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Article ; Online: Induced asymmetries in membranes.

Girard, Martin / Bereau, Tristan

2022 Volume 122, Issue 11, Page(s) 2092–2098

Abstract: Lipid asymmetry in plasma membrane of eukaryotes is ubiquitous. The first measurements reported compositional asymmetry: phosphatidylethanolamine and phosphatidylserine are mostly on the cytoplasmic leafet, while phosphatidylcholine and sphingomyelin are ...

Abstract	Lipid asymmetry in plasma membrane of eukaryotes is ubiquitous. The first measurements reported compositional asymmetry: phosphatidylethanolamine and phosphatidylserine are mostly on the cytoplasmic leafet, while phosphatidylcholine and sphingomyelin are mostly on the exoplasmic leaflet. More recent experiments using lipidomics have evidenced the presence of saturation asymmetry between the two leaflets. A question that naturally arises is why such an asymmetry? To complicate matters, it is still largely unknown in which leaflet cholesterol lies. Here, we use chemical potentials to mimic flippase proteins responsible for maintenance of compositional asymmetry in silico. We show that saturation asymmetry naturally arises as a byproduct of phospholipid number asymmetry and sphingomyelin contents, thereby showing that some reported asymmetries may naturally result from others and do not necessarily require being externally driven. We also show that plasmalogen lipids' tendency to be highly unsaturated is also natural. Additionally, we tackle the problem of cholesterol and show that, while it is influenced by all asymmetries, the resulting cholesterol asymmetry tends to be fairly mild.
MeSH term(s)	Sphingomyelins/metabolism ; Cell Membrane/metabolism ; Phospholipids/chemistry ; Membranes/metabolism ; Cholesterol/metabolism
Chemical Substances	Sphingomyelins ; Phospholipids ; Cholesterol (97C5T2UQ7J)
Language	English
Publishing date	2022-12-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2022.12.004
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Article ; Online: Condensed-Phase Molecular Representation to Link Structure and Thermodynamics in Molecular Dynamics.

Mohr, Bernadette / van der Mast, Diego / Bereau, Tristan

Journal of chemical theory and computation

2023 Volume 19, Issue 14, Page(s) 4770–4779

Abstract: Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an atomic ... ...

Abstract	Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an atomic representation originally developed for electronic properties: the Spectrum of London and Axilrod-Teller-Muto representation (SLATM). SLATM's expansion in one-, two-, and three-body interactions makes it amenable to probing structural ordering in molecular liquids. We show that such representation encodes enough critical information to permit the learning of thermodynamic properties via linear methods. We demonstrate our approach on the preferential insertion of small solute molecules toward cardiolipin membranes and monitor selectivity against a similar lipid. Our analysis reveals simple, interpretable relationships between two- and three-body interactions and selectivity, identifies key interactions to build optimal prototypical solutes, and charts a two-dimensional projection that displays clearly separated basins. The methodology is generally applicable to a variety of thermodynamic properties.
Language	English
Publishing date	2023-07-03
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.3c00201
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Article ; Online: Computer simulations of lipid regulation by molecular semigrand canonical ensembles.

Girard, Martin / Bereau, Tristan

Biophysical journal

2021 Volume 120, Issue 12, Page(s) 2370–2373

Abstract: The plasma membrane is the interface between cells and exterior media. Although its existence has been known for a long time, organization of its constituent lipids remain a challenge. Recently, we have proposed that lipid populations may be controlled ... ...

Abstract	The plasma membrane is the interface between cells and exterior media. Although its existence has been known for a long time, organization of its constituent lipids remain a challenge. Recently, we have proposed that lipid populations may be controlled by chemical potentials of different lipid species, resulting in semigrand canonical thermodynamic ensembles. However, the currently available molecular dynamics software packages do not facilitate the control of chemical potentials at the molecular level. Here, we propose a variation of existing algorithms that efficiently characterizes and controls the chemical nature of each lipid. Additionally, we allow coupling with collective variables and show that it can be used to dynamically create asymmetric membranes. This algorithm is openly available as a plugin for the HOOMD-Blue molecular dynamics engine.
MeSH term(s)	Algorithms ; Cell Membrane ; Computer Simulation ; Lipid Bilayers ; Molecular Dynamics Simulation ; Thermodynamics
Chemical Substances	Lipid Bilayers
Language	English
Publishing date	2021-05-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.04.025
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Article ; Online: Finite-size transitions in complex membranes.

