Membrane models for molecular simulations of peripheral membrane proteins
Peripheral membrane proteins (PMPs) bind temporarily to the surface of biological membranes. They also exist in a soluble form and their tertiary structure is often known. Yet, their membrane-bound form and their interfacial-binding site with membrane lipids remain difficult to observe directly. The...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2021-01-01
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| Series: | Advances in Physics: X |
| Online Access: | http://dx.doi.org/10.1080/23746149.2021.1932589 |
| _version_ | 1818585165341917184 |
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| author | Mahmoud Moqadam Thibault Tubiana Emmanuel E. Moutoussamy Nathalie Reuter |
| author_facet | Mahmoud Moqadam Thibault Tubiana Emmanuel E. Moutoussamy Nathalie Reuter |
| author_sort | Mahmoud Moqadam |
| collection | DOAJ |
| description | Peripheral membrane proteins (PMPs) bind temporarily to the surface of biological membranes. They also exist in a soluble form and their tertiary structure is often known. Yet, their membrane-bound form and their interfacial-binding site with membrane lipids remain difficult to observe directly. Their binding and unbinding mechanism, the conformational changes of the PMPs and their influence on the membrane structure are notoriously challenging to study experimentally. Molecular dynamics simulations are particularly useful to fill some knowledge-gaps and provide hypothesis that can be experimentally challenged to further our understanding of PMP-membrane recognition. Because of the time-scales of PMP-membrane binding events and the computational costs associated with molecular dynamics simulations, membrane models at different levels of resolution are used and often combined in multiscale simulation strategies. We here review membrane models belonging to three classes: atomistic, coarse-grained and implicit. Differences between models are rooted in the underlying theories and the reference data they are parameterized against. The choice of membrane model should therefore not only be guided by its computational efficiency. The range of applications of each model is discussed and illustrated using examples from the literature. |
| first_indexed | 2024-12-16T08:32:44Z |
| format | Article |
| id | doaj.art-edf82aaaaf7f4af0a644dae6e2cd38a9 |
| institution | Directory Open Access Journal |
| issn | 2374-6149 |
| language | English |
| last_indexed | 2024-12-16T08:32:44Z |
| publishDate | 2021-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Advances in Physics: X |
| spelling | doaj.art-edf82aaaaf7f4af0a644dae6e2cd38a92022-12-21T22:37:50ZengTaylor & Francis GroupAdvances in Physics: X2374-61492021-01-016110.1080/23746149.2021.19325891932589Membrane models for molecular simulations of peripheral membrane proteinsMahmoud Moqadam0Thibault Tubiana1Emmanuel E. Moutoussamy2Nathalie Reuter3University of BergenUniversity of BergenUniversity of BergenUniversity of BergenPeripheral membrane proteins (PMPs) bind temporarily to the surface of biological membranes. They also exist in a soluble form and their tertiary structure is often known. Yet, their membrane-bound form and their interfacial-binding site with membrane lipids remain difficult to observe directly. Their binding and unbinding mechanism, the conformational changes of the PMPs and their influence on the membrane structure are notoriously challenging to study experimentally. Molecular dynamics simulations are particularly useful to fill some knowledge-gaps and provide hypothesis that can be experimentally challenged to further our understanding of PMP-membrane recognition. Because of the time-scales of PMP-membrane binding events and the computational costs associated with molecular dynamics simulations, membrane models at different levels of resolution are used and often combined in multiscale simulation strategies. We here review membrane models belonging to three classes: atomistic, coarse-grained and implicit. Differences between models are rooted in the underlying theories and the reference data they are parameterized against. The choice of membrane model should therefore not only be guided by its computational efficiency. The range of applications of each model is discussed and illustrated using examples from the literature.http://dx.doi.org/10.1080/23746149.2021.1932589 |
| spellingShingle | Mahmoud Moqadam Thibault Tubiana Emmanuel E. Moutoussamy Nathalie Reuter Membrane models for molecular simulations of peripheral membrane proteins Advances in Physics: X |
| title | Membrane models for molecular simulations of peripheral membrane proteins |
| title_full | Membrane models for molecular simulations of peripheral membrane proteins |
| title_fullStr | Membrane models for molecular simulations of peripheral membrane proteins |
| title_full_unstemmed | Membrane models for molecular simulations of peripheral membrane proteins |
| title_short | Membrane models for molecular simulations of peripheral membrane proteins |
| title_sort | membrane models for molecular simulations of peripheral membrane proteins |
| url | http://dx.doi.org/10.1080/23746149.2021.1932589 |
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