Lipid-protein interaction induced domains: Kinetics and conformational changes in multicomponent vesicles

Mesoscale simulations: An indispensable approach to understand biomembranes

Computer simulation techniques form a versatile tool, a computational microscope, for exploring biological processes. This tool has been particularly effective in exploring different features of biological membranes. In recent years, thanks to elegant multiscale simulation schemes, some fundamental limitations of investigations by distinct simulation techniques have been resolved. As a result, we are now capable of exploring processes spanning multiple scales beyond the capacity of any single technique. In this perspective, we argue that mesoscale simulations require more attention and must be further developed to fill evident gaps in a quest toward simulating and modeling living cell membranes.

Crowding-induced membrane remodeling: Interplay of membrane tension, polymer density, architecture

The plasma membrane hosts a wide range of biomolecules, mainly proteins and carbohydrates, that mediate cellular interactions with its environment. The crowding of such biomolecules regulates cellular morphologies and cellular trafficking. Recent discoveries have shown that the structure and density of cell surface polymers and hence the signaling machinery change with the state of the cell, especially in cancer progression. The alterations in membrane-attached glycocalyx and glycosylation of proteins and lipids are common features of cancer cells. The overexpression of glycocalyx polymers, such as mucin and hyaluronan, strongly correlates with cancer metastasis. Here, we present a mesoscale biophysics-based model that accounts for the shape regulation of membranes by crowding of membrane-attached biopolymer-glycocalyx and actin networks. Our computational model is based on the dynamically triangulated Monte Carlo model for membranes and coarse-grained representations of polymer chains. The model allows us to investigate the crowding-induced shape transformations in cell membranes in a tension- and graft polymer density-dependent manner. Our results show that the number of membrane protrusions and their shape depend on membrane tension, with higher membrane tension inducing more tubular protrusions than the vesicular shapes formed at low tension at high surface coverage of polymers. The shape transformations occur above the threshold density predicted by the polymer brush theory, but this threshold also depends on the membrane tension. Increasing the size of the polymer, either by changing the length or by adding side chains, is shown to increase the crowding-induced curvature. The effect of crowding is more prominent for flexible polymers than for semiflexible rigid polymers. We also present an extension of the model that incorporates properties of the actin-like filament networks and demonstrate how tubular structures can be generated by biopolymer crowding on the cytosolic side of cell membranes.

Binding of thermalized and active membrane curvature-inducing proteins

The phase behavior of a membrane induced by the binding of curvature-inducing proteins is studied by a combination of analytical and numerical approaches. In thermal equilibrium under the detailed balance between binding and unbinding, the membrane exhibits three phases: an unbound uniform flat phase (U), a bound uniform flat phase (B), and a separated/corrugated phase (SC). In the SC phase, the bound proteins form hexagonally-ordered bowl-shaped domains. The transitions between the U and SC phases and between the B and SC phases are second order and first order, respectively. At a small spontaneous curvature of the protein or high surface tension, the transition between B and SC phases becomes continuous. Moreover, a first-order transition between the U and B phases is found at zero spontaneous curvature driven by the Casimir-like interactions between rigid proteins. Furthermore, nonequilibrium dynamics is investigated by the addition of active binding and unbinding at a constant rate. The active binding and unbinding processes alter the stability of the SC phase.

Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales

At the micron scale, where cell organelles display an amazing complexity in their shape and organization, the physical properties of a biological membrane can be better-understood using continuum models subject to thermal (stochastic) undulations. Yet, the chief orchestrators of these complex and intriguing shapes are a specialized class of membrane associating often peripheral proteins called curvature remodeling proteins (CRPs) that operate at the molecular level through specific protein-lipid interactions. We review multiscale methodologies to model these systems at the molecular as well as at the mesoscopic and cellular scales, and also present a free energy perspective of membrane remodeling through the organization and assembly of CRPs. We discuss the morphological space of nearly planar to highly curved membranes, methods to include thermal fluctuations, and review studies that model such proteins as curvature fields to describe the emergent curved morphologies. We also discuss several mesoscale models applied to a variety of cellular processes, where the phenomenological parameters (such as curvature field strength) are often mapped to models of real systems based on molecular simulations. Much insight can be gained from the calculation of free energies of membranes states with protein fields, which enable accurate mapping of the state and parameter values at which the membrane undergoes morphological transformations such as vesiculation or tubulation. By tuning the strength, anisotropy, and spatial organization of the curvature-field, one can generate a rich array of membrane morphologies that are highly relevant to shapes of several cellular organelles. We review applications of these models to budding of vesicles commonly seen in cellular signaling and trafficking processes such as clathrin mediated endocytosis, sorting by the ESCRT protein complexes, and cellular exocytosis regulated by the exocyst complex. We discuss future prospects where such models can be combined with other models for cytoskeletal assembly, and discuss their role in understanding the effects of cell membrane tension and the mechanics of the extracellular microenvironment on cellular processes.