Elucidating molecular mechanisms of protoxin-2 state-specific binding to the human NaV1.7 channel
Data files
Dec 14, 2023 version files 10.14 GB
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Molecular_Dynamics.zip
9.97 GB
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README.md
36.73 KB
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Structural_Modeling.zip
170.03 MB
Abstract
Human voltage-gated sodium (hNaV) channels are responsible for initiating and propagating action potentials in excitable cells and mutations have been associated with numerous cardiac and neurological disorders. hNaV1.7 channels are expressed in peripheral neurons and are promising targets for pain therapy. The tarantula venom peptide protoxin-2 (PTx2) has high selectivity for hNaV1.7 and is a valuable scaffold for designing novel therapeutics to treat pain. Here, we used computational modeling to study the molecular mechanisms of the state-dependent binding of PTx2 to hNaV1.7 voltage-sensing domains (VSDs). Using Rosetta structural modeling methods, we constructed atomistic models of the hNaV1.7 VSD II and IV in the activated and deactivated states with docked PTx2. We then performed microsecond-long all-atom molecular dynamics (MD) simulations of the systems in hydrated lipid bilayers. Our simulations revealed that PTx2 binds most favorably to the deactivated VSD II and activated VSD IV. These state-specific interactions are mediated primarily by PTx2’s residues R22, K26, K27, K28, and W30 with VSD and the surrounding membrane lipids. Our work revealed important protein-protein and protein-lipid contacts that contribute to high-affinity state-dependent toxin interaction with the channel. The workflow presented will prove useful for designing novel peptides with improved selectivity and potency for more effective and safe treatment of pain.
https://doi.org/10.5061/dryad.jq2bvq8gj
Brief Description: The data were obtained from Rosetta structural modeling and molecular dynamics simulations focusing on the interaction of Protoxin-2 (PTx2) with the human Voltage-Sensing Domain (hNaV1.7) II and IV in both deactivated and activated states.
Author Information:
A. Principal Investigator Contact Information
Name: Igor Vorobyov
Institution: University of California, Davis
Address: Davis, CA USA
Email: ivorobyov@ucdavis.edu
B. Associate or Co-investigator Contact Information
Name: Vladimir Yarov-Yarovoy
Institution:University of California, Davis
Address: Davis, CA USA
Email: yarovoy@ucdavis.edu
3. Date of data collection (single date, range, approximate date): 2022-2023
Abbreviations and Terminology Definitions
PTx2: Protoxin-2
VSD: Voltage-Sensing Domain
RMSD: Root Mean Square Deviation
MM/PBSA: Molecular Mechanics Poisson-Boltzmann Surface Area, an approach to characterize protein-ligand binding energetics
AMBER: A suite of biomolecular simulation programs
Rosetta: A suite of molecular modeling and docking programs
Description of the data and file structure
Molecular Dynamics/
|- PTx2_DeactivatedVSD2/ (PTx2 – hNaV1.7 deactivated VSD II)
| |- 1/
| | |- deactVSD2_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
| |- 2/
| | |- deactVSD2_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
| |- 3/
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- deactVSD2_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
|- PTx2_DeactivatedVSD4/ (PTx2 – hNaV1.7 deactivated VSD IV)
| |- 1/
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- deactVSD4_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
| |- 2/
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- deactVSD4_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
| |- 3/
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- deactVSD4_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
|- PTx2_ActivatedVSD2/ (PTx2 – hNaV1.7 activated VSD II)
| |- 1/
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- actVSD2_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| |- 2/
| | |- actVSD2_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
| |- 3/
| | |- actVSD2_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
