Search for: All records

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 Synaptotagmin (syt) 1, a Ca²⁺sensor for synaptic vesicle exocytosis, functions in vivo as a multimer. Syt1 senses Ca²⁺via tandem C2-domains that are connected to a single transmembrane domain via a juxtamembrane linker. Here, we show that this linker segment harbors a lysine-rich, intrinsically disordered region that is necessary and sufficient to mediate liquid-liquid phase separation (LLPS). Interestingly, condensate formation negatively regulates the Ca²⁺-sensitivity of syt1. Moreover, Ca²⁺and anionic phospholipids facilitate the observed phase separation, and increases in [Ca²⁺]_ipromote the fusion of syt1 droplets in living cells. Together, these observations suggest a condensate-mediated feedback loop that serves to fine-tune the ability of syt1 to trigger release, via alterations in Ca²⁺binding activity and potentially through the impact of LLPS on membrane curvature during fusion reactions. In summary, the juxtamembrane linker of syt1 emerges as a regulator of syt1 function by driving self-association via LLPS. 

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. 

Biomolecular phase separation has emerged as an essential mechanism for cellular organization. How cells respond to environmental stimuli in a robust and sensitive manner to build functional condensates at the proper time and location is only starting to be understood. Recently, lipid membranes have been recognized as an important regulatory center for biomolecular condensation. However, how the interplay between the phase behaviors of cellular membranes and surface biopolymers may contribute to the regulation of surface condensation remains to be elucidated. Using simulations and a mean-field theoretical model, we show that two key factors are the membrane’s tendency to phase-separate and the surface polymer’s ability to reorganize local membrane composition. Surface condensate forms with high sensitivity and selectivity in response to features of biopolymer when positive co-operativity is established between coupled growth of the condensate and local lipid domains. This effect relating the degree of membrane–surface polymer co-operativity and condensate property regulation is shown to be robust by different ways of tuning the co-operativity, such as varying membrane protein obstacle concentration, lipid composition, and the affinity between lipid and polymer. The general physical principle emerged from the current analysis may have implications in other biological processes and beyond.