of ϕ = 0.20 being equivalent to the QENS RBC lysate sample [61]. This result was in agreement with previous reports on globular, multi-domain and intrinsically disordered proteins [5,59,[62][63][64][65].…”

Dynamics of proteins in solution

“…However, a later NSE study by Ameseder et al (2018a) indicated that presence of the sulfur bonds leads to a suppression of low-frequency Zimm modes (see section 'Relations of protein dynamics to structure: from globular to intrinsically disordered proteins'). 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. As suggested by Ameseder et al (2018b), in the denatured protein, the slow process may become the predominating contribution to the dynamics (e.g. if the additional mobile atoms were mostly slow), practically obscuring the faster one.…”

“…There exists an analytical form of the Fourier transform of Eq. (53) ( Kneller and Hinsen, 2004) (without resolution function term), but practically its calculation is often performed numerically (Toppozini et al, 2015;Ameseder et al, 2018b). To describe non-exponential relaxations, also the fractional Brownian dynamics (FBD) model can be employed.…”

“…The effect of chemical denaturation on BSA at lower concentrations (∼30 mg ml −1 ) induced by 6 M guanidinium hydrochloride (GndCl) at T = 295 K was studied with TOF and NBS by Ameseder et al (2018aAmeseder et al ( , 2018b. Moreover, also the effect of the reduction of disulfide bridges in denatured BSA induced by 6 M GndCl 150 mM β-mercaptoethanol (β-met) was investigated.…”