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  Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations

Bubnis, G., & Grubmüller, H. (2020). Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations. Biophysical Journal, In Press. doi:10.1016/j.bpj.2020.10.037.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0007-7BFC-4 Version Permalink: http://hdl.handle.net/21.11116/0000-0007-7BFE-2
Genre: Journal Article

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Bubnis, G.1, Author              
Grubmüller, H.2, Author              
Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for Biophysical Chemistry, Max Planck Society, ou_578631              
2Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

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 Abstract: Membrane topology changes such as poration, stalk formation, and hemifusion rupture are essential to cellular function, but their molecular details, energetics, and kinetics are still not fully understood. Here, we present a unified energetic and mechanistic picture of metastable pore defects in tensionless lipid membranes. We used an exhaustive committor analysis to test and select optimal reaction coordinates and also to determine the nucleation mechanism. These reaction coordinates were used to calculate free-energy landscapes that capture the full process and end states. The identified barriers agree with the committor analysis. To enable sufficient sampling of the complete transition path for our molecular dynamics simulations, we developed a “gizmo” potential biasing scheme. The simulations suggest that the essential step in the nucleation is the initial merger of lipid headgroups at the nascent pore center. To facilitate this event, an indentation pathway is energetically preferred to a hydrophobic defect. Continuous water columns that span the indentation were determined to be on-path transients that precede the nucleation barrier. This study gives a quantitative description of the nucleation mechanism and energetics of small metastable pores and illustrates a systematic approach to uncover the mechanisms of diverse cellular membrane remodeling processes.

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Language(s): eng - English
 Dates: 2020-11-13
 Publication Status: Published online
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 Rev. Type: Peer
 Identifiers: DOI: 10.1016/j.bpj.2020.10.037
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Title: Biophysical Journal
Source Genre: Journal
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