Coarse-grained simulation of mechanical properties of single microtubules with micrometer length
Microtubules are one of the most important components in the cytoskeleton and play a vital role in maintaining the shape and function of cells. Because single microtubules are some micrometers long, it is difficult to simulate such a large system using an all-atom model. In this work, we use the new...
| Main Authors: | , , , , |
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| Format: | Journal Article |
| Language: | English |
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2021
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| Online Access: | https://hdl.handle.net/10356/151757 |
| _version_ | 1824455755367972864 |
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| author | Zha, Jinyin Zhang, Yuwei Xia, Kelin Gräter, Frauke Xia, Fei |
| author2 | School of Physical and Mathematical Sciences |
| author_facet | School of Physical and Mathematical Sciences Zha, Jinyin Zhang, Yuwei Xia, Kelin Gräter, Frauke Xia, Fei |
| author_sort | Zha, Jinyin |
| collection | NTU |
| description | Microtubules are one of the most important components in the cytoskeleton and play a vital role in maintaining the shape and function of cells. Because single microtubules are some micrometers long, it is difficult to simulate such a large system using an all-atom model. In this work, we use the newly developed convolutional and K-means coarse-graining (CK-CG) method to establish an ultra-coarse-grained (UCG) model of a single microtubule, on the basis of the low electron microscopy density data of microtubules. We discuss the rationale of the micro-coarse-grained microtubule models of different resolutions and explore microtubule models up to 12-micron length. We use the devised microtubule model to quantify mechanical properties of microtubules of different lengths. Our model allows mesoscopic simulations of micrometer-level biomaterials and can be further used to study important biological processes related to microtubule function. |
| first_indexed | 2025-02-19T03:43:15Z |
| format | Journal Article |
| id | ntu-10356/151757 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2025-02-19T03:43:15Z |
| publishDate | 2021 |
| record_format | dspace |
| spelling | ntu-10356/1517572023-02-28T19:49:35Z Coarse-grained simulation of mechanical properties of single microtubules with micrometer length Zha, Jinyin Zhang, Yuwei Xia, Kelin Gräter, Frauke Xia, Fei School of Physical and Mathematical Sciences School of Biological Sciences Science::Biological sciences Microtubule Persistence Length Microtubules are one of the most important components in the cytoskeleton and play a vital role in maintaining the shape and function of cells. Because single microtubules are some micrometers long, it is difficult to simulate such a large system using an all-atom model. In this work, we use the newly developed convolutional and K-means coarse-graining (CK-CG) method to establish an ultra-coarse-grained (UCG) model of a single microtubule, on the basis of the low electron microscopy density data of microtubules. We discuss the rationale of the micro-coarse-grained microtubule models of different resolutions and explore microtubule models up to 12-micron length. We use the devised microtubule model to quantify mechanical properties of microtubules of different lengths. Our model allows mesoscopic simulations of micrometer-level biomaterials and can be further used to study important biological processes related to microtubule function. Ministry of Education (MOE) Nanyang Technological University Published version This work was supported by the National Natural Science Foundation of China (Grant Nos. 21773065 and 22073029), Nanyang Technological University Startup Grant M4081842, Singapore Ministry of Education Academic Research fund Tier 1 RG31/18 and RG109/19, Tier 2 MOE2018-T2-1-033. FG acknowledges support by the Klaus Tschira Foundation and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy–2082/1–390761711. 2021-07-15T09:32:23Z 2021-07-15T09:32:23Z 2021 Journal Article Zha, J., Zhang, Y., Xia, K., Gräter, F. & Xia, F. (2021). Coarse-grained simulation of mechanical properties of single microtubules with micrometer length. Frontiers in Molecular Biosciences, 7, 632122-. https://dx.doi.org/10.3389/fmolb.2020.632122 2296-889X https://hdl.handle.net/10356/151757 10.3389/fmolb.2020.632122 33659274 2-s2.0-85101907827 7 632122 en M4081842 RG31/18 RG109/19 MOE2018-T2-1-033 Frontiers in Molecular Biosciences © 2021 Zha, Zhang, Xia, Gräter and Xia. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. application/pdf |
| spellingShingle | Science::Biological sciences Microtubule Persistence Length Zha, Jinyin Zhang, Yuwei Xia, Kelin Gräter, Frauke Xia, Fei Coarse-grained simulation of mechanical properties of single microtubules with micrometer length |
| title | Coarse-grained simulation of mechanical properties of single microtubules with micrometer length |
| title_full | Coarse-grained simulation of mechanical properties of single microtubules with micrometer length |
| title_fullStr | Coarse-grained simulation of mechanical properties of single microtubules with micrometer length |
| title_full_unstemmed | Coarse-grained simulation of mechanical properties of single microtubules with micrometer length |
| title_short | Coarse-grained simulation of mechanical properties of single microtubules with micrometer length |
| title_sort | coarse grained simulation of mechanical properties of single microtubules with micrometer length |
| topic | Science::Biological sciences Microtubule Persistence Length |
| url | https://hdl.handle.net/10356/151757 |
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