Coarse grained molecular dynamic simulation of mammalian mechanosensitive ion channel TRPV2
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Molecular dynamics simulation is a powerful biophysical tool to gain theoretical insights into protein action. In mechanobiology, conformational change of bacterial mechanosensitive ion channels has been studied extensively. Here we studied transient receptor potential cation channel subfamily V member 2 (TRPV2), a mammalian mechanosensitive ion channel, using coarse grained molecular dynamics simulation. Coarse grained geometry of TRPV2 was generated based on a full atomic cryo-electron microscopy structure (PDB ID: 5HI9). The TRPV2 protein was embedded in a membrane composed of POPC/POPS phospholipid bilayer and solvated. The structure of TRPV2 homotetramer was stable during 1 μs simulation period. While a bacterial mechanosensitive channel MscS showed significant increase in pore radius in response to membrane tension, TRPV2 did not, as suggested by previous experimental studies. Transmembrane helix tilt, which was observed in mechanosensitive opening of MscS, was not observed in TRPV2 in membrane tension. This result suggests that mechanosensitive alteration of TRPV2 structure requires external force other than the membrane tension.
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Monitoring neural activities by optical imaging
Monitoring neural activities by optical imaging along with the use of genetic modification provides better spatio-temporal resolution to study single neural firing and hence very useful in understanding the neural process and dynamics. This is just a glimpse of few articles reported their outcome of such imaging.
Chen_et_al-2008-Genes_to_Cells
This document describes the identification of a putative human mitochondrial thymidine monophosphate kinase (TMPK2). The researchers cloned and characterized a cDNA encoding TMPK2 that contains a mitochondrial targeting sequence. They showed that TMPK2 localizes to mitochondria and overexpression increases cellular dTTP levels and the conversion of radioactive thymidine and dTMP to dTDP and dTTP in mitochondria. TMPK2 expression was detected in various tissues and cell lines, and was upregulated during monocyte/macrophage differentiation, suggesting its role in mitochondrial DNA synthesis during cellular differentiation.
Actual Poster for SIP
This study identified five olfactory receptors expressed in human airway smooth muscle cells. Short-chain fatty acids like propionate and acetate, ligands for one receptor OR51E2, decreased cell stiffness, cytoskeletal dynamics, and inhibited proliferation in a time- and dose-dependent manner. This suggests olfactory signaling in airway smooth muscle may be exploited for new therapies for obstructive lung diseases.
Micro-Neuro-Sensor Recording of STN Neurons of the Human Brain
What cause to the neurons of the human brain cells when they are damaged. They become inactive. So damage to subthalamiuc nucleus (STN) neurons of the human brain causing larger involuntary movements and thereby attacking the Parkinson’s disease (PD). Deep brain stimulation (DBS) of bilateral sub thalamic nuclei (STN) is an efficient method of rehabilitation technique in subjects with advanced idiopathic Parkinson’s (or Parkinson) disease. Accurate targeting of STN neurons and placement of microelectrodes/ (neurosensors) are paramount importance for optimal results after STN-DBS method.In this paper, microminiaturized electrode recordings (MER) of STN neurons were detected in a mean of 3.5 ±1.1 channels on right hemisphere and 3.6 ±1.04 on left hemisphere.Final channel selected were most commonly central seen in 42.3% followed by anterior in 33.7%. When a high current is delivered to STN or GPi neurons of basal ganglia (a component of human brain), causing their inhibition and improved indication of symptoms. It is now known that there is a significant change in the firing pattern and a reorganization of the entire basal ganglia circuit with DBS. The MER of STN neurons has identified a specific high frequency irregular larger amplitude firing patterns seen only in disease states and hence used to detect the neurons of ST nucleus during functional surgery. Microelectrode recording is so useful to confirm the right path but has to be taken in consideration with effects on macro stimulation.
Rowitch, David
This document discusses oligodendrocytes, the cells that form myelin in the central nervous system. It describes their role in development, diseases like multiple sclerosis where remyelination fails, and potential therapies to promote remyelination. A clinical trial was conducted using neural progenitor cell transplantation to treat Pelizaeus-Merzbacher disease, a fatal leukodystrophy caused by myelin deficiency. Research suggests the Wnt signaling pathway inhibits oligodendrocyte differentiation and myelination, and a small molecule Wnt inhibitor was found to accelerate remyelination in mice.
NKCC1 Poster for SIRS 2010
Poster I presented at the Schizophrenia International Research Society conference in Florence in April, 2010.