|- PTx2_ActivatedVSD4/ (PTx2 – hNaV1.7 activated VSD IV)
| |- 1/
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- actVSD4_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
| |- 2/
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- actVSD4_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
| |- 3/
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- actVSD4_1us_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- rmsd_BINDINGSITE.dat (RMSD for the PTx2-VSD binding region during simulation)
| | |- rmsd_TOX.dat (RMSD for the toxin during simulation)
| | |- rmsd_VSD.dat (RMSD for the VSD during simulation)
| | |- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- LIE_ligand_with_receptor_and_memb/ (AMBER computed linear interaction energy for each PTx2 residues with VSD and the surrounding lipids)
| | | |- [1-letter residue name][residue number].dat
| | |- LIE_receptor_with_ligand/ (AMBER computed linear interaction energy for each VSD residue with PTx2)
| | | |- [1-letter residue name][residue number].dat
| | |- rmsd_TOX_relative_to_VSD.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD)
| | |- rmsd_COMPLEX.dat (RMSD for the toxin-VSD complex when the entire trajectory is aligned to the VSD)
|- PTx2_ActivatedFullChannel/ (PTx2 – hNaV1.7 activated VSD II and IV systems - full channel simulation)
| |- 1/
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- act_300ns_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- rmsd_VSD4.dat (RMSD for the VSD IV during simulation)
| | |- rmsd_VSD2.dat (RMSD for the VSD II during simulation)
| | |- rmsd_BINDINGSITE_VSD2.dat (RMSD for the PTx2-VSD II binding region during simulation)
| | |- rmsd_BINDINGSITE_VSD4.dat (RMSD for the PTx2-VSD IV binding region during simulation)
| | |- rmsd_TOX_VSD2.dat (RMSD for the toxin binding to VSD II during simulation)
| | |- rmsd_TOX_VSD4.dat (RMSD for the toxin binding to VSD IV during simulation)
| | |- MMPBSA_VSD2
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- MMPBSA_VSD4/
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- rmsd_COMPLEX_VSD2.dat (RMSD for the toxin-VSD II complex when the entire trajectory is aligned to the VSD II)
| | |- rmsd_TOX_relative_to_VSD2.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD II)
| | |- rmsd_COMPLEX_VSD4.dat (RMSD for the toxin-VSD IV complex when the entire trajectory is aligned to the VSD IV)
| | |- rmsd_TOX_relative_to_VSD4.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD IV)
| |- 2/
| | |- rmsd_VSD4.dat (RMSD for the VSD IV during simulation)
| | |- rmsd_VSD2.dat (RMSD for the VSD II during simulation)
| | |- rmsd_BINDINGSITE_VSD2.dat (RMSD for the PTx2-VSD II binding region during simulation)
| | |- rmsd_BINDINGSITE_VSD4.dat (RMSD for the PTx2-VSD IV binding region during simulation)
| | |- rmsd_TOX_VSD2.dat (RMSD for the toxin binding to VSD II during simulation)
| | |- rmsd_TOX_VSD4.dat (RMSD for the toxin binding to VSD IV during simulation)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- act_300ns_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- MMPBSA_VSD2/
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- MMPBSA_VSD4/
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame
| | |- rmsd_COMPLEX_VSD2.dat (RMSD for the toxin-VSD II complex when the entire trajectory is aligned to the VSD II)
| | |- rmsd_TOX_relative_to_VSD2.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD II)
| | |- rmsd_COMPLEX_VSD4.dat (RMSD for the toxin-VSD IV complex when the entire trajectory is aligned to the VSD IV)
| | |- rmsd_TOX_relative_to_VSD4.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD IV)
| |- 3/
| | |- rmsd_VSD4.dat (RMSD for the VSD IV during simulation)
| | |- rmsd_VSD2.dat (RMSD for the VSD II during simulation)
| | |- rmsd_BINDINGSITE_VSD2.dat (RMSD for the PTx2-VSD II binding region during simulation)
| | |- rmsd_BINDINGSITE_VSD4.dat (RMSD for the PTx2-VSD IV binding region during simulation)
| | |- rmsd_TOX_VSD2.dat (RMSD for the toxin binding to VSD II during simulation)
| | |- rmsd_TOX_VSD4.dat (RMSD for the toxin binding to VSD IV during simulation)
