Molecular Dynamics Reveal Key Steps in BAR-Related Membrane Remodeling
Abstract
:1. Introduction
2. Materials and Methods
2.1. Systems of MD Simulation
2.2. Time-Resolved Force Distribution Analysis
2.3. Interaction Area, Secondary Structure Analysis, and Helix Kink
3. Results
3.1. Structure Change in the BAR Dimer and Interaction of the BAR Dimer–Membrane
3.2. Brief Analysis of the Bending Mechanism of Membrane Curvature
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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System | Number | Time/ns | Size |
---|---|---|---|
4ATM + membrane | 20 | 300 | 10.0 × 34.5 × 20.9 nm3 |
Membrane only | 1 | 300 | 7.6 × 23.0 × 15.2 nm3 |
Lipid Molecule | Proportion |
---|---|
Cholesterol | ~32% |
DOPC | ~35% |
DOPE | ~17% |
DOPS | ~2% |
PI (4,5) P2 | ~3% |
Brain SM | ~11% |
Ranking | Helix 1–Helix 2 | Helix 1–Helix 3 | Helix 2–Helix 3 |
---|---|---|---|
1 | LYS 132 | GLU 52 | ARG 134 |
2 | GLU 50 | ARG 198 | ARG 138 |
3 | GLU 153 | GLN 49 | TYR 145 |
4 | TRP 106 | TRP 195 | PHE 180 |
5 | PHE 46 | TYR 202 | PHE 173 |
6 | GLN 71 | TYP 63 | LEU 212 |
7 | ARG 138 | GLU 213 | PHE 183 |
8 | ARG 149 | TYP 42 | GLU 190 |
9 | HIS 82 | LEU 191 | PHE 216 |
10 | LEU 64 | GLN 188 | LEU 223 |
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Song, S.; Li, T.; Stevens, A.O.; Shorty, T.; He, Y. Molecular Dynamics Reveal Key Steps in BAR-Related Membrane Remodeling. Pathogens 2024, 13, 902. https://doi.org/10.3390/pathogens13100902
Song S, Li T, Stevens AO, Shorty T, He Y. Molecular Dynamics Reveal Key Steps in BAR-Related Membrane Remodeling. Pathogens. 2024; 13(10):902. https://doi.org/10.3390/pathogens13100902
Chicago/Turabian StyleSong, Shenghan, Tongtong Li, Amy O. Stevens, Temair Shorty, and Yi He. 2024. "Molecular Dynamics Reveal Key Steps in BAR-Related Membrane Remodeling" Pathogens 13, no. 10: 902. https://doi.org/10.3390/pathogens13100902
APA StyleSong, S., Li, T., Stevens, A. O., Shorty, T., & He, Y. (2024). Molecular Dynamics Reveal Key Steps in BAR-Related Membrane Remodeling. Pathogens, 13(10), 902. https://doi.org/10.3390/pathogens13100902