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Nanoplastics, small plastic particles smaller than microplastics, have been suggested to have a wide-range of unique interactions when they encounter lipid membranes. Recent studies have demonstrated that the smaller size of nanoplastic particles may allow them to penetrate and dissolve in lipid membranes. Following this penetration, however, there is not yet a clear picture of how such particles impact the local lipid environment. A recent study by the present authors found that when lipid vesicles that included laurdan, a fluorescent dye molecule typically thought to report on the membrane phase, were exposed to polystyrene nanoparticles, they exhibited a concentration-dependent blue shift consistent with a fluid-to-gel phase transition. However, coarse-grained simulations suggested that no such transition was taking place; instead, the simulations observed that polymer chains from the polystyrene nanoparticles penetrated into the liposome membrane. In the present work, we use all-atom molecular dynamics simulations to demonstrate that the inclusion of polystyrene within a lipid membrane causes significant changes to the local hydration and structure of that membrane while maintaining the membrane phase. Specifically, through the explicit incorporation of laurdan within the present simulations, we demonstrate that the local hydration environment of the dye molecule changes significantly but continuously as membranes are exposed to polystyrene, thus suggesting a possible explanation for the previously reported experimental observation. The present results provide a picture of the complex heterogeneity generated within polymer-containing membranes. 

Understanding the cell membrane penetration process of biomedical nanosystems and its dependence on nanomaterial properties and surface functionalization is crucial for the rational design of safe and efficient cellular internalization strategies. Computer simulations are powerful tools to evaluate the thermodynamic aspects of the process and to elucidate its underlying molecular mechanisms. In this work, the interaction between uncoated or polymer-coated graphene oxide (GO) dots and lipid bilayer models is investigated by coarse-grained (CG) molecular dynamics (MD) simulations. We first validate the coarse-grained model against all-atom MD simulations (AAMD). Then, we perform CGMD simulations and free energy calculations to assess the effect of the polymeric coating and of its features (grafting density, polymer end-group charge and polymer hydrophilic/hydrophobic character) on the interaction between GO dots of realistic size and lipid membranes. We find that the membrane penetration of GO dots is spontaneous when coated with a low-density polyethylene glycol (PEG) layer, while a high-density PEG coating prevents the penetration, and a mixed PEG/polyethylene (PE) coating excessively stabilizes the nanosystem in the inner membrane region. These findings will help to fine-tune how GO dots interact with cellular membranes. 

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 computational spectroscopy of water has proven to be a powerful tool for probing the structure and dynamics of chemical systems and for providing atomistic insight into experimental vibrational spectroscopic results. However, such calculations have been limited for biochemical systems due to the lack of empirical vibrational frequency maps for the TIP3P water model, which is used in many popular biomolecular force fields. Here, we develop an empirical map for the TIP3P model and evaluate its efficacy for reproducing the experimental vibrational spectroscopy of water. We observe that the calculated infrared and Raman spectra are blueshifted and narrowed compared to the experimental spectra. Further analysis finds that the blueshift originates from a shifted distribution of frequencies, rather than other dynamical effects, suggesting that the TIP3P model forms a significantly different electrostatic environment than other three-point water models. This is explored further by examining the two-dimensional infrared spectra, which demonstrates that the blueshift is significant for the first two vibrational transitions. Similarly, spectral diffusion timescales, evaluated through both the center line slope and the frequency–frequency time correlation function demonstrate that TIP3P exhibits significantly faster spectral dynamics than other three-point models. Finally, sum-frequency generation spectroscopy calculations suggest that despite these challenges, the TIP3P empirical map can provide phenomenological, qualitative, insight into the behavior of water at the air–water and lipid–water interfaces. As these interfaces are models for hydrophobic and hydrophilic environments observed in biochemical systems, the presently developed empirical map will be useful for future studies of biochemical systems. 

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.