Free energy, rates, and mechanism of transmembrane dimerization in lipid bilayers from dynamically unbiased molecular dynamics simulations
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arXiv
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| Autores principales: | , , |
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| Formato: | Preprint |
| Publicado: |
2024
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| _version_ | 1866911975314817024 |
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| author | Jackel, Emil Lazzeri, Gianmarco Covino, Roberto |
| author_facet | Jackel, Emil Lazzeri, Gianmarco Covino, Roberto |
| contents | The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics simulations do not cover the time scales required to sample the typical transmembrane assembly. Hence, most studies rely on enhanced sampling schemes that steer the dynamics of transmembrane proteins along a collective variable that should encode all slow degrees of freedom. However, given the complexity of the condensed-phase lipid environment, this is far from trivial, with the consequence that free energy profiles of dimerization can be poorly converged. Here, we introduce an alternative approach, which relies only on simulating short, dynamically unbiased trajectory segments, avoiding using collective variables or biasing forces. By merging all trajectories, we obtain free energy profiles, rates, and mechanisms of transmembrane dimerization with the same set of simulations. We showcase our algorithm by sampling the spontaneous association and dissociation of a transmembrane protein in a lipid bilayer, the popular coarse-grained Martini force field. Our algorithm represents a promising way to investigate assembly processes in biologically relevant membranes, overcoming some of the challenges of conventional methods. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2408_01407 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Free energy, rates, and mechanism of transmembrane dimerization in lipid bilayers from dynamically unbiased molecular dynamics simulations Jackel, Emil Lazzeri, Gianmarco Covino, Roberto Soft Condensed Matter Chemical Physics Biomolecules The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics simulations do not cover the time scales required to sample the typical transmembrane assembly. Hence, most studies rely on enhanced sampling schemes that steer the dynamics of transmembrane proteins along a collective variable that should encode all slow degrees of freedom. However, given the complexity of the condensed-phase lipid environment, this is far from trivial, with the consequence that free energy profiles of dimerization can be poorly converged. Here, we introduce an alternative approach, which relies only on simulating short, dynamically unbiased trajectory segments, avoiding using collective variables or biasing forces. By merging all trajectories, we obtain free energy profiles, rates, and mechanisms of transmembrane dimerization with the same set of simulations. We showcase our algorithm by sampling the spontaneous association and dissociation of a transmembrane protein in a lipid bilayer, the popular coarse-grained Martini force field. Our algorithm represents a promising way to investigate assembly processes in biologically relevant membranes, overcoming some of the challenges of conventional methods. |
| title | Free energy, rates, and mechanism of transmembrane dimerization in lipid bilayers from dynamically unbiased molecular dynamics simulations |
| topic | Soft Condensed Matter Chemical Physics Biomolecules |
| url | https://arxiv.org/abs/2408.01407 |