Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach
Abstract
:1. Introduction
2. Materials and Methods
2.1. Systems Studied
2.2. UNRES Model of Polypeptide Chains
2.3. Coarse-Grained Molecular Dynamics with UNRES
2.4. Simulation Procedure
2.4.1. The 4YY2 System
2.4.2. The 6SD5 System
2.4.3. The 2BL2 System
2.5. Hardware Platform and Timing
2.6. Determining the Rotation Angle
3. Results
3.1. The 4YY2 System
3.2. The 6SD5 System
3.3. The 2BL2 System
4. Discussion and Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ATP | Adenosine-5’-Tri-Phosphate |
CHARMM-GUI | Chemistry at HARvard Macromolecular Mechanics Graphical User Interface |
GDT_TS | Global Distance Test Total Score |
MD | Molecular Dynamics |
MREMD | Multiplexed Replica Exchange Molecular Dynamics |
NVE | constant Number of particles, constant Volume, constant Energy |
NVT | constant Number of particles, constant Volume, constant Temperature |
PDB | Protein Data Bank |
RMSD | Root Mean Square Deviation |
UNRES | UNited RESidue model of proteins |
WHAM | Weighted Histogram Analysis Method |
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Liwo, A.; Pyrka, M.; Czaplewski, C.; Peng, X.; Niemi, A.J. Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach. Biomolecules 2023, 13, 941. https://doi.org/10.3390/biom13060941
Liwo A, Pyrka M, Czaplewski C, Peng X, Niemi AJ. Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach. Biomolecules. 2023; 13(6):941. https://doi.org/10.3390/biom13060941
Chicago/Turabian StyleLiwo, Adam, Maciej Pyrka, Cezary Czaplewski, Xubiao Peng, and Antti J. Niemi. 2023. "Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach" Biomolecules 13, no. 6: 941. https://doi.org/10.3390/biom13060941
APA StyleLiwo, A., Pyrka, M., Czaplewski, C., Peng, X., & Niemi, A. J. (2023). Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach. Biomolecules, 13(6), 941. https://doi.org/10.3390/biom13060941