| | |- step5_input.psf (protein structure file which define the molecular topology)
| | |- act_300ns_noequil.dcd (trajectory file containing the coordinates of the system)
| | |- step5_input.pdb (protein structure file containing the entire system used in molecular dynamics simulation)
| | |- step5_input.parm7 (parameter file for AMBER)
| | |- MMPBSA_VSD2/
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- MMPBSA_VSD4/
| | | |- en.average.txt (MM/PBSA computed enthalpy)
| | | |- en.std.txt (MM/PBSA enthalpy standard deviations)
| | | |- entro.entropy.txt (MM/PBSA computed entropy)
| | | |- entro.final.txt (MM/PBSA interaction energy values in vacuum for each computed frame)
| | | |- en.final.txt (MM/PBSA enthalpy values for each computed frame)
| | |- rmsd_TOX_relative_to_VSD2.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD II)
| | |- rmsd_COMPLEX_VSD2.dat (RMSD for the toxin-VSD II complex when the entire trajectory is aligned to the VSD II)
| | |- rmsd_COMPLEX_VSD4.dat (RMSD for the toxin-VSD IV complex when the entire trajectory is aligned to the VSD IV)
| | |- rmsd_TOX_relative_to_VSD4.dat (RMSD for the toxin when the entire trajectory is aligned to the VSD IV)
Analysis Scripts/
|- plot_concat_heatmaps.py (plot contact maps showcasing PTx2 – VSD residue or POPC lipid interactions averaged over three MD simulation replicas)
|- plot_per_residue_energy_AMBER.py (plot linear interaction energy computed using AMBER)
|- ttest_MMPBSA_barplots.py (perform t-test on energy results)
|- simulation_interaction_analysis.py (analyze interactions formed during the provided simulation trajectory)
|- aux_scripts/
| |- prot_center.tcl (center the trajectory to specific part of the protein)
| |- pbcwrap.tcl (wrap the trajectory file to ensure the protein complex to be in the center of the simulation box)
|- MMPBSA/ (energy calculations performed using the Molecular Mechanics Poisson-Boltzmann Surface Area approach)
| |- z-energies-process-awk-PBSA-entropy.sh (compute entropy values)
| |- mmpbsa.in (input file for MMPBSA with implicit membrane)
| |- mmpbsa-no.in (input file for MMPBSA without implicit membrane)
| |- z-energies-process-awk-PBSA.sh (compute binding energy values)
| |- run_MMPBSA.sh (bash command for executing MM/PBSA calculations)
|- energy.cpptraj (perform linear interaction energy analysis for each residues in the system)
|- plot_MMPBSA.py (plot time series of MM/PBSA energy values for PTx2 - isolated VSD systems)
|- plot_MMPBSA_fullchannel.py (plot time series of MM/PBSA energy values for PTx2 - VSD attached to full channel systems)
|- plot_RMSD.py (plot time series of RMSD values for PTx2 - isolated VSD systems)
|- plot_RMSD_fullchannel.py (plot time series of RMSD values for PTx2 - VSD attached to full channel systems)
Figures/ (figures used in the manuscript)
|- fig1.png
|- fig2.tif
|- fig3.tif
|- fig4.tif
|- fig5.tif
|- fig6.tif
|- fig7.tif
|- fig8.tif
|- fig9.tif
|- fig10.tif
|- fig11.tif
|- SI/ (figures used in the supplementary information)
| |- figS1.tif
| |- figS2.tif
| |- figS3.tif
| |- figS4.tif
| |- figS5.tif
| |- figS6.tif
| |- figS7.tif
| |- figS8.tif
| |- figS9.tif
| |- figS10.tif
| |- figS11.tif
| |- figS12.tif
| |- figS13.tif
Structural Modeling/
|- 1-Deactivated-VSDII-modeling/ (code and files used to model the VSDII from NaV1.7 in a deactivated conformation using Rosetta Comparative Modeling)
| |- sendJob-Hybridize.sh (bash code to execute rosettascripts comparative modeling protocol)
| |- rosetta_cm.xml (Rosettascripts protocol for comparative modeling)
| |- nav1.7-vsdii.fa (fasta sequence of the VSDII from NaV1.7)
| |- nav1.7-vsdii.span (file containing the information about the transmembrane spans of the VSDII)
| |- 6n4r-relaxed.pdb (experimental structure of chimera Nav channel with deactivated VSD used as template in the comparative modeling)
| |- FRAGMENT_FILES_MISSING
|- 2-EMdensity-refinement/ (code and files used to refine the experimental CryoEM structures 6J8J and 6NT4 used in subsequent steps using Rosetta EM density refinement method)
