Decoding the Effect of Hydrostatic Pressure on TRPV1 Lower-Gate Conformation by Molecular-Dynamics Simulation.
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ABSTRACT: In response to hydrostatic pressure, the cation channel transient receptor potential vanilloid 1 (TRPV1) is essential in signaling pathways linked to glaucoma. When activated, TRPV1 undergoes a gating transition from a closed to an open state that allows the influx of Ca2+ ions. However, the gating mechanism of TRPV1 in response to hydrostatic pressure at the molecular level is still lacking. To understand the effect of hydrostatic pressure on the activation of TRPV1, we conducted molecular-dynamics (MD) simulations on TRPV1 under different hydrostatic pressure configurations, with and without a cell membrane. The TRPV1 membrane-embedded model is more stable than the TPRV1-only model, indicating the importance of including the cell membrane in MD simulation. Under elevated pressure at 27.6 mmHg, we observed a more dynamic and outward motion of the TRPV1 domains in the lower-gate area than in the simulation under normal pressure at 12.6 mmHg. While a complete closed-to-open-gate transition was not evident in the limited course of our MD simulations, an increase in the channel radius at the lower gate was observed at 27.6 mmHg versus that at 12.6 mmHg. These findings provide novel information regarding the effect of hydrostatic pressure on TRPV1 channels.
Project description:The porcine lens response to a hyperosmotic stimulus involves an increase in the activity of an ion cotransporter sodium-potassium/two-chloride cotransporter 1 (NKCC1). Recent studies with agonists and antagonists pointed to a mechanism that appears to depend on activation of transient receptor potential vanilloid 1 (TRPV1) ion channels. Here, we compare responses in lenses and cultured lens epithelium obtained from TRPV1-/- and wild type (WT) mice. Hydrostatic pressure (HP) in lens surface cells was determined using a manometer-coupled microelectrode approach. The TRPV1 agonist capsaicin (100 nM) caused a transient HP increase in WT lenses that peaked after ∼30 min and then returned toward baseline. Capsaicin did not cause a detectable change of HP in TRPV1-/- lenses. The NKCC inhibitor bumetanide prevented the HP response to capsaicin in WT lenses. Potassium transport was examined by measuring Rb+ uptake. Capsaicin increased Rb+ uptake in cultured WT lens epithelial cells but not in TRPV1-/- cells. Bumetanide, A889425, and the Akt inhibitor Akti prevented the Rb+ uptake response to capsaicin. The bumetanide-sensitive (NKCC-dependent) component of Rb+ uptake more than doubled in response to capsaicin. Capsaicin also elicited rapid (<2 min) NKCC1 phosphorylation in WT but not TRPV1-/- cells. HP recovery was shown to be absent in TRPV1-/- lenses exposed to hyperosmotic solution. Bumetanide and Akti prevented HP recovery in WT lenses exposed to hyperosmotic solution. Taken together, responses to capsaicin and hyperosmotic solution point to a functional role for TRPV1 channels in mouse lens. Lack of NKCC1 phosphorylation and Rb+ uptake responses in TRPV1-/- mouse epithelium reinforces the notion that a hyperosmotic challenge causes TRPV1-dependent NKCC1 activation. The results are consistent with a role for the TRPV1-activated signaling pathway leading to NKCC1 stimulation in lens osmotic homeostasis.
Project description:We examined whether hydrostatic-pressure induced nuclear DAF-16 functions as a transcription factor. The expression changes were monitored by using DNA microarray analyses, after the WT adult hermaphrodites were exposed to a pressure of ≥30 MPa for 5 minutes. The results showed significant and reproducible increase of 31 genes after 30 minutes
Project description:As a member of the transient receptor potential (TRP) channels superfamily, the TRPV1 channel undergoes a closed-to-open gating transition in response to various physical and chemical stimuli including heat. Thanks to recent progress in cryo-electron microscopy, high-resolution structures are becoming available for various TRP channels including TRPV1. This has enabled us to study the molecular mechanism of TRPV1 channel gating by using molecular simulation. Here we review recent progress in molecular simulations of TRPV1 channel by us and others, with focus on our molecular dynamics (MD) simulations of TRPV1 at different temperatures. While no consensus has been reached on the heat activation mechanism of TRPV1, the simulations have offered specific predictions and models for future experimental studies to test.