Girard, Martin / Bereau, Tristan

Biophysical journal

2021 Volume 120, Issue 12, Page(s) 2436–2443

Abstract: The lipid-raft hypothesis postulates that cell membranes possess some degree of lateral organization. The hypothesis has attracted much attention while remaining controversial, with an underlying mechanism that remains elusive. One idea that supports ... ...

Abstract	The lipid-raft hypothesis postulates that cell membranes possess some degree of lateral organization. The hypothesis has attracted much attention while remaining controversial, with an underlying mechanism that remains elusive. One idea that supports rafts relies on the membrane lying near a critical point. Although supported by experimental evidence, holding a many-component membrane at criticality requires a delicate tuning of all components-a daunting task. Here, we propose a coherent framework to reconcile critical behavior and lipid regulation. Using a lattice model, we show that lipid regulation of a complex membrane, i.e., allowing composition to fluctuate based on relative chemical potentials, can lead to critical behavior. The results are robust against specific values of the chemical potentials. Instead of a conventional transition point, criticality is observed over a large temperature range. This surprising behavior arises from finite-size effects, causing nonequivalent time and space averages. The instantaneous lipid distribution effectively develops a translational symmetry, which we relate to long-wavelength Goldstone modes. The framework is robust and reproduces important experimental trends; membrane-demixing temperature closely follows cell-growth temperature. It also ensures criticality of fixed-composition extracts, such as giant plasma membrane vesicles. Our clear picture provides a strong argument in favor of the critical-membrane hypothesis, without the need for specific sensing mechanisms.
MeSH term(s)	Cell Membrane ; Lipids ; Membrane Microdomains ; Membranes ; Temperature
Chemical Substances	Lipids
Language	English
Publishing date	2021-05-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.03.043
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Article ; Online: Reweighting non-equilibrium steady-state dynamics along collective variables.

Bause, Marius / Bereau, Tristan

The Journal of chemical physics

2021 Volume 154, Issue 13, Page(s) 134105

Abstract: Computer simulations generate microscopic trajectories of complex systems at a single thermodynamic state point. We recently introduced a Maximum Caliber (MaxCal) approach for dynamical reweighting. Our approach mapped these trajectories to a Markovian ... ...

Abstract	Computer simulations generate microscopic trajectories of complex systems at a single thermodynamic state point. We recently introduced a Maximum Caliber (MaxCal) approach for dynamical reweighting. Our approach mapped these trajectories to a Markovian description on the configurational coordinates and reweighted path probabilities as a function of external forces. Trajectory probabilities can be dynamically reweighted both from and to equilibrium or non-equilibrium steady states. As the system's dimensionality increases, an exhaustive description of the microtrajectories becomes prohibitive-even with a Markovian assumption. Instead, we reduce the dimensionality of the configurational space to collective variables (CVs). Going from configurational to CV space, we define local entropy productions derived from configurationally averaged mean forces. The entropy production is shown to be a suitable constraint on MaxCal for non-equilibrium steady states expressed as a function of CVs. We test the reweighting procedure on two systems: a particle subject to a two-dimensional potential and a coarse-grained peptide. Our CV-based MaxCal approach expands dynamical reweighting to larger systems, for both static and dynamical properties, and across a large range of driving forces.
Language	English
Publishing date	2021-04-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0042972
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Article ; Online: Broad chemical transferability in structure-based coarse-graining.

Kanekal, Kiran H / Rudzinski, Joseph F / Bereau, Tristan

The Journal of chemical physics

2022 Volume 157, Issue 10, Page(s) 104102

Abstract: Compared to top-down coarse-grained (CG) models, bottom-up approaches are capable of offering higher structural fidelity. This fidelity results from the tight link to a higher resolution reference, making the CG model chemically specific. Unfortunately, ... ...

