Concentration sensing in crowded environments

Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells

Macromolecular crowding in the cellular cytoplasm can potentially impact diffusion rates of proteins, their intrinsic structural stability, binding of proteins to their corresponding partners as well as biomolecular organization and phase separation. While such intracellular crowding can have a large impact on biomolecular structure and function, the molecular mechanisms and driving forces that determine the effect of crowding on dynamics and conformations of macromolecules are so far not well understood. At a molecular level, computational methods can provide a unique lens to investigate the effect of macromolecular crowding on biomolecular behavior, providing us with a resolution that is challenging to reach with experimental techniques alone. In this review, we focus on the various physics-based and data-driven computational methods developed in the past few years to investigate macromolecular crowding and intracellular protein condensation. We review recent progress in modeling and simulation of biomolecular systems of varying sizes, ranging from single protein molecules to the entire cellular cytoplasm. We further discuss the effects of macromolecular crowding on different phenomena, such as diffusion, protein-ligand binding, and mechanical and viscoelastic properties, such as surface tension of condensates. Finally, we discuss some of the outstanding challenges that we anticipate the community addressing in the next few years in order to investigate biological phenomena in model cellular environments by reproducing in vivo conditions as accurately as possible.

An Unstructured Mesh Reaction-Drift-Diffusion Master Equation with Reversible Reactions

We develop a convergent reaction-drift-diffusion master equation (CRDDME) to facilitate the study of reaction processes in which spatial transport is influenced by drift due to one-body potential fields within general domain geometries. The generalized CRDDME is obtained through two steps. We first derive an unstructured grid jump process approximation for reversible diffusions, enabling the simulation of drift-diffusion processes where the drift arises due to a conservative field that biases particle motion. Leveraging the Edge-Averaged Finite Element method, our approach preserves detailed balance of drift-diffusion fluxes at equilibrium, and preserves an equilibrium Gibbs-Boltzmann distribution for particles undergoing drift-diffusion on the unstructured mesh. We next formulate a spatially-continuous volume reactivity particle-based reaction-drift-diffusion model for reversible reactions of the form A + B ↔ C . A finite volume discretization is used to generate jump process approximations to reaction terms in this model. The discretization is developed to ensure the combined reaction-drift-diffusion jump process approximation is consistent with detailed balance of reaction fluxes holding at equilibrium, along with supporting a discrete version of the continuous equilibrium state. The new CRDDME model represents a continuous-time discrete-space jump process approximation to the underlying volume reactivity model. We demonstrate the convergence and accuracy of the new CRDDME through a number of numerical examples, and illustrate its use on an idealized model for membrane protein receptor dynamics in T cell signaling.

Is There a Need for a More Precise Description of Biomolecule Interactions to Understand Cell Function?

An important goal of biological research is to explain and hopefully predict cell behavior from the molecular properties of cellular components. Accordingly, much work was done to build extensive “omic” datasets and develop theoretical methods, including computer simulation and network analysis to process as quantitatively as possible the parameters contained in these resources. Furthermore, substantial effort was made to standardize data presentation and make experimental results accessible to data scientists. However, the power and complexity of current experimental and theoretical tools make it more and more difficult to assess the capacity of gathered parameters to support optimal progress in our understanding of cell function. The purpose of this review is to focus on biomolecule interactions, the interactome, as a specific and important example, and examine the limitations of the explanatory and predictive power of parameters that are considered as suitable descriptors of molecular interactions. Recent experimental studies on important cell functions, such as adhesion and processing of environmental cues for decision-making, support the suggestion that it should be rewarding to complement standard binding properties such as affinity and kinetic constants, or even force dependence, with less frequently used parameters such as conformational flexibility or size of binding molecules.