New biophysics data collected at ILL and ESRF will help biochemists make in vitro experiments more physiologically relevant by taking into account macromolecular ‘crowding’ inside cells. Researchers found that crowding has a significant effect on protein diffusion at the nanosecond timescale. This has implications for all biochemical processes and reaction rates when comparing lab results to cell physiology.
A publication in PNAS
When conducting in vitro (laboratory) investigations into biological processes, biochemists carefully allow for factors such as pH, ionic strength and composition (the amount and type of positive and negative ions present), and concentration of relevant metabolites. However, the fact that 40% of the cell’s aqueous environment is occupied by large molecules is rarely considered.
Macromolecules undergo random motions in the intracellular water, which affects the rate of protein diffusion. This is important because movement of proteins is key for all cellular processes and signalling, from transport of metabolites to reaction kinetics.
Now physicists from the Universities of Tübingen and Oxford, ESRF and ILL have used neutron and X-ray data to compare the diffusion of bovine serum albumin (BSA), a globular protein, in aqueous solution with a simplified diffusion model from colloid physics.
Although BSA is a globular protein it is not an exact sphere; it actually has a complicated and floppy shape with a heterogenous surface charge. This is a problem for theoretical physics which can at present only model hard spheres with a homogenous surface charge.
The researchers investigated whether the theory was a suitable basis for a model of macromolecular crowding by calculating the equivalent sphere size of a single BSA protein and comparing the theoretical and computer simulation predictions of its rate of movement with experimental data.
They found that the predictions quantitatively matched up with the measurements. This is the first time that both the theory and computer simulation have been confirmed by systematic experimental data.
Roosen-Runge F et al, Protein self-diffusion in crowded solutions, PNAS July 2011