Speaker
Description
We investigate the effect of crowding on the short-time tracer diffusion of model proteins on the nanometer length and (sub-)nanosecond timescales both experimentally and with the aid of computer simulations [1]. Experimentally, we dissolve polyclonal immunoglobulin (Ig) antibody proteins of natural isotopic abundance as tracers in perdeuterated Escherichia coli cell lysate as crowder to mimic a biological environment and at the same time optimize the sensitivity for the tracers using incoherent quasi-elastic neutron scattering. We subsequently compare the ensemble-averaged dynamics of Ig in lysate to the dynamics of Ig in pure water as a function of concentration. In both cases, remarkably, the diffusion of Ig only depends on the total macromolecular volume fraction φ in the sample, within the experimental accuracy. To shed light on how polydispersity affects the short-time self-diffusion of proteins in crowded environments, we perform computer simulations which have proven to provide accurate information on the diffusion of proteins in crowed environments [2,3] and to interpret and rationalize neutron scattering experiments [4,5]. Because of the short times scales involve in our experiments, diffusion is mainly modulated by hydrodynamic interactions (HI) mediated by the aqueous media and therefore an accurate description of the HI most be included in the simulation scheme. For these reason, we perform simulations based on Stokesian Dynamics [6] in which HI are considered explicitly and short-time properties can be calculated. In our approach, the lysate polydisperse system is modeled using hard spheres. We demonstrate an intricate dependency between the diffusion of a tracer on the crowder composition, specifically on the ensemble effective radius, Reff = (<Ri^3>)^1/3. For tracers with a radius close to Reff, the tracer diffusion is similar to that of a monodisperse system, whereas deviations are observed for significantly different tracer radii. Notably, the hydrodynamic radius of Ig is close to the lysate effective radius, which explains the surprising insensitivity to the polydispersity observed in the experiments. The simulation results further show that polydispersity slows down larger macromolecules more effectively than smaller ones even at nanosecond timescales. This has obvious implications for the functioning of the cellular machinery. Our simulations also confirms the predictive power, on the nanosecond timescale, of coarse-grained molecular dynamics simulations.
[1] Grimaldo M., Lopez H., et al. (2019) J. Phys. Chem. Lett. 10, 1709–1715
[2] McGuffee, S. R.; Elcock, A. H. (2010) PLoS Comput. Biol. 6, e1000694.
[3] Ando, T.; Skolnick, J. (2010) Proc. Natl. Acad. Sci. USA 107, 18457–18462.
[4] Bucciarelli, S. et al. (2016) Science Advances 2, e1601432.
[5] Wang, G. et al. (2018) J. Phys. Chem. B 122, 2867–2880
[6] Brady, J. F.; Bossis, G. (1988) Annu. Rev. Fluid Mech. 20, 111–157