Project description:S. cerevisiae Y440 Mat a leu2 was grown in YEPD at 28 degrees C with aeration to exponential growth phase and was subjected to a hydrostatic pressure of 50 and 200 MPa for 30 minutes at room temperature. Total RNA was extracted using phenol/chloroform and further precipitated with 3 M sodium acetate / absolute ethanol. Extracted RNA samples were treated for 10 min with 0.5 U of RNAse-free DNAse I / ]g RNA at 37 oC to remove any residual genomic DNA. RNA pellets were washed in 70 % ethanol and resuspended in DEPC treated water. Purified mRNA from pressurized and unpressurized cells was reversed-transcribed, labeled with fluorescent-tagged nucleotides, and hybridized against a common refernce pool of mRNA for 18 h at 65 0C on cDNA microarray. After several washes, arrays were scanned using a commercially available scanning laser microscope (GenePix 4000) from Axon Instruments (Foster City, CA), the data obtained was normalized (mean value) applying a linear regression method. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract Keywords: Computed
Project description:Uterine regeneration using decellularization scaffolds provides a novel treatment for uterine factor infertility. Decellularized scaffolds require maximal removal of cellular components and minimal damage to the extracellular matrix (ECM). Among many decellularization methods, the hydrostatic pressure (HP) method stands out due to its low cytotoxicity and superior ECM preservation compared to the traditional detergent methods. Conventionally, 980 MPa was utilized in HP decellularization, including the first successful implementation of uterine decellularization previously reported by our team. However, structural protein denaturation caused by exceeding pressure led to a limited regeneration outcome in our previous research. This factor urged the study on the effects of pressure conditions in HP methods on decellularized scaffolds. The authors, therefore, fabricated a decellularized uterine scaffold at varying pressure conditions and evaluated the scaffold qualities from the perspective of cell removal and ECM preservation. The results show that by using lower decellularization pressure conditions of 250 MPa, uterine tissue can be decellularized with more preserved structural protein and mechanical properties, which is considered to be promising for decellularized uterine scaffold fabrication applications.
Project description:The physical and chemical properties of typical nitrate energetic materials under hydrostatic compression and uniaxial compression were studied using the ReaxFF/lg force field combined with the molecular dynamics simulation method. Under hydrostatic compression, the P-V curve and the bulk modulus (B 0) obtained using the VFRS equation of state show that the compressibility of the three crystals is nitroglycerine (NG) > erythritol tetranitrate (ETN) > 2,3-bis-hydroxymethyl-2,3-dinitro-1,4-butanediol tetranitrate (NEST-1). The a- and c-axis of ETN are easy to compress under the action of hydrostatic pressure, but the b-axis is not easy to compress. The b-axis of NEST-1 is the most compressible, while the a- and c-axis can be compressed slightly when the initial pressure increases and then remains unchanged afterward. The a-, b-, and c-axes of NG all have similar compressibilities. By analyzing the change trend of the main bond lengths of the crystals, it can be seen that the most stable of the three crystals is the N-O bond and the largest change is in the O-NO2 bond. The stability of the C-O bond shows that the NO3 produced by nitrates is not from the C-O bond fracture. Under uniaxial compression, the stress tensor component, the average principal stress, and the hydrostatic pressure have similar trends and amplitudes, indicating that the anisotropy behaviors of the three crystals ETN, NEST-1, and NG are weak. There is no significant correlation between maximum shear stress and sensitivity. The maximum shear stresses τ xy and τ yz of the ETN in the [010] direction are 1.5 GPa higher than τ xz . However, the maximum shear stress of NG shows irregularity in different compression directions, indicating that there is no obvious correlation between the maximum shear stress and sensitivity.
