DOI: 10.5061/dryad.jq2bvq8gj
title: Elucidating molecular mechanisms of protoxin-2 state-specific binding to the human NaV1.7 channel

description: 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.
description: 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)
description: # Elucidating molecular mechanisms of protoxin-2 state-specific binding to
 the human NaV1.7 channel 
 **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
 (hNa<sub>V</sub>1.7) 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:
 B. Associate or Co-investigator Contact
 Information Name: Vladimir Yarov-Yarovoy Institution:University of
 California, Davis Address: Davis, CA USA Email:
 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:
 PDB 6NT4:
 **Code/Software** The Rosetta
 software suite can be downloaded from the following link:
 The
 AMBER software suite can be downloaded from the following link:
 **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)