Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations
High-speed atomic force microscopy (HS-AFM) is a powerful technique to image the structural dynamics of biomolecules. We can obtain atomic-resolution structural information from the measured AFM image by superimposing a structural model on the image. We previously developed a flexible fitting molecu...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-04-01
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| Series: | Frontiers in Molecular Biosciences |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2022.882989/full |
| _version_ | 1818150447705227264 |
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| author | Sotaro Fuchigami Shoji Takada |
| author_facet | Sotaro Fuchigami Shoji Takada |
| author_sort | Sotaro Fuchigami |
| collection | DOAJ |
| description | High-speed atomic force microscopy (HS-AFM) is a powerful technique to image the structural dynamics of biomolecules. We can obtain atomic-resolution structural information from the measured AFM image by superimposing a structural model on the image. We previously developed a flexible fitting molecular dynamics (MD) simulation method that allows for modest conformational changes when superimposed on an AFM image. In this study, for a molecular motor, myosin V (which changes its chemical state), we examined whether the conformationally distinct state in each HS-AFM image could be inferred via flexible fitting MD simulation. We first built models of myosin V bound to the actin filament in two conformational states, the “down-up” and “down-down” states. Then, for the previously obtained HS-AFM image of myosin bound to the actin filament, we performed flexible-fitting MD simulations using the two states. By comparing the fitting results, we inferred the conformational and chemical states from the AFM image. |
| first_indexed | 2024-12-11T13:23:05Z |
| format | Article |
| id | doaj.art-264a3a2a699047ccb41fe99d7b984c18 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-12-11T13:23:05Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-264a3a2a699047ccb41fe99d7b984c182022-12-22T01:05:41ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2022-04-01910.3389/fmolb.2022.882989882989Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular SimulationsSotaro FuchigamiShoji TakadaHigh-speed atomic force microscopy (HS-AFM) is a powerful technique to image the structural dynamics of biomolecules. We can obtain atomic-resolution structural information from the measured AFM image by superimposing a structural model on the image. We previously developed a flexible fitting molecular dynamics (MD) simulation method that allows for modest conformational changes when superimposed on an AFM image. In this study, for a molecular motor, myosin V (which changes its chemical state), we examined whether the conformationally distinct state in each HS-AFM image could be inferred via flexible fitting MD simulation. We first built models of myosin V bound to the actin filament in two conformational states, the “down-up” and “down-down” states. Then, for the previously obtained HS-AFM image of myosin bound to the actin filament, we performed flexible-fitting MD simulations using the two states. By comparing the fitting results, we inferred the conformational and chemical states from the AFM image.https://www.frontiersin.org/articles/10.3389/fmolb.2022.882989/fullatomic force microscopymyosin Vactin filamentflexible fittingcoarse-grained molecular simulationCafeMol |
| spellingShingle | Sotaro Fuchigami Shoji Takada Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations Frontiers in Molecular Biosciences atomic force microscopy myosin V actin filament flexible fitting coarse-grained molecular simulation CafeMol |
| title | Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations |
| title_full | Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations |
| title_fullStr | Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations |
| title_full_unstemmed | Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations |
| title_short | Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations |
| title_sort | inferring conformational state of myosin motor in an atomic force microscopy image via flexible fitting molecular simulations |
| topic | atomic force microscopy myosin V actin filament flexible fitting coarse-grained molecular simulation CafeMol |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2022.882989/full |
| work_keys_str_mv | AT sotarofuchigami inferringconformationalstateofmyosinmotorinanatomicforcemicroscopyimageviaflexiblefittingmolecularsimulations AT shojitakada inferringconformationalstateofmyosinmotorinanatomicforcemicroscopyimageviaflexiblefittingmolecularsimulations |