Exploring internal protein dynamics by neutron spin echo spectroscopy

Abstract

The activity of proteins is often related to configuration changes that concern single atoms or amino acids or entire subdomains within the protein. The corresponding length and timescale reach from subAngstrom and picoseconds to nanometers and several tens of nanoseconds and beyond. We focus here on the slow motions on several ten nanosecond timescales of complete domains and show that and how these can be accessed by means of small angle neutron scattering and neutron spin-echo spectroscopy. In particular neutron spin echo spectroscopy is able to access timescales up to several hundred nanoseconds. Further insight into domain dynamics can be achieved by modelling the dynamics in comparison with the experimental data.

Structure and domain dynamics of human lactoferrin in solution and the influence of Fe(III)-ion ligand binding

“…For proteins in solution the contrast and H/D exchange have to be considered according to Jacrot [48]. A concentration series allows to extrapolate to c = 0 for each Q-value from the concentration-normalized scattering intensity I(Q)/c to obtain the form factor F(Q) (with S(Q,c = 0) = 1) and to extract the structure factor S(Q,c) successively [19]. …”

“…Only the highest concentration of c = 50 mg/ml of each sample condition was measured. The background contribution of the buffer solution was measured independently and the data for the protein sample was corrected accordingly [19]. Full measurements are shown in the Additional file 1: Figure S3a-c.…”

“…The effect of the direct interactions is measured in SANS as the structure factor S(Q,c). The solvent-mediated interactions are included in the hydrodynamic function H(Q), which can be assumed to be Q-independent for flexible globular proteins [19] in contrast to rigid globular proteins [57]. From known D 0 (Q) and S(Q,c), the value of H can be determined by DLS and NSE at low Q, where only translational diffusion is observed.…”

“…With its space-time resolution on the molecular scale, NSE is sensitive to internal protein dynamics on the nanometer and nanosecond scale. A detailed normal mode analysis allows the description of main domain movements and a determination of their motion amplitudes and timescales [19]. …”

The spin-echo spectrometer at the Spallation Neutron Source (SNS)

“…The observed dynamics is dominated by the center of mass diffusion of the protein. Depending on the observed wavevector the effective diffusion exhibits Q-dependent additional contributions from rotational diffusion and contributions that convey information on the internal domain motions [20,21]. The aim is to determine how the large-scale flexibility of the protein pertains to its function.…”