Biology subjects

Park, Y. C.

Publications and source records attributed to Park, Y. C..

5 recordsLinked to original sources

bioRxiv2026

On the effect of lateral stretch on the deformation energetics of biological membranes and the lipid dynamics within

A broad range of cellular functions involve transient or persistent changes in the morphology of lipid membranes, from the organellar to the molecular scale. By and large, the thermodynamics of protein-mediated remodeling, which often distort the membrane beyond its thermally accessible undulations, remain to be understood. Molecular Dynamics simulations enhanced by advanced sampling methods are uniquely suited to examine and quantitate these phenomena. Here, we leverage the Multi-Map simulation method to directly quantify how applied lateral tension impacts the energetics of both global and localized membrane perturbations induced extrinsically. We obtain free-energy profiles of curvature and thickness deformations with and without tension, which allow us to test the quadratic approximations of Helfrich-based continuum theories. We find that these continuum models are applicable up to ~ 20 kBT, beyond which they under-estimate the free-energy cost of bending. However, we find that the effect of tension on these deformations is primarily driven by changes in the projected area of the membrane, and therefore consistent with continuum theory, even beyond 30 kBT. These changes outpace the effects of tension on lipid packing and diffusion, and importantly we find that tension levels preceding rupture ([≤] 10 mN/m) do not impede complete lipid mixing. Finally, we investigate the free-energy landscapes of membrane thickness and lipid enrichment with a heterogeneous lipid composition and show that strong enrichment can be sustained even under steady exchange of the constituent lipid molecules.

biophysics↗

bioRxiv2025

TMC1 and TMC2 are cholesterol-dependent scramblases that regulate membrane homeostasis in auditory hair cells

TMC1 and TMC2, the pore-forming subunits of the mechanoelectrical transduction (MET) complex in inner ear sensory hair cells, are essential for auditory and vestibular function. Pathogenic mutations in TMC1 are a leading cause of genetic hearing loss, but their underlying cellular mechanisms remain poorly understood. Here, we reveal that TMC1 and TMC2 are cholesterol-regulated lipid scramblases whose activity modulates plasma membrane asymmetry. Using reconstituted proteoliposomes and molecular dynamics simulations, we demonstrate that both proteins facilitate phospholipid translocation across membrane bilayers, a process tuned by cholesterol and enhanced by deafness-causing TMC1 mutations. We show that this scramblase activity correlates with TMC1-dependent externalization of phosphatidylserine and membrane blebbing in murine auditory hair cells, linking TMC1-dependent membrane homeostasis dysregulation to auditory sensory cell pathology. These findings identify TMCs as a novel family of lipid scramblases, advancing our understanding of MET complex biology and offering mechanistic insight into membrane-driven forms of hereditary deafness.

neuroscience↗

bioRxiv2022

State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels

The force-from-lipids hypothesis of cellular mechanosensation posits that membrane channels open and close in response to changes in the physical state of the lipid bilayer, induced for example by lateral tension. Here, we investigate the molecular basis for this transduction mechanism by studying the mechanosensitive ion channel MscS from Escherichia coli and its eukaryotic homolog, MSL1 from Arabidopsis thaliana. First, we use single-particle cryo-EM to determine the structure of a novel open conformation of wild-type MscS, stabilized in a thinned lipid nanodisc. Compared with the closed state, the structure shows a reconfiguration of helices TM1, TM2 and TM3a, and widening of the central pore. Based on these structures, we examined how the morphology of the lipid bilayer is altered upon gating, using molecular dynamics simulations. The simulations reveal that closed-state MscS causes drastic protrusions in the inner leaflet of the lipid bilayer, both in the absence and presence of lateral tension, and for different lipid compositions. These deformations arise to provide adequate solvation to hydrophobic features of the protein surface in this conformation, and clearly reflect a high energy conformation for the membrane, particularly under tension. Strikingly, these protrusions are largely eradicated upon channel opening. An analogous computational study of open and closed MSL1 recapitulates these findings. The gating equilibrium of MscS channels thus appears to be dictated by two opposing conformational preferences, namely those of the lipid membrane and of the protein structure. We propose a membrane deformation model of mechanosensation, which posits that tension shifts the gating equilibrium towards the conductive state not because it alters the mode in which channel and lipids interact but because it increases the energetic cost of the morphological perturbations in the membrane induced by to the closed state.

biophysics↗

bioRxiv2022

Long-term Antibody Release Polycaprolactone (PCL) Capsule and the Release Kinetics In Natural and Accelerated Degradation

Although therapy using monoclonal antibodies (mAbs) has been steadily successful over the last 20 years, the means of delivery of mAbs has not been optimized, especially for long-term delivery. Frequent injections or infusions have been current standard of care. In this study, we have developed a long-term antibody biodegradable implant using a porous polycaprolactone (PCL) capsule. It released Bevacizumab (Bev) slowly for 8 months to date. The Bev release kinetics fit a drug release model with experimental data of the diffusion coefficient and partition coefficient through the polymer capsule. Since screening drug release profiles for the long-term (> 6 months) is time consuming, an accelerated degradation method was used after validating characteristics of the PCL capsule in natural and accelerated degradation conditions. The correlation of time period between the natural and the accelerated degradation was determined. Overall, the study suggests mAbs can be released from a porous PCL capsule without an effect of the polymer degradation over the long period (~ 6 months) and the long-term release kinetics can be determined by the accelerated degradation within 14 days.

bioengineering↗

bioRxiv2021

The functional evolution of termite gut microbiota

Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species, but remains largely unknown in other taxa. We intend to feel this gap and provide a global understanding of the functional evolution of termite gut microbiota. We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that key nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways. Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared [~]150 million years ago. Therefore, the "world smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception.

evolutionary biology↗