Elucidating molecular mechanisms of protoxin-2 state-specific binding to the human NaV1.7 channel

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 ..., 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(Mi..., , # 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 (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:

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-...