Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach
Molecular motors are essential for the movement and transportation of macromolecules in living organisms. Among them, rotatory motors are particularly efficient. In this study, we investigated the long-term dynamics of the designed left-handed alpha/alpha toroid (PDB: 4YY2), the RBM2 flagellum prote...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-06-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/13/6/941 |
| _version_ | 1797595833371197440 |
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| author | Adam Liwo Maciej Pyrka Cezary Czaplewski Xubiao Peng Antti J. Niemi |
| author_facet | Adam Liwo Maciej Pyrka Cezary Czaplewski Xubiao Peng Antti J. Niemi |
| author_sort | Adam Liwo |
| collection | DOAJ |
| description | Molecular motors are essential for the movement and transportation of macromolecules in living organisms. Among them, rotatory motors are particularly efficient. In this study, we investigated the long-term dynamics of the designed left-handed alpha/alpha toroid (PDB: 4YY2), the RBM2 flagellum protein ring from <i>Salmonella</i> (PDB: 6SD5), and the V-type Na<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mo>+</mo></msup></semantics></math></inline-formula>-ATPase rotor in <i>Enterococcus hirae</i> (PDB: 2BL2) using microcanonical and canonical molecular dynamics simulations with the coarse-grained UNRES force field, including a lipid-membrane model, on a millisecond laboratory time scale. Our results demonstrate that rotational motion can occur with zero total angular momentum in the microcanonical regime and that thermal motions can be converted into net rotation in the canonical regime, as previously observed in simulations of smaller cyclic molecules. For 6SD5 and 2BL2, net rotation (with a ratcheting pattern) occurring only about the pivot of the respective system was observed in canonical simulations. The extent and direction of the rotation depended on the initial conditions. This result suggests that rotatory molecular motors can convert thermal oscillations into net rotational motion. The energy from ATP hydrolysis is required probably to set the direction and extent of rotation. Our findings highlight the importance of molecular-motor structures in facilitating movement and transportation within living organisms. |
| first_indexed | 2024-03-11T02:42:06Z |
| format | Article |
| id | doaj.art-bc5e920880a34a19b1ae31af38e0ccbc |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-11T02:42:06Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-bc5e920880a34a19b1ae31af38e0ccbc2023-11-18T09:30:58ZengMDPI AGBiomolecules2218-273X2023-06-0113694110.3390/biom13060941Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained ApproachAdam Liwo0Maciej Pyrka1Cezary Czaplewski2Xubiao Peng3Antti J. Niemi4Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, PolandFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, PolandFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, PolandCenter for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, ChinaNordita, Stockholm University and Uppsala University, Roslagstullsbacken 23, SE-106 91 Stockholm, SwedenMolecular motors are essential for the movement and transportation of macromolecules in living organisms. Among them, rotatory motors are particularly efficient. In this study, we investigated the long-term dynamics of the designed left-handed alpha/alpha toroid (PDB: 4YY2), the RBM2 flagellum protein ring from <i>Salmonella</i> (PDB: 6SD5), and the V-type Na<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mo>+</mo></msup></semantics></math></inline-formula>-ATPase rotor in <i>Enterococcus hirae</i> (PDB: 2BL2) using microcanonical and canonical molecular dynamics simulations with the coarse-grained UNRES force field, including a lipid-membrane model, on a millisecond laboratory time scale. Our results demonstrate that rotational motion can occur with zero total angular momentum in the microcanonical regime and that thermal motions can be converted into net rotation in the canonical regime, as previously observed in simulations of smaller cyclic molecules. For 6SD5 and 2BL2, net rotation (with a ratcheting pattern) occurring only about the pivot of the respective system was observed in canonical simulations. The extent and direction of the rotation depended on the initial conditions. This result suggests that rotatory molecular motors can convert thermal oscillations into net rotational motion. The energy from ATP hydrolysis is required probably to set the direction and extent of rotation. Our findings highlight the importance of molecular-motor structures in facilitating movement and transportation within living organisms.https://www.mdpi.com/2218-273X/13/6/941molecular motorsfalling cat motionmolecular dynamicscoarse grainingUNRES force field |
| spellingShingle | Adam Liwo Maciej Pyrka Cezary Czaplewski Xubiao Peng Antti J. Niemi Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach Biomolecules molecular motors falling cat motion molecular dynamics coarse graining UNRES force field |
| title | Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach |
| title_full | Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach |
| title_fullStr | Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach |
| title_full_unstemmed | Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach |
| title_short | Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach |
| title_sort | long time dynamics of selected molecular motor components using a physics based coarse grained approach |
| topic | molecular motors falling cat motion molecular dynamics coarse graining UNRES force field |
| url | https://www.mdpi.com/2218-273X/13/6/941 |
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