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In this chapter, we discuss the analysis of membrane remodeling by proteins, pep- tides and nanoparticles using multi-scale computational methods; these include mainly molecular dynamics simulations at atomistic and coarse-grained levels, al- though we will also touch upon continuum mechanics models. The discussions will cover several systems that we have analyzed in recent studies, which include Sar1, the ESCRTIII complex, complexin and peptides from SARS-COVID-2; as comparison, we also briefly discuss the impact of polyelectrolyte coacervates and functionalized nanoparticles on membrane properties, including generation of membrane curvature and potential disruption of liposomes. These examples illustrate different molecular properties and mechanisms that are potentially relevant to membrane remodeling at different length scales. The results highlight both the values and limitations of different computational models for the analysis of membrane remodeling, thus underscoring the importance of integrating different computational approaches to cross-validate the results. 

The backbone hydrogen bonds of a peptide assembly derived from FUS-LC gain excess stability at the anionic membrane-water and air–water interfaces due to distinctive interfacial solvation properties. 

Abstract Curvature-generating proteins that direct membrane trafficking assemble on the surface of lipid bilayers to bud transport intermediates, which move protein and lipid cargoes from one cellular compartment to another. However, it remains unclear what controls the overall shape of the membrane bud once curvature induction has begun. In vitro experiments showed that excessive concentrations of the COPII protein Sar1 promoted the formation of membrane tubules from synthetic vesicles, while COPII-coated transport intermediates in cells are generally more spherical or lobed in shape. To understand the origin of these morphological differences, we employ atomistic, coarse-grained (CG), and continuum mesoscopic simulations of membranes in the presence of multiple curvature-generating proteins. We first characterize the membrane-bending ability of amphipathic peptides derived from the amino terminus of Sar1, as a function of interpeptide angle and concentration using an atomistic bicelle simulation protocol. Then, we employ CG simulations to reveal that Sec23 and Sec24 control the relative spacing between Sar1 protomers and form the inner-coat unit through an attachment with Sar1. Finally, using dynamical triangulated surface simulations based on the Helfrich Hamiltonian, we demonstrate that the uniform distribution of spacer molecules among curvature-generating proteins is crucial to the spherical budding of the membrane. Overall, our analyses suggest a new role for Sec23, Sec24, and cargo proteins in COPII-mediated membrane budding process in which they act as spacers to preserve a dispersed arrangement of Sar1 protomers and help determine the overall shape of the membrane bud. 

Abstract Surface interactions are responsible for many properties of condensed matter, ranging from crystal faceting to the kinetics of phase transitions. Usually, these interactions are polar along the normal to the interface and apolar within the interface. Here we demonstrate that polar in-plane surface interactions of a ferroelectric nematic N F produce polar monodomains in micron-thin planar cells and stripes of an alternating electric polarization, separated by $${180}^{{{{{{\rm{o}}}}}}}$$ 180 o domain walls, in thicker slabs. The surface polarity binds together pairs of these walls, yielding a total polarization rotation by $${360}^{{{{{{\rm{o}}}}}}}$$ 360 o . The polar contribution to the total surface anchoring strength is on the order of 10%. The domain walls involve splay, bend, and twist of the polarization. The structure suggests that the splay elastic constant is larger than the bend modulus. The $${360}^{{{{{{\rm{o}}}}}}}$$ 360 o pairs resemble domain walls in cosmology models with biased vacuums and ferromagnets in an external magnetic field.