Finger prick testing- physics and problems
2nd part of 2 part seminar for 2nd semester of nanotechnology course. It is continuation from 1st seminar, throws light on biosensor, low-dimensional anomalies, Luminescence, Surface plasmon resonance, Drop by drop variations of blood.
Note- This is just concise part I made for seminar, any scientific inaccuracies is probable and highly regretted. Any constructive criticism is welcome.
Positron emission tomographic scan
PET scans use radioactive tracers and detectors to generate 3D images of metabolic processes in the body. They have various applications in neurology for diagnosing and monitoring conditions like dementia, epilepsy, movement disorders, and brain tumors. For example, PET can help differentiate Alzheimer's from other dementias based on patterns of hypometabolism in temporal and parietal lobes. It is also useful for localizing epileptic foci before epilepsy surgery. The document discusses the history, mechanisms, common tracers, and limitations of PET scanning as well as its role in evaluating specific neurological conditions and potential future applications.
Abdulla, ICBO2011, Composite annotation for heart development
This document summarizes research on annotating multiscale models of heart development. It describes the anatomy, tissues, cells and proteins involved in heart development. It discusses using the Gene Ontology and other ontologies to annotate models pre-composition, and ontologies like PATO and EHDA for post-composition annotation. The research uses Compucell3D and SBML to build a multiscale model of heart development involving genes, proteins, cells and tissues. It concludes that post-composition annotation is necessary for multiscale developmental models but is more challenging than pre-composition.
Micro-Neuro-Sensor Recording of STN Neurons of the Human Brain
Abstract-What cause to the neurons of the human brain cells when they are damaged. They become inactive. So damage to subthalamiuc ucleus (STN) neurons of the human brain causing larger involuntary movements and thereby attacking the Parkinson’s disease (PD). Deep brain stimulation (DBS) of bilateral sub thalamic nuclei (STN) is an efficient method of rehabilitation technique in subjects with advanced idiopathic Parkinson’s (or Parkinson) disease. Accurate targeting of STN neurons and placement of microelectrodes/ (neurosensors) are paramount importance for optimal results after STN-DBS method.In this paper, microminiaturized electrode recordings (MER) of STN neurons were detected in a mean of 3.5 ±1.1 channels on right hemisphere and 3.6 ±1.04 on left hemisphere.Final channel selected were most commonly central seen in 42.3% followed by anterior in 33.7%. When a high current is delivered to STN or GPi neurons of basal ganglia (a component of human brain), causing their inhibition and improved indication of symptoms. It is now known that there is a significant change in the firing pattern and a reorganization of the entire basal ganglia circuit with DBS. The MER of STN neurons has identified a specific high frequency irregular larger amplitude firing patterns seen only in disease states and hence used to detect the neurons of ST nucleus during functional surgery. Micro electrode recording is so useful to confirm the right path but has to be taken in consideration with effects on macro stimulation.
Radiopharmacutical coordination chemistry approach
Here is a 1 page report on how my research involves transition metals:
My research focuses on developing new radiopharmaceuticals for diagnostic imaging and therapy. Radiopharmaceuticals are drugs that contain a radionuclide, which allows the drug to be detected by imaging modalities like PET or SPECT. The radionuclide is often attached to a targeting molecule like a peptide or antibody to allow specific delivery to tissues of interest.
Many commonly used radionuclides in radiopharmaceuticals are transition metals. For example, technetium-99m is the most widely used medical isotope due to its ideal nuclear properties for imaging with gamma cameras. I develop new 99mTc-labeled compounds by manipulating the coordination
Biosefty Committee.pptx
The document discusses the Na+/K+-ATPase pump, which imports 2K+ and exports 3Na+ across cell membranes using ATP hydrolysis, and the role of FXYD proteins in modulating the kinetic properties of the pump. It outlines a proposed study to express and purify human Na+/K+ pump isoforms and FXYD proteins, examine the effects of FXYD proteins on pump kinetics, and screen natural compounds for isoform-selective inhibitors/activators of the human pump. Materials, methods, and references are provided to support the proposed work.
Functional neuroimaging.pptx
Dr. Sunil Kumar Sharma's document discusses various functional neuroimaging modalities including fMRI, PET, and SPECT. It provides details on how each modality works, its advantages and disadvantages, and examples of its applications in mapping brain functions and depicting disease-related changes. Specific conditions discussed in relation to imaging findings include dementia, Parkinsonism, brain tumors, and epilepsy.
