Cmem Builder: An Automated Tool for Curved Membrane Construction in Molecular Dynamics Simulations
Jiabin Guo1, Kin Lei1, Jixing Liu1
1Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR 999078, China.
Journal of Chemical Theory and Computation
|July 28, 2025
Summary
Cmem Builder is a new web server that automates the creation of curved membrane models for molecular dynamics simulations. It accurately generates complex membrane geometries and protein interactions, aiding research into membrane curvature.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Membrane curvature is crucial for cellular processes like endocytosis and mechanotransduction.
- Molecular dynamics (MD) simulations offer atomistic insights into curved membrane systems.
- Existing tools lack comprehensive support for generating defined curved membrane geometries and integrating protein-specific curvature data.
Purpose of the Study:
- To develop a user-friendly web server, Cmem Builder, for automated generation of curved lipid membranes and membrane-protein complexes.
- To enable coarse-grained (CG) MD simulations using the MARTINI force field with accurate protein-lipid interactions in curved environments.
- To provide a platform supporting Z-axis symmetric curved shapes, OPM database-derived or custom curvature profiles, and detailed control over lipid composition.
Main Methods:
- Developed Cmem Builder, a web server automating curved membrane generation for CG MD simulations.
- Implemented Z-axis symmetry for curved membrane shapes.
- Integrated OPM database for protein curvature and allowed custom geometry inputs.
- Incorporated geometric sampling for precise lipid placement and control over lipid composition.
Main Results:
- Successfully generated curved membrane models for systems involving Piezo1 and BAR proteins.
- Modeled plasma membranes with asymmetric lipid compositions accurately.
- Demonstrated the accuracy and efficiency of Cmem Builder in creating complex membrane structures.
- Validated the tool's capability in simulating curvature-driven phenomena and protein-membrane interactions.
Conclusions:
- Cmem Builder provides a robust and accessible platform for researchers studying curved membrane systems.
- The tool facilitates accurate modeling of protein-lipid interactions in curved environments.
- Automates the generation of complex membrane geometries, enhancing the study of membrane dynamics.
- Freely available at https://cmembuilder.com, promoting wider accessibility in the scientific community.
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