Significant Differences in RNA Structure Destabilization by HIV-1 Gag∆p6 and NCp7 Proteins
Abstract
:1. Introduction
2. Materials and Methods
2.1. Hairpin Construct Synthesis
2.2. Gag Polyprotein Preparation
2.3. Single Molecule Optical Tweezers
2.4. Hairpin Energies from Mfold
3. Results
3.1. TAR Hairpin Length Is Unaffected by Gag∆p6
3.2. Gag∆p6 Reduces the Energy of Unfolding
3.3. Gag∆p6 Lowers but Does Not Shift the Energy Barrier
3.4. Landscape Models Locate Gag∆p6 Binding
4. Discussion
4.1. Both NCp7 and Gag∆p6 Chaperone Nucleic Acids
4.2. While NCp7 Strongly Facilitates TAR Opening, Gag∆p6 Does Not
Author Contributions
Funding
Conflicts of Interest
Appendix A. Polymer Models of Elasticity
Appendix B. Equilibrium Energies from Non-Equilibrium Measurements
Appendix C. Kinetic Models and the Transition State
Appendix D. Modeling the Energy Landscape
References
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Experiment | Δxop | ΔGop | F½ | |||
---|---|---|---|---|---|---|
(bases) | (kBT) | (pN) | (nm) | (kBT) | (s−1) | |
TAR (OT) | 48.2 ± 0.6 | 42.1 ± 1.5 | 10.6 ± 0.2 | 10.9 ± 0.7 | 28.0 ± 1.4 | (0.7 ± 0.4) × 10−8 |
TAR (mfold) | 48 ± 1 | 41.5 ± 1.5 | 10.1 ± 0.1 | 11.3 ± 0.9 | 30.7 ± 2.0 | - |
TAR + Gag∆p6 (OT) | 47.5 ± 0.7 | 28.9 ± 1.5 | 7.7 ± 0.2 | 9.2 ± 0.7 | 18.1 ± 0.9 | (10 ± 6) × 10−8 |
TAR + Gag∆p6 (mfold) | 48 ± 1 | 26.0 ± 1.5 | 8.0 ± 0.2 | 8.6 ± 1.0 | 20.1 ± 1.5 | |
TAR + NCp7 (OT) | 48.4 ± 0.5 | 28.3 ± 0.9 | 7.7 ± 0.2 | 4.8 ± 0.6 | 14.3 ± 1.3 | (1.2 ± 0.8) × 10−4 |
TAR + NCp7 (mfold) | 48 ± 1 | 25.6 ± 1.5 | 7.9 ± 0.1 | 4.7 ± 0.9 | 14.8 ± 1.2 | - |
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McCauley, M.J.; Rouzina, I.; Li, J.; Núñez, M.E.; Williams, M.C. Significant Differences in RNA Structure Destabilization by HIV-1 Gag∆p6 and NCp7 Proteins. Viruses 2020, 12, 484. https://doi.org/10.3390/v12050484
McCauley MJ, Rouzina I, Li J, Núñez ME, Williams MC. Significant Differences in RNA Structure Destabilization by HIV-1 Gag∆p6 and NCp7 Proteins. Viruses. 2020; 12(5):484. https://doi.org/10.3390/v12050484
Chicago/Turabian StyleMcCauley, Micah J., Ioulia Rouzina, Jasmine Li, Megan E. Núñez, and Mark C. Williams. 2020. "Significant Differences in RNA Structure Destabilization by HIV-1 Gag∆p6 and NCp7 Proteins" Viruses 12, no. 5: 484. https://doi.org/10.3390/v12050484