Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.bios.2023.115318

researchmap

Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

The field of supramolecular chemistry has witnessed tremendous progress in bringing the system away from equilibrium for traditionally inaccessible structures and functions. Vesicular assemblies with complex energy landscapes and pathways, which are reminiscent of diverse cellular vesicles like exosomes, remain exceedingly rare. Here, relying on the activation of oligo(ethylene glycol) (OEG) interdigitation and the encoded conformational freedom in monodisperse Janus dendrimers, we reveal a rich landscape and a pathway selection of distinct vesicles. The interdigitation can be selectively switched on and off using temperature ramps, and the critical temperatures can be further determined by molecular design. Our findings suggest that synthetic vesicles, with different energy states and unexpected transition pathways, emulate dynamic cellular vesicles in nature. We anticipate that vesicles with an activated OEG corona conformation will open new routes for nanomedicine and advanced materials.

DOI： 10.1021/jacs.3c04285

PubMed

researchmap

Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jacs.3c00389

researchmap

Publishing type：Research paper (scientific journal)  

We conducted a series of coarse-grained molecular dynamics (CG-MD) simulations to investigate the complicated actions of melittin, which is an antimicrobial peptide (AMP) derived from honey bee venom, on a lipid membrane. To accurately simulate the AMP action, we developed and used a protein CG model as an extension of the pSPICA force field (FF), which was designed to reproduce several thermodynamic quantities and structural properties. At a low peptide-to-lipid (P/L) ratio (1/102), no defect was detected. At P/L = 1/51, toroidal pore formation was observed due to collective insertion of multiple melittin peptides from the N-termini. The pore formation was initiated by a local increase in membrane curvature in the vicinity of the peptide aggregate. At a higher P/L ratio (1/26), two more modes were detected, seemingly not controlled by the P/L ratio but by a local arrangement of melittin peptides: 1. Pore formation accompanied by lipid extraction by melittin peptides:a detergent-like mechanism. 2. A rapidly formed large pore in a significantly curved membrane: bursting. Thus, we observed three pore formation modes (toroidal pore formation, lipid extraction, and bursting) depending on the peptide concentration and local arrangement. These observations were consistent with experimental observations and hypothesized melittin modes. Through this study, we found that the local arrangements and population of melittin peptides and the area expansion rate by membrane deformation were key to the initiation of and competition among the multiple pore formation mechanisms.

DOI： 10.1016/j.bbamem.2022.183955

Scopus

PubMed

researchmap

Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jctc.1c01207

Scopus

PubMed

researchmap

Publishing type：Research paper (scientific journal)  

We present a coarse-grained (CG) force field (FF), pSPICA, for lipid membranes that incorporates a CG polar water model, which guarantees a reasonable dielectric response for water. Using a relatively simple functional form for the interaction, the CG parameters were systematically optimized to reproduce surface/interfacial tension, density, solvation or transfer free energy, as well as distribution functions obtained from all-atom molecular dynamics trajectory generated with the CHARMM FF, following the scheme used in the SPICA FF. Lipid membranes simulated using the present CG FF demonstrate reasonable membrane area and thickness, elasticity, and line tension, which ensure that the simulated lipid membranes exhibit proper mesoscopic morphology. The major advantages of the pSPICA FF with a polar water model were its ability to simulate membrane electroporation and its superior performance in the morphological characterization of charged lipid aggregates. We also demonstrated that the pSPICA can better describe the membrane permeation of hydrophilic segments involving a water string formation.

DOI： 10.1021/acs.jctc.9b00946

Scopus

PubMed

researchmap

Publishing type：Research paper (scientific journal)  

We combined two reverse mapping methods, a predetermined fragment database and fragment rotation, to generate atomistic configurations from coarse-grained structures. The combined method together with molecular dynamics simulations was applied to simulate perfluorosulfonic acid (PFSA) membranes with large length scales and to explore the origin of fracture under a uniaxial tensile loading. Through the analysis of voids in the deformed membrane, we found that void growth with tensile loading takes place at the boundary of the hydrophobic and hydrophilic regions, which may be the origin of the fracture in the PFSA membrane. This study demonstrates an efficient reverse mapping method, which is useful for simulating proton exchange membranes with realistic chain lengths.

DOI： 10.1016/j.polymer.2019.121766

Scopus

researchmap

Publishing type：Research paper (scientific journal)  

The average conformation of the methyl-branched chains of archaeal lipid phosphatidyl glycerophosphate methyl ester (PGP-Me) was examined in a hydrated bilayer membrane based on the 2H nuclear magnetic resonance (NMR) of enantioselectively 2H-labeled compounds that were totally synthesized for the first time in this study. The NMR results in combination with molecular dynamics simulations revealed that the PGP-Me chain appeared to exhibit behavior different from that of typical membrane lipids such as dimyristoylphosphatidylcholine (DMPC). The C-C bonds of the PGP-Me chain adopt alternative parallel and tilted orientations to the membrane normal as opposed to a DMPC chain where all of the C-C bonds tilt in the same way on average. This characteristic orientation causes the intertwining of PGP-Me chains, which plays an important role in the excellent thermal and high-salinity stabilities of archaeal lipid bilayers and membrane proteins.

DOI： 10.1021/acs.biochem.9b00469

Scopus

PubMed

researchmap

Publishing type：Research paper (scientific journal)  

Understanding the molecular mechanism underlying pore formation in lipid membranes by antimicrobial peptides is of great importance in biological sciences as well as in drug design applications. Melittin has been widely studied as a pore forming peptide, though the molecular mechanism for pore formation is still illusive. We examined the free energy barrier for the creation of a pore in lipid membranes with and without multiple melittin peptides. It was found that six melittin peptides significantly stabilized a pore, though a small barrier (a few kBT) for the formation still existed. With five melittin peptides or fewer, the pore formation barrier was much higher, though the established pore was in a local energy minimum. Although seven melittins effectively reduced the free energy barrier, a single melittin peptide left the pore after a long time MD simulation probably because of the overcrowded environment around the bilayer pore. Thus, it is highly selective for the number of melittin peptides to stabilize the membrane pore, as was also suggested by the line tension evaluations. The free energy cost required to insert a single melittin into the membrane is too high to explain the one-by-one insertion mechanism for pore formation, which also supports the collective melittin mechanism for pore formation.

DOI： 10.1016/j.bbamem.2019.03.002

Scopus

PubMed

researchmap

Publishing type：Research paper (scientific journal)  

In studying large molecular systems, insights can better be extracted by selecting a limited number of physical quantities for analysis rather than treating every atomic coordinate in detail. Some information may, however, be lost by projecting the total system onto a small number of coordinates. For such problems, the generalized Langevin equation (GLE) is shown to provide a useful framework to examine the interaction between the observed variables and their environment. Starting with the GLE obtained from the time series of the observed quantity, we perform a transformation to introduce a set of variables that describe dynamical modes existing in the environment. The introduced variables are shown to effectively recover the essential information of the total system that appeared to be lost by the projection.

DOI： 10.1063/1.4962065

Scopus

researchmap