Duke neuro 1.10
The document summarizes research on ankyrin proteins and their role in localizing membrane proteins in specialized membrane domains. Ankyrins function as adaptors that bind to membrane proteins through unstructured motifs, targeting them to axon initial segments, nodes of Ranvier, photoreceptor outer segments, cardiomyocyte intercalated discs and costameres. Knockdown of ankyrins leads to loss of localization of binding partners and disruption of these membrane domains.
Xin Yu Education Course_ISMRM
The speaker declares no conflicts of interest regarding the presentation. The presentation will discuss functional MRI (fMRI) and manganese-enhanced MRI (MEMRI) studies of the mouse brain. It will cover issues with BOLD fMRI in mice such as spatial resolution requirements and anesthesia effects. It will also discuss applications of MEMRI for mapping neural activity and connectivity in olfactory and auditory systems of mouse models.
Biotech FVG 2014 - Alfonso Franciosi, Elettra-Sincrotrone Trieste
Il sistema scientifico del Friuli Venezia Giulia e la collaborazione tra Ricerca, Impresa e Governance Pubblica nell'ambito delle Biotecnologie
Stem cell Biobridge
1) The study investigated the hypothesis that neural stem cells from the subventricular zone (SVZ) and dentate gyrus (DG) are recruited to injured brain sites via extracellular factors to aid repair.
2) It found that transplantation of mesenchymal stem cells into the injured cortex led to increased extracellular metalloproteinases, decreased cell death, increased host cell proliferation and regeneration, and improved motor and neurological functions.
3) This suggests stem cells may act as "bio bridges" recruiting endogenous stem cells through metalloproteinase expression to reconnect neurogenic niches to injured sites and promote repair.
CSHL Poster draft 1
1) The study investigates the roles of off-track (otk) and off-track 2 (otk2) in Drosophila embryonic motor axon guidance.
2) It finds that both otk and otk2 mutants exhibit defects in motor neuron projections, including the MN12s projecting anteriorly instead of posteriorly.
3) The results suggest otk and otk2 may form a receptor complex and are required for axons' responses to the repellent Wnt4, with otk2 playing an uncharacterized role in motor axon guidance.
Ikrar Et Al (Cell Type Specific Regulation Of Cortical Excitability Through T...
This study investigated using the allatostatin receptor (AlstR) system to selectively inhibit neuronal activity in specific cell types in the cortex. The researchers expressed AlstRs in either excitatory or inhibitory neurons in mouse brain slices using Cre-driven expression. They found that applying the allatostatin peptide ligand strongly reduced spiking in AlstR-expressing neurons but not others. When targeting excitatory neurons, it constrained activity propagation, but enhancing it when targeting inhibitory neurons. Expressing AlstRs in excitatory neurons also effectively suppressed induced seizure activity. This work demonstrates the AlstR system can regulate cortical excitability in a cell-type specific manner.
Similar to Coarse grained molecular dynamic simulation of mammalian mechanosensitive ion channel TRPV2 (20)
Micro-Neuro-Sensor Recording of STN Neurons of the Human Brain
Micro-Neuro-Sensor Recording of STN Neurons of the Human Brain
Abdulla, ICBO2011, Composite annotation for heart development
Abdulla, ICBO2011, Composite annotation for heart development
Micro-Neuro-Sensor Recording of STN Neurons of the Human Brain
Micro-Neuro-Sensor Recording of STN Neurons of the Human Brain
Radiopharmacutical coordination chemistry approach
Radiopharmacutical coordination chemistry approach
Biotech FVG 2014 - Alfonso Franciosi, Elettra-Sincrotrone Trieste
Biotech FVG 2014 - Alfonso Franciosi, Elettra-Sincrotrone Trieste
Ikrar Et Al (Cell Type Specific Regulation Of Cortical Excitability Through T...
Ikrar Et Al (Cell Type Specific Regulation Of Cortical Excitability Through T...
Recently uploaded
Signatures of wave erosion in Titan’s coasts
The shorelines of Titan’s hydrocarbon seas trace flooded erosional landforms such as river valleys; however, it isunclear whether coastal erosion has subsequently altered these shorelines. Spacecraft observations and theo-retical models suggest that wind may cause waves to form on Titan’s seas, potentially driving coastal erosion,but the observational evidence of waves is indirect, and the processes affecting shoreline evolution on Titanremain unknown. No widely accepted framework exists for using shoreline morphology to quantitatively dis-cern coastal erosion mechanisms, even on Earth, where the dominant mechanisms are known. We combinelandscape evolution models with measurements of shoreline shape on Earth to characterize how differentcoastal erosion mechanisms affect shoreline morphology. Applying this framework to Titan, we find that theshorelines of Titan’s seas are most consistent with flooded landscapes that subsequently have been eroded bywaves, rather than a uniform erosional process or no coastal erosion, particularly if wave growth saturates atfetch lengths of tens of kilometers.