| |- simple-EM-relax.sh (bash code to execute rosettascripts EM density refinement protocol)
| |- B_relax_density.xml (Rosettascripts protocol for EM density refinement)
| |- 6j8j-original.pdb (Original 6J8J experimental structure download from the PDB database)
| |- 6nt4-original.pdb (Original 6NT4 experimental structure download from the PDB database)
| |- emd_9782-ProTx-II.map (EM map for 6J8J)
| |- emd_0501.map (EM map for 6NT4)
| |- final-models/
| | |- 6j8j-A-relaxed_A.pdb (EM density refined top model for 6J8J)
| | |- 6nt4-A-relaxed_A.pdb (EM density refined top model for 6NT4)
|- 3-Loop-Modeling/ (code and files used to model the missing S3S4 loop in the NaV1.7 activated VSDII from the 6J8J experimental structure)
| |- 1-build-loop/ (code and files used to build the missing residues in the S3S4 loop of VSDII from 6J8J)
| | |- 6j8j-A-relaxed_A.pdb (input pdb with missing loop)
| | |- 6j8j-A-relaxed_A.remodel (blueprint file that specifies the missing residues that should be modeled)
| | |- sendJobRemodel.sh (bash code to execute Rosetta remodel application)
| |- 2-optimize-loop/ (code and files used to relax/optimize the missing residues in the S3S4 loop of VSDII from 6J8J)
| | |- 6j8j-A-relaxed_A_lm_c00.pdb (input structure with S3S4 loop already modelled)
| | |- protocol-LoopModeler.xml (rosettascripts protocol for loop optimization and relaxation)
| | |- sendJob-LM.sh (bash code to execute Rosetta scripts)
|- 4-Toxin-VSD-complex-modeling/ (code and files used to model the interactions between PTx2 and the VSDs of NaV1.7 using RosettaDock)
| |- 1-prepacking/
| | |- 6j8j-A-relaxed_A_site4-lm-PrTx2-VSDII-[1-3]-TM_AF.pdb (input PDBs for prepacking for activated VSDII - Ptx2 modeling with the toxin at 3 different locations around the binding site)
| | |- 6j8j-A-relaxed_A_site4-lm-PrTx2-VSDII-TM_AF.span (file containing the information about the transmembrane spans of 6J8J to use the membrane docking framework)
| | |- 6j8j-tm-A-relaxed_A-PrTx2-VSDIV_[1-3]AF.pdb (input PDBs for prepacking for activated VSDIV - Ptx2 modeling with the toxin at 3 different locations around the binding site)
| | |- 6nt4-vsdiv_prtx2_cAF_TM_relaxed[1-3].pdb (input PDBs for prepacking for deactivated VSDIV - Ptx2 modeling with the toxin at 3 different locations around the binding site)
| | |- 6nt4-vsdiv_prtx2_cAF_TM_relaxed.span (file containing the information about the transmembrane spans of 6NT4 to use the membrane docking framework)
| | |- protx2-dvsdii-TM-[1-3]AE.pdb (input PDBs for prepacking for deactivated VSDII - Ptx2 modeling with the toxin at 3 different locations around the binding site)
| | |- sendJob-docking-prepack-membrane.sh (bash code to execute Rosetta docking prepacking protocol in the membrane framework: franklin2019n energy function)
| |- 2-docking/
| | |- 6j8j-A-relaxed_A_site4-lm-PrTx2-VSDII-[1-3]-TM_AF_prepack.pdb (input PDBs for RosettaDock for activated VSDII - Ptx2 modeling with the toxin at 3 different locations around the binding site after prepacking)
| | |- 6j8j-A-relaxed_A_site4-lm-PrTx2-VSDII-TM_AF.span (file containing the information about the transmembrane spans of 6J8J to use the membrane docking framework)
| | |- 6j8j-tm-A-relaxed_A-PrTx2-VSDIV_[1-3]AF_prepack.pdb (input PDBs for RosettaDock for activated VSDIV - Ptx2 modeling with the toxin at 3 different locations around the binding site after prepacking)
| | |- 6nt4-vsdiv_prtx2_cAF_TM_relaxed[1-3]_prepack.pdb (input PDBs for RosettaDock for deactivated VSDIV - Ptx2 modeling with the toxin at 3 different locations around the binding site after prepacking)
| | |- 6nt4-vsdiv_prtx2_cAF_TM_relaxed.span (file containing the information about the transmembrane spans of 6NT4 to use the membrane docking framework)
| | |- protx2-dvsdii-TM-[1-3]_AE_prepack.pdb (input PDBs for RosettaDock for deactivated VSDII - Ptx2 modeling with the toxin at 3 different locations around the binding site after prepacking)
| | |- sendJobF2019Docking.sh (bash code to execute RosettaDock in the membrane framework: franklin2019n energy function)
