Biology subjects

Shinoda, W.

Publications and source records attributed to Shinoda, W..

5 recordsLinked to original sources

bioRxiv2025

pH-Sensitive Amino Lipid-Driven Pore Formation Enables Endosomal Escape of Lipid Nanoparticles

Lipid nanoparticles (LNPs) have transformed nucleic acid delivery for vaccines and gene therapies, yet their efficiency remains limited by incomplete endosomal escape. While experimental studies have revealed endosomal membrane disruption facilitating cytosolic release, the molecular basis of this process remains poorly understood. Here, we employ molecular simulations to elucidate how LNPs fuse with the endosomal membrane and release their payloads. We identify multiple fusion pathways, with a dominant stalk-pore mechanism. Our simulations reproduce and rationalize key experimental observations, including the transfer of ionizable lipids from LNPs to the membrane, which promotes nucleic acid reorientation and facilitates stalk formation and expansion. Furthermore, lipid shape, pH sensitivity, membrane tension, and nucleic acid encapsulation emerge as critical molecular determinants of endosomal escape efficiency. These findings advance our mechanistic understanding of intracellular delivery and provide a framework for the rational design of LNPs with improved performance for gene therapies and RNA vaccines.

biophysics↗

bioRxiv2025

Asymmetry and Heterogeneity in the Plasma Membrane

Plasma membranes (PMs) exhibit asymmetry between their two leaflets in terms of phospholipid headgroups, unsaturation, and resulting membrane properties such as packing and fluidity. Lateral heterogeneity, including the formation of lipid domains, is another crucial aspect of PMs with significant biological implications. However, the nature and even the existence of lipid domains in the two leaflets of PMs remain elusive, hindering a complete understanding of the significance of lipid asymmetry. Using coarse-grained molecular dynamics simulation of the asymmetric PM, we find that the outer leaflet predominantly adopts a liquid-ordered state, whereas the inner leaflet separates into nanoscale ({approx}10 nm) liquid-ordered and liquid-disordered domains, exhibiting highly dynamic fusion and fission events. This structural asymmetry is further reinforced by asymmetric lateral stress resulting from a cholesterol bias toward the outer leaflet. These findings suggest distinct functional roles for the two leaflets, modulated by asym-metric lateral stress. Additionally, comparing the phase behavior of asymmetric and fully scrambled PMs reveals a key determinant of domain size: intact PMs maintain nanoscale domains, while cell-derived giant PM vesicles, which have lost the strict lipid asymmetry, exhibit microscale domains.

biophysics↗

bioRxiv2023

Improved Protein Model in SPICA Force Field

The previous version of the SPICA coarse-grained (CG) force field (FF) protein model focused primarily on membrane proteins and successfully reproduced the dimerization free energies of several transmembrane helices and stable structures of various membrane protein assemblies. However, that model had limited accuracy when applied to other proteins, such as intrinsically disordered proteins (IDPs) and peripheral proteins, because the dimensions of the IDPs in an aqueous solution were too compact, and protein binding on the lipid membrane surface was over-stabilized. To improve the accuracy of the SPICA FF model for the simulation of such systems, in this study we introduce protein secondary structure-dependent nonbonded interaction parameters to the backbone segments and re-optimize almost all nonbonded parameters for amino acids. The improved FF proposed here successfully reproduces the radius of gyration of various IDPs, the binding sensitivity of several peripheral membrane proteins, and the dimerization free energies of several transmembrane helices. The new model also shows improved agreement with experiments on the free energy of peptide association in water. In addition, an extensive library of nonbonded interactions between proteins and lipids, including various glycerophospholipids, sphingolipids, and cholesterol, allows the study of specific interactions between lipids and peripheral and transmembrane proteins. Hence, the new SPICA FF (version 2) proposed herein is applicable with high accuracy for simulating a wide range of protein systems. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/557852v2_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@8b026dorg.highwire.dtl.DTLVardef@4c622forg.highwire.dtl.DTLVardef@c2081forg.highwire.dtl.DTLVardef@a34b69_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2021

The SPICA Coarse-Grained Force Field for Proteins and Peptides

A coarse-grained (CG) model for peptides and proteins was developed as an extension of the SPICA (Surface Property fItting Coarse grAined) force field (FF). The model was designed to examine membrane proteins that are fully compatible with the lipid membranes of the SPICA FF. A preliminary version of this protein model was created using thermodynamic properties, including the surface tension and density in the SPICA (formerly called SDK) FF. In this study, we improved the CG protein model to facilitate molecular dynamics (MD) simulation with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. The side chain analogs reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable dimerization free energies in water compared to those from AA-MD. A series of peptides/proteins adsorbed or penetrated into the membrane simulated by the CG-MD correctly predicted the penetration depths and tilt angles of peripheral and transmembrane peptides/proteins comparable to those in the orientation of protein in membrane (OPM) database. In addition, the dimerization free energies of several transmembrane helices within a lipid bilayer were comparable to those from experimental estimation. Application studies on a series of membrane protein assemblies, scramblases, and poliovirus capsids demonstrated a good performance of the SPICA FF.

biophysics↗

bioRxiv2020

Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure

Lipid droplets (LD) are intracellular organelles responsible for lipid storage, and they emerge from the endoplasmic reticulum (ER) upon the accumulation of neutral lipids, mostly triglycerides (TG), between the two leaflets of the ER membrane. LD biogenesis takes place at ER sites that are marked by the protein seipin, which subsequently recruits additional proteins to catalyse LD formation. Deletion of seipin, however, does not abolish LD biogenesis, and its precise role in controlling LD assembly remains unclear. Here we use molecular dynamics simulations to investigate the molecular mechanism through which seipin promotes LD formation. We find that seipin clusters TG molecules inside its unconventional ring-like oligomeric structure, and that both its luminal and transmembrane regions contribute to this process. Diacylglycerol, the precursor of TG, also clusters inside the seipin oligomer, in turn promoting TG accumulation. Our results suggest that seipin remodels the membrane of specific ER sites to prime them for LD biogenesis. Significance statementMetabolic disorders related to aberrant fat accumulation, including lipodystrophy and obesity, are a particularly serious health concern. In cells, fat accumulates in intracellular organelles, named lipid droplets (LDs). LDs form in the endoplasmic reticulum, where triglycerides, the most abundant form of fat, is produced. The Bernardinelli-Seip congenital lipodystrophy type 2 protein, seipin, has been identified as a key regulator of LD formation, but its mechanism of action remains debated and its molecular details mostly obscure. Here, we use molecular dynamics simulations to investigate the mechanism of seipin. We find that seipin can cluster and trap both triglycerides and its precursor, diacylglycerol. Our results suggest that seipin organizes the lipid composition of specific ER sites to prime them for LD biogenesis.

cell biology↗