Discovery of An Apparent Red, High-Velocity Type Ia Supernova at 𝐳 = 2.9 wi...
We present the JWST discovery of SN 2023adsy, a transient object located in a host galaxy JADES-GS
+
53.13485
−
27.82088
with a host spectroscopic redshift of
2.903
±
0.007
. The transient was identified in deep James Webb Space Telescope (JWST)/NIRCam imaging from the JWST Advanced Deep Extragalactic Survey (JADES) program. Photometric and spectroscopic followup with NIRCam and NIRSpec, respectively, confirm the redshift and yield UV-NIR light-curve, NIR color, and spectroscopic information all consistent with a Type Ia classification. Despite its classification as a likely SN Ia, SN 2023adsy is both fairly red (
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) despite a host galaxy with low-extinction and has a high Ca II velocity (
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Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
Music and Medieval History
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
Magmatic iron-meteorite parent bodies are the earliest planetesimals in the Solar System,and they preserve information about conditions and planet-forming processes in thesolar nebula. In this study, we include comprehensive elemental compositions andfractional-crystallization modeling for iron meteorites from the cores of five differenti-ated asteroids from the inner Solar System. Together with previous results of metalliccores from the outer Solar System, we conclude that asteroidal cores from the outerSolar System have smaller sizes, elevated siderophile-element abundances, and simplercrystallization processes than those from the inner Solar System. These differences arerelated to the formation locations of the parent asteroids because the solar protoplane-tary disk varied in redox conditions, elemental distributions, and dynamics at differentheliocentric distances. Using highly siderophile-element data from iron meteorites, wereconstruct the distribution of calcium-aluminum-rich inclusions (CAIs) across theprotoplanetary disk within the first million years of Solar-System history. CAIs, the firstsolids to condense in the Solar System, formed close to the Sun. They were, however,concentrated within the outer disk and depleted within the inner disk. Future modelsof the structure and evolution of the protoplanetary disk should account for this dis-tribution pattern of CAIs.
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
Ozturkcan, S., Berndt, A., & Angelakis, A. (2024). Mending clothing to support sustainable fashion. Presented at the 31st Annual Conference by the Consortium for International Marketing Research (CIMaR), 10-13 Jun 2024, University of Gävle, Sweden.
Candidate young stellar objects in the S-cluster: Kinematic analysis of a sub...
Context. The observation of several L-band emission sources in the S cluster has led to a rich discussion of their nature. However, a definitive answer to the classification of the dusty objects requires an explanation for the detection of compact Doppler-shifted Brγ emission. The ionized hydrogen in combination with the observation of mid-infrared L-band continuum emission suggests that most of these sources are embedded in a dusty envelope. These embedded sources are part of the S-cluster, and their relationship to the S-stars is still under debate. To date, the question of the origin of these two populations has been vague, although all explanations favor migration processes for the individual cluster members. Aims. This work revisits the S-cluster and its dusty members orbiting the supermassive black hole SgrA* on bound Keplerian orbits from a kinematic perspective. The aim is to explore the Keplerian parameters for patterns that might imply a nonrandom distribution of the sample. Additionally, various analytical aspects are considered to address the nature of the dusty sources. Methods. Based on the photometric analysis, we estimated the individual H−K and K−L colors for the source sample and compared the results to known cluster members. The classification revealed a noticeable contrast between the S-stars and the dusty sources. To fit the flux-density distribution, we utilized the radiative transfer code HYPERION and implemented a young stellar object Class I model. We obtained the position angle from the Keplerian fit results; additionally, we analyzed the distribution of the inclinations and the longitudes of the ascending node. Results. The colors of the dusty sources suggest a stellar nature consistent with the spectral energy distribution in the near and midinfrared domains. Furthermore, the evaporation timescales of dusty and gaseous clumps in the vicinity of SgrA* are much shorter ( 2yr) than the epochs covered by the observations (≈15yr). In addition to the strong evidence for the stellar classification of the D-sources, we also find a clear disk-like pattern following the arrangements of S-stars proposed in the literature. Furthermore, we find a global intrinsic inclination for all dusty sources of 60 ± 20◦, implying a common formation process. Conclusions. The pattern of the dusty sources manifested in the distribution of the position angles, inclinations, and longitudes of the ascending node strongly suggests two different scenarios: the main-sequence stars and the dusty stellar S-cluster sources share a common formation history or migrated with a similar formation channel in the vicinity of SgrA*. Alternatively, the gravitational influence of SgrA* in combination with a massive perturber, such as a putative intermediate mass black hole in the IRS 13 cluster, forces the dusty objects and S-stars to follow a particular orbital arrangement. Key words. stars: black holes– stars: formation– Galaxy: center– galaxies: star formation
Male reproduction physiology by Suyash Garg .pptx
Physiology of Male reproduction.
