Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments

Applying molecular crowding models to simulations of virus capsid assembly in vitro

Virus capsid assembly has been widely studied as a biophysical system, both for its biological and medical significance and as an important model for complex self-assembly processes. No current technology can monitor assembly in detail and what information we have on assembly kinetics comes exclusively from in vitro studies. There are many differences between the intracellular environment and that of an in vitro assembly assay, however, that might be expected to alter assembly pathways. Here, we explore one specific feature characteristic of the intracellular environment and known to have large effects on macromolecular assembly processes: molecular crowding. We combine prior particle simulation methods for estimating crowding effects with coarse-grained stochastic models of capsid assembly, using the crowding models to adjust kinetics of capsid simulations to examine possible effects of crowding on assembly pathways. Simulations suggest a striking difference depending on whether or not a system uses nucleation-limited assembly, with crowding tending to promote off-pathway growth in a nonnucleation-limited model but often enhancing assembly efficiency at high crowding levels even while impeding it at lower crowding levels in a nucleation-limited model. These models may help us understand how complicated assembly systems may have evolved to function with high efficiency and fidelity in the densely crowded environment of the cell.

Reaching new levels of realism in modeling biological macromolecules in cellular environments

An increasing number of studies are aimed at modeling cellular environments in a comprehensive and realistic fashion. A major challenge in these efforts is how to bridge spatial and temporal scales over many orders of magnitude. Furthermore, there are additional challenges in integrating different aspects ranging from questions about biomolecular stability in crowded environments to the description of reactive processes on cellular scales. In this review, recent studies with models of biomolecules in cellular environments at different levels of detail are discussed in terms of their strengths and weaknesses. In particular, atomistic models, implicit representations of cellular environments, coarse-grained and spheroidal models of biomolecules, as well as the inclusion of reactive processes via reaction-diffusion models are described. Furthermore, strategies for integrating the different models into a comprehensive description of cellular environments are discussed.

Formation of protein complexes in crowded environments--from in vitro to in vivo

Traditionally, biochemical studies are performed in dilute homogenous solutions, which are very different from the dense mixture of molecules found in cells. Thus, the physiological relevance of these studies is in question. This recognition motivated scientists to formulate the effect of crowded solutions in general, and excluded volume in particular, on biochemical processes. Using polymers or proteins as crowders, it was shown that while crowding tends to significantly enhance the formation of complexes containing many subunits, dimerizations are only mildly affected. Computer simulations, together with experimental evidence, indicate soft interactions and diffusion as critical factors that operate in a concerted manner with excluded volume to modulate protein binding. Yet, these approaches do not truly mimic the cellular environment. In vivo studies may overcome this shortfall. The few studies conducted thus far suggest that in cells, binding and folding occur at rates close to those determined in dilute solutions. Obtaining quantitative biochemical information on reactions inside living cells is currently a main challenge of the field, as the complexity of the intracellular milieu was what motivated crowding research to begin with.