Abstract	Compared to top-down coarse-grained (CG) models, bottom-up approaches are capable of offering higher structural fidelity. This fidelity results from the tight link to a higher resolution reference, making the CG model chemically specific. Unfortunately, chemical specificity can be at odds with compound-screening strategies, which call for transferable parameterizations. Here, we present an approach to reconcile bottom-up, structure-preserving CG models with chemical transferability. We consider the bottom-up CG parameterization of 3441 C
MeSH term(s)	Mechanical Phenomena
Language	English
Publishing date	2022-05-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0104914
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Article ; Online: Better Together: Lipopeptide Micelle Formation Enhances Antimicrobial Selectivity.

Bereau, Tristan

Biophysical journal

2015 Volume 109, Issue 4, Page(s) 668–669

MeSH term(s)	Anti-Infective Agents/chemistry ; Lipopeptides/chemistry ; Membrane Fusion ; Micelles
Chemical Substances	Anti-Infective Agents ; Lipopeptides ; Micelles
Language	English
Publishing date	2015-08-18
Publishing country	United States
Document type	Comment ; Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2015.07.012
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Article ; Online: Regulating Lipid Composition Rationalizes Acyl Tail Saturation Homeostasis in Ectotherms.

Girard, Martin / Bereau, Tristan

Biophysical journal

2020 Volume 119, Issue 5, Page(s) 892–899

Abstract: Cell membranes mainly consist of lipid bilayers with an actively regulated composition. The underlying processes are still poorly understood, in particular, how the hundreds of components are controlled. Cholesterol has been found to correlate with ... ...

Abstract	Cell membranes mainly consist of lipid bilayers with an actively regulated composition. The underlying processes are still poorly understood, in particular, how the hundreds of components are controlled. Cholesterol has been found to correlate with phospholipid saturation for reasons that remain unclear. To better understand the link between cell membrane regulation and chemical composition, we establish a computational framework based on chemical reaction networks, resulting in multiple semigrand canonical ensembles. By running computer simulations, we show that regulating the chemical potential of lipid species is sufficient to reproduce the experimentally observed increase in acyl tail saturation with added cholesterol. Our model proposes a different picture of lipid regulation in which components can be regulated passively instead of actively. In this picture, phospholipid acyl tail composition naturally adapts to added molecules such as cholesterol or proteins. A comparison between regulated membranes with commonly studied ternary model membranes shows stark differences: for instance, correlation lengths and viscosities observed are independent of lipid chemical affinity.
MeSH term(s)	Cell Membrane ; Cholesterol ; Homeostasis ; Lipid Bilayers ; Phospholipids
Chemical Substances	Lipid Bilayers ; Phospholipids ; Cholesterol (97C5T2UQ7J)
Language	English
Publishing date	2020-08-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2020.07.024
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Article ; Online: Coarse-grained conformational surface hopping: Methodology and transferability.

Rudzinski, Joseph F / Bereau, Tristan

The Journal of chemical physics

2020 Volume 153, Issue 21, Page(s) 214110

Abstract: Coarse-grained (CG) conformational surface hopping (SH) adapts the concept of multisurface dynamics, initially developed to describe electronic transitions in chemical reactions, to accurately describe classical molecular dynamics at a reduced level. The ...

Abstract	Coarse-grained (CG) conformational surface hopping (SH) adapts the concept of multisurface dynamics, initially developed to describe electronic transitions in chemical reactions, to accurately describe classical molecular dynamics at a reduced level. The SH scheme couples distinct conformational basins (states), each described by its own force field (surface), resulting in a significant improvement of the approximation to the many-body potential of mean force [T. Bereau and J. F. Rudzinski, Phys. Rev. Lett. 121, 256002 (2018)]. The present study first describes CG SH in more detail, through both a toy model and a three-bead model of hexane. We further extend the methodology to non-bonded interactions and report its impact on liquid properties. Finally, we investigate the transferability of the surfaces to distinct systems and thermodynamic state points, through a simple tuning of the state probabilities. In particular, applications to variations in temperature and chemical composition show good agreement with reference atomistic calculations, introducing a promising "weak-transferability regime," where CG force fields can be shared across thermodynamic and