Video mentioned at page no. 23 as summary for better understanding
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
Neutralizing antibodies, pivotal in immune defense, specifically bind and inhibit viral pathogens, thereby playing a crucial role in protecting against and mitigating infectious diseases. In this slide, we will introduce what antibodies and neutralizing antibodies are, the production and regulation of neutralizing antibodies, their mechanisms of action, classification and applications, as well as the challenges they face.
The cost of acquiring information by natural selection
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
It's based on the first part of this research paper:
The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
11.1 Role of physical biological in deterioration of grains.pdf
Storagedeteriorationisanyformoflossinquantityandqualityofbio-materials.
Themajorcausesofdeteriorationinstorage
•Physical
•Biological
•Mechanical
•Chemical
Storageonlypreservesquality.Itneverimprovesquality.
Itisadvisabletostartstoragewithqualityfoodproduct.Productwithinitialpoorqualityquicklydepreciates
Farming systems analysis: what have we learnt?.pptx
Presentation given at the official farewell of Prof Ken Gillet at Wageningen on 13 June 2024
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDS
The pathway(s) to seeding the massive black holes (MBHs) that exist at the heart of galaxies in the present and distant Universe remains an unsolved problem. Here we categorise, describe and quantitatively discuss the formation pathways of both light and heavy seeds. We emphasise that the most recent computational models suggest that rather than a bimodal-like mass spectrum between light and heavy seeds with light at one end and heavy at the other that instead a continuum exists. Light seeds being more ubiquitous and the heavier seeds becoming less and less abundant due the rarer environmental conditions required for their formation. We therefore examine the different mechanisms that give rise to different seed mass spectrums. We show how and why the mechanisms that produce the heaviest seeds are also among the rarest events in the Universe and are hence extremely unlikely to be the seeds for the vast majority of the MBH population. We quantify, within the limits of the current large uncertainties in the seeding processes, the expected number densities of the seed mass spectrum. We argue that light seeds must be at least 103 to 105 times more numerous than heavy seeds to explain the MBH population as a whole. Based on our current understanding of the seed population this makes heavy seeds (Mseed > 103 M⊙) a significantly more likely pathway given that heavy seeds have an abundance pattern than is close to and likely in excess of 10−4 compared to light seeds. Finally, we examine the current state-of-the-art in numerical calculations and recent observations and plot a path forward for near-future advances in both domains.
Recently uploaded (20)
Discovery of An Apparent Red, High-Velocity Type Ia Supernova at 𝐳 = 2.9 wi...
Discovery of An Apparent Red, High-Velocity Type Ia Supernova at 𝐳 = 2.9 wi...
Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
Introduction_Ch_01_Biotech Biotechnology course .pptx
Introduction_Ch_01_Biotech Biotechnology course .pptx
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
Juaristi, Jon. - El canon espanol. El legado de la cultura española a la civi...
Candidate young stellar objects in the S-cluster: Kinematic analysis of a sub...
Candidate young stellar objects in the S-cluster: Kinematic analysis of a sub...
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...
