Potency-Enhancing Mutations of Gating Modifier Toxins for the Voltage-Gated Sodium Channel NaV1.7 Can Be Predicted Using Accurate Free-Energy Calculations
Abstract
:1. Introduction
2. Results
2.1. Retrospective Performance of FEP on Mutagenesis Data
2.1.1. Overall Performance
2.1.2. Performance by GMT and Physicochemical Category
2.1.3. Performance for Mutations with Proximity to the Membrane
2.2. Stability of GMT:VSD Complex during FEP Simulations
2.3. Improvement of ProTx-II Potency for NaV1.7 in Silico
3. Discussion
3.1. FEP Accurately Predicts the Relative Change in Potency of GMT Mutants for NaV1.7 Using Cryo-EM Structures
3.2. Including an Explicit Membrane in FEP Simulations Improves the Model
3.3. A Workflow Consisting of WaterMap, MM-GB/SA, and FEP Can Rapidly Identify NSAAs Predicted to Increase Potency of ProTx-II for NaV1.7 in Silico
4. Materials and Methods
4.1. Protein Structure Preparation
4.2. Selection and Categorization of Mutants
4.3. Construction of NSAA Library of Tryptophan Analogues
4.4. WaterMap Calculations
4.5. MM-GB/SA Calculations and Analysis
4.6. FEP Calculations for GMT Mutations
4.7. Calculation of iRMSD for GMT Pose Stability Analysis
4.8. Statistics
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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FEP | MM-GB/SA | |||||
---|---|---|---|---|---|---|
Category | N | Min and Max ΔΔG in kcals/mol (Range) | RMSE | R2 | RMSE | R2 |
Overall | 47 | −1.4–7 (8.4) | 1.00 ± 0.1 | 0.66 | 3.89 ± 0.82 | 0.56 |
By Toxin | ||||||
ProTx-II | 10 | −1.4–7 (8.4) | 1.70 ± 0.16 | 0.78 | 7.57 ± 1.48 | 0.68 |
HwTx-IV | 37 | −1.09–1.88 (2.97) | 0.69 ± 0.07 | 0.19 | 1.95 ± 0.64 | 0.24 |
By Property | ||||||
Charge change mutations | 24 | −1.09–7 (8.09) | 0.96 ± 0.15 | 0.81 | 3.75 ± 1.3 | 0.79 |
Neutral mutations | 23 | −1.4–1.88 (3.28) | 1.02 ± 0.14 | 0.02 | 4.04 ± 1.3 | 0.23 |
By Position | ||||||
Mutations facing into the membrane | 19 | −1.09–1.88 (2.97) | 0.71 ± 0.10 | 0.31 | 1.65 ± 0.32 | 0.25 |
Mutations facing into the channel | 16 | −1.4–7 (8.4) | 1.41 ± 0.15 | 0.70 | 6.4 ± 1.3 | 0.61 |
Mutations facing into the solvent | 12 | −0.96–0.68 (1.64) | 0.53 ± 0.11 | 0.02 | 0.70 ± 0.21 | 0.03 |
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Katz, D.; Sindhikara, D.; DiMattia, M.; Leffler, A.E. Potency-Enhancing Mutations of Gating Modifier Toxins for the Voltage-Gated Sodium Channel NaV1.7 Can Be Predicted Using Accurate Free-Energy Calculations. Toxins 2021, 13, 193. https://doi.org/10.3390/toxins13030193
Katz D, Sindhikara D, DiMattia M, Leffler AE. Potency-Enhancing Mutations of Gating Modifier Toxins for the Voltage-Gated Sodium Channel NaV1.7 Can Be Predicted Using Accurate Free-Energy Calculations. Toxins. 2021; 13(3):193. https://doi.org/10.3390/toxins13030193
Chicago/Turabian StyleKatz, Dana, Dan Sindhikara, Michael DiMattia, and Abba E. Leffler. 2021. "Potency-Enhancing Mutations of Gating Modifier Toxins for the Voltage-Gated Sodium Channel NaV1.7 Can Be Predicted Using Accurate Free-Energy Calculations" Toxins 13, no. 3: 193. https://doi.org/10.3390/toxins13030193
APA StyleKatz, D., Sindhikara, D., DiMattia, M., & Leffler, A. E. (2021). Potency-Enhancing Mutations of Gating Modifier Toxins for the Voltage-Gated Sodium Channel NaV1.7 Can Be Predicted Using Accurate Free-Energy Calculations. Toxins, 13(3), 193. https://doi.org/10.3390/toxins13030193