SMARTINI3 parametrization of multi-scale membrane models via unsupervised learning methods.

Autor: Soleimani A; Institute for Theoretical Physics, Georg-August-University Göttingen, 37077, Göttingen, Germany.; Department of Physics, Technical University Dortmund, 44221, Dortmund, Germany., Risselada HJ; Institute for Theoretical Physics, Georg-August-University Göttingen, 37077, Göttingen, Germany. jelger.risselada@tu-dortmund.de.; Department of Physics, Technical University Dortmund, 44221, Dortmund, Germany. jelger.risselada@tu-dortmund.de.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2024 Oct 28; Vol. 14 (1), pp. 25714. Date of Electronic Publication: 2024 Oct 28.
DOI: 10.1038/s41598-024-75490-2
Abstrakt: In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (ultra-CG) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its compatibility with realistic membrane proteins, for example, modeled within the Martini coarse-grained (CG) model, as well as with the widely used GROMACS software for molecular simulations. Our objective is to parameterize this ultra-CG model to accurately reproduce the experimentally observed structural and thermodynamic properties of Phosphatidylcholine (PC) membranes in real units, including properties such as area per lipid, area compressibility, bending modulus, line tension, phase transition temperature, density profile, and radial distribution function. In our example, we specifically focus on the properties of a POPC membrane, although the developed membrane model could be perceived as a generic model of lipid membranes. To optimize the performance of the model (the fitness), we conduct a series of evolutionary runs with diverse random initial population sizes (ranging from 96 to 384). We demonstrate that the ultra-CG membrane model we developed exhibits authentic lipid membrane behaviors, including self-assembly into bilayers, vesicle formation, membrane fusion, and gel phase formation. Moreover, we demonstrate compatibility with the Martini coarse-grained model by successfully reproducing the behavior of a transmembrane domain embedded within a lipid bilayer. This facilitates the simulation of realistic membrane proteins within an ultra-CG bilayer membrane, enhancing the accuracy and applicability of our model in biophysical studies.
(© 2024. The Author(s).)
Databáze: MEDLINE
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