The cost of acquiring information by natural selection
The cost of acquiring information by natural selection
11.1 Role of physical biological in deterioration of grains.pdf
11.1 Role of physical biological in deterioration of grains.pdf
Microbiology of Central Nervous System INFECTIONS.pdf
Microbiology of Central Nervous System INFECTIONS.pdf
Farming systems analysis: what have we learnt?.pptx
Farming systems analysis: what have we learnt?.pptx
Nutaceuticsls herbal drug technology CVS, cancer.pptx
Nutaceuticsls herbal drug technology CVS, cancer.pptx
Coarse grained molecular dynamic simulation of mammalian mechanosensitive ion channel TRPV2
- 1. Coarse grained molecular dynamic simulation of mammalian mechanosensitive ion channel TRPV2 Ken Takahashi, Keiji Naruse Department of Cardiovascular Physiology Graduate School of Medicine, Dentistry and Pharmaceutical Sciences Okayama University ISMB 2017, Singapore, Dec 14
- 2. Molecular dynamics (MD) simulation MscL MscS )cos(1)(V )cos()cos( 2 1 )(V )( 2 1 )(V 4 )(V 4)(V dddihedral 2 aaangle 2 bbbond 0 el 612 Jones-Lennard ijklijkl ijkijk ijij ijrel ji ij ij ij ij ij ijij nK K ddKd r qq r rr r Potential energy functions:
- 3. Coarse-grained molecular dynamics (CGMD) Marrink, J Phys Chem B, 2007Acetylcholine receptor All atom Coarse-grained
- 4. CGMD mimics nature Monticelli, JCTC, 2008 Marrink, J Phys Chem B, 2004
- 5. TRPV2 channel TRPV2 senses: 1. Heat 2. Mechanical stimulus 3. Lipid Romero-Romero, Proteins, 2017 Organ Cells Function Related disease Brain Neuron, astrocyte Synaptic and glial transmission Depression DRG Neuron Axon outgrowth --- DRG Neuron Nociception Pain Heart Myocyte Myocardial conduction Cardiac hypertrophy Pancreas β-Cells Insulin secretion Diabetes Intestine Myenteric neuron Intestinal motility Irritable bowel syndrome Spleen Macrophage, mast cell, lymphocyte Immune response Immunodeficiency Urinary bladder Epithelial cell Sensing stretch Bladder cancer Prostate Epithelial cell LPC receptor Prostate cancer Bone Osteoclast Calcium oscillation Cancer Muscle Skeletal and cardiac muscle cells Sensing stretch Muscular dystrophy Blood vessel Smooth muscle, endothelial cell Blood pressure control Cardiomyopathy Shibasaki, J Physiol Sci, 2016
- 6. TRPV2 structure PDB ID: 5HI9
- 8. PDB ID: 5HI9 TRPV2 structure
- 9. Molecule Quantity TRPV2 1 POPC 936 POPS 927 Water (CG) 97,282 Sodium 955 Simulation model GROMACS Martini CG forcefield
- 10. Membrane stretch Bilayer tension: -71.5 dyn/cm Duration: 4,000 ns
- 11. Minimum pore radius 0 1 2 3 4 5 6 7 0 500 1000 1500 2000 2500 3000 3500 4000 minimumporeradius(Å) time (ns) 0 1 2 3 4 5 6 7 0 500 1000 1500 2000 minimumporeradius(Å) time (ns) MscS TRPV2
- 12. Helix tilt 0 10 20 30 40 50 60 70 0 500 1000 1500 2000 2500 3000 3500 4000 helixtiltangle(degree) time (ns) s1 s2 s3 s4 s5 s6 0 10 20 30 40 50 60 70 0 500 1000 1500 2000 helixtiltangle(degree) time (ns) TM1 TM2 TM3MscS TRPV2
- 13. Interaction energy POPC POPS S1 S2 S3 S4 S5 PORE S6 POPC POPS S1 S2 S3 S4 S5 PORE S6Total energies LJ-SR energies Coulomb-SR energies POPS POPC POPC POPS S1 S2 S3 S4 S5 PORE S6 POPC POPS S1 S2 S3 S4 S5 PORE S6
- 14. Conclusion 1. TRPV2 transmembrane helices were stable against lipid bilayer tension. 2. Pore radius of TRPV2 channel did not increase in response to lipid bilayer tension. 3. Interactions between helices/lipids may determine the mechanosensitive behavior of TRPV2 channel.
- 15. Acknowledgment Nagoya University Yuichiro Imaichi Tatsuro Yokoyama Okayama University Kensaku Toda Kazuya Saruwatari Yutaka Kuriyama Keiji Naruse This study was supported by Grant-in-Aid for Scientific Research on Innovative Areas, No. 15H05936.
Editor's Notes
- MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download for most Unix/Linux systems, Windows, and Mac. Modeller was developed by UCSF. PDB ID: 5HI9 homotetramer
- MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download for most Unix/Linux systems, Windows, and Mac. Modeller was developed by UCSF.
- POPC 936 POPS 927 Water 97282 Sodium 955
- 3.6–3.8-Å-radius sphere for pottasium