Project description:As a prototype cellular sensor, the TRPV1 cation channel undergoes a closed-to-open gating transition in response to various physical and chemical stimuli including noxious heat. Despite recent progress, the molecular mechanism of heat activation of TRPV1 gating remains enigmatic. Toward decrypting the structural basis of TRPV1 heat activation, we performed extensive molecular dynamics simulations (with cumulative simulation time of ?11 ?s) for the wild-type channel and a constitutively active double mutant at different temperatures (30, 60, and 72°C), starting from a high-resolution closed-channel structure of TRPV1 solved by cryo-electron microscopy. In the wild-type simulations, we observed heat-activated conformational changes (e.g., expansion or contraction) in various key domains of TRPV1 (e.g., the S2-S3 and S4-S5 linkers) to prime the channel for gating. These conformational changes involve a number of dynamic hydrogen-bond interactions that were validated with previous mutational studies. Next, our mutant simulations observed channel opening after a series of conformational changes that propagate from the channel periphery to the channel pore via key intermediate domains (including the S2-S3 and S4-S5 linkers). The gating transition is accompanied by a large increase in the protein-water electrostatic interaction energy, which supports the contribution of desolvation of polar/charged residues to the temperature-sensitive TRPV1 gating. Taken together, our molecular dynamics simulations and analyses offered, to our knowledge, new structural, dynamic, and energetic information to guide future mutagenesis and functional studies of the TRPV1 channels and development of TRPV1-targeting drugs.
Project description:Transient receptor potential vanilloid subtype 1 (TRPV1) is a heat-sensitive ion channel also involved in pain sensation, and is the receptor for capsaicin, the active ingredient of hot chili peppers. The recent structures of TRPV1 revealed putative ligand density within the S1 to S4 voltage-sensor-like domain of the protein. However, questions remain regarding the dynamic role of the lipid bilayer in ligand binding to TRPV1. Molecular dynamics simulations were used to explore behavior of capsaicin in a 1-palmitoyl-2-oleoyl phosphatidylcholine bilayer and with the target S1-S4 transmembrane helices of TRPV1. Equilibrium simulations reveal a preferred interfacial localization for capsaicin. We also observed a capsaicin molecule flipping from the extracellular to the intracellular leaflet, and subsequently able to access the intracellular TRPV1 binding site. Calculation of the potential of mean force (i.e., free energy profile) of capsaicin along the bilayer normal confirms that it prefers an interfacial localization. The free energy profile indicates that there is a nontrivial but surmountable barrier to the flipping of capsaicin between opposing leaflets of the bilayer. Molecular dynamics of the S1-S4 transmembrane helices of the TRPV1 in a lipid bilayer confirm that Y511, known to be crucial to capsaicin binding, has a distribution along the bilayer normal similar to that of the aromatic group of capsaicin. Simulations were conducted of the TRPV1 S1-S4 transmembrane helices in the presence of capsaicin placed in the aqueous phase, in the lipid, or docked to the protein. No stable interaction between ligand and protein was seen for simulations initiated with capsaicin in the bilayer. However, interactions were seen between TRPV1 and capsaicin starting from the cytosolic aqueous phase, and capsaicin remained stable in the majority of simulations from the docked pose. We discuss the significance of capsaicin flipping from the extracellular to the intracellular leaflet and mechanisms of binding site access by capsaicin.
Project description:The solidification experiments of TC8 alloy under both microgravity and normal gravity were conducted using a drop tube. The solidification microstructure were found composed of fine equiaxed grains formed at early stage and bigger elongated grains formed at later stage. Between the two kinds of grains a curved transition interface was observed in 1g sample, while that in μg sample was almost flat. Generally, the amounts and aspect ratios of the grains are larger, and the grain sizes are smaller in 1g sample. Besides, no visible element macrosegregation occurred in both samples. The results suggest that the solidification velocities of the samples were rapid, and consequently the convection effect and solute transport effect caused by gravity had little influence on the solidification microstructure. Therefore, the solidification process was mainly controlled by thermal diffusion, and hydrostatic pressure and wall effect played a great role in it.