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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
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:
Coarse-grained molecular dynamics (CGMD)
Marrink, J Phys Chem B, 2007Acetylcholine receptor
All atom
Coarse-grained
CGMD mimics nature
Monticelli, JCTC, 2008
Marrink, J Phys Chem B, 2004
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
TRPV2 structure
PDB ID: 5HI9
TRPV2 structure
S1
S2
S3
S4
S5S6
pore helix
PDB ID: 5HI9
TRPV2 structure
Molecule Quantity
TRPV2 1
POPC 936
POPS 927
Water (CG) 97,282
Sodium 955
Simulation model
GROMACS
Martini CG forcefield
Membrane stretch
Bilayer tension: -71.5 dyn/cm
Duration: 4,000 ns
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
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
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
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.
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.

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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
  • 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

  1. 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
  2. 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.
  3. POPC 936 POPS 927 Water 97282 Sodium 955
  4. 3.6–3.8-Å-radius sphere for pottasium