| |- 3-final-EMdf/ (code and files to relax/optimize the Ptx2 top docked models into the EM density, only for activated VSDII and VSDIV)
| | |- 6j8j-A-relaxed_A_site4-lm-PrTx2-VSDII-1-TM_AF_prepack_local_dock.pdb (top model after docking ptx2 to activated VSDII)
| | |- 6j8j-A-relaxed_A_site4-lm-PrTx2-VSDII-TM_AF.span (file containing the information about the transmembrane spans of 6J8J to use the membrane energy function)
| | |- 6j8j-tm-A-relaxed_A-PrTx2-VSDIV_1_AF_prepack_local_dock.pdb (top model after docking ptx2 to activated VSDIV)
| | |- B_relax_density-toxin-only.xml (Rosettascripts protocol for EM density refinement, adapted so that only the toxin gets fitted and the interface optimized)
| | |- emd_9782-ProTx-II.map (EM map for 6J8J)
| | |- sendJob-PrTx2-EMdf.sh (bash code to execute rosettascripts protocol)
| |- final-models/ (final models that were used as input for MD simulations)
| | |- ProTxII_Nav17_VSDII_deactivated.pdb
| | |- ProTxII_Nav17_VSDIV_deactivated.pdb
| | |- ProTxII_Nav17-VSDIV-activated.pdb
| | |- ProTxII-Nav17-VSDII-activated.pdb
| | |- hNav1.7-PrTx2-VSDII-VSDIV-docked.pdb (full NaV1.7 channel with PTx2 bound to both activated VSDII and VSDIV, built by combining ProTxII-Nav17-VSDII-activated.pdb file with ProTxII_Nav17-VSDIV-activated.pdb and running a simple docking refinement)
Sharing/Access information
Experimental PDB files and EM maps were downloaded from the Protein Data Bank
PDB 6J8J: https://www.rcsb.org/structure/6J8J
PDB 6NT4: https://www.rcsb.org/structure/6NT4
Code/Software
The Rosetta software suite can be downloaded from the following link: https://www.rosettacommons.org/software/license-and-download
The AMBER software suite can be downloaded from the following link: https://ambermd.org/GetAmber.php
Relationship between files, if important: None
Additional related data collected that was not included in the current data package: None
Are there multiple versions of the dataset? No
#########################################################################
DATA-SPECIFIC INFORMATION FOR: en.final.txt, entro.final.txt
Number of variables: 1
Variable List: computed enthalpy (en.final.txt) or interaction energy in a vacuum (entro.final.txt) for each frame (1 row = 1 frame)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: rmsd_BINDINGSITE.dat, rmsd_COMPLEX.dat, rmsd_TOX.dat, rmsd_TOX_relative_to_VSD.dat, rmsd_VSD.dat
Number of variables: 2
Variable List: Simulation Frame Number, Root mean square deviation in Angstroms (1 row = 1 frame)
#########################################################################
DATA-SPECIFIC INFORMATION FOR: .dat files in "LIE_ligand_with_receptor_and_member" and "LIE_receptor_with_ligand directory"
Number of variables: 3
Variable List: Simulation Frame Number, Electrostatics Energy (kcal/mol), Van de Waals Energy (kcal/mol) (1 row = 1 frame)
Structures were generated using the Rosetta structural modeling software suite(Rohl et al., 2004) based on experimental cryo-EM structures. All-atom molecular dynamics (MD) simulations were performed using the Amber20 software package (Salomon-Ferrer et al., 2013) and the standard all-atom Chemistry at Harvard Macromolecular Mechanics (CHARMM) force fields for proteins (CHARMM36m), lipids (C36), and ions(Huang and MacKerell Jr, 2013; Klauda et al., 2010; Best et al., 2012) as well as the TIP3P water model. Afterward, protein-ligand interactions were characterized in each set of simulations using in-house Python scripts incorporating the protein–ligand interaction profiler (PLIP) Python module.(Salentin et al., 2015) Binding free energy calculations were performed using the Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) approach(Srinivasan et al., 1998; Kollman et al., 2000; Wang et al., 2016a) with all-atom MD simulation trajectories by MMPBSA.py program in Amber Tools(Miller et al., 2012). To calculate the energy contribution of each residue to the binding process for each system, we computed the electrostatic and van der Waals interaction energies of PTx2 with POPC lipids and VSD II/IV using AMBER linear interaction energy analysis.(Salomon-Ferrer et al., 2013; Roe and Cheatham, 2013)