Multi-Scale Simulations Yield Insight into Protein Diffusion and Stability in Crowded Environments

Abstract

In living cells, proteins operate in a highly crowded environment where a large fraction of the volume is filled by macromolecules. Despite intensive research, the effects of macromolecular crowding on protein mobility, stability, and ultimately function have not yet been fully elucidated. The need for a detailed microscopic understanding calls for insights from computer simulations; however, the wide spread of time- and length scales involved in crowding poses a serious challenge for current in silico approaches. Our novel multi-scale scheme, combining lattice Boltzmann molecular dynamics (LBMD) with all-atom replica exchange simulations, bridges a gap between existing simulation techniques and provides a computational framework for exploring protein diffusion and stability in the intracellular environment. Our LBMD simulations, employing the OPEP coarse-grain model, reproduce the experimentally observed diffusion slowdown in several crowded binary protein mixtures and allow us to characterize the timescales of protein reshuffling as well as the typical geometries of local packing around the proteins. Furthermore, we use our computational scheme to shed light on the unfolding of superoxide dismutase 1 (SOD1) in crowded conditions, a process implicated in amyotrophic lateral sclerosis (ALS). We show that the thermal stability of a SOD1 barrel depends on its interactions with the surrounding proteins. As a consequence, the different states of local packing result in crowding-induced heterogeneity of SOD1 thermal stabilities. Thus, our results highlight the importance of considering the local environment when investigating protein function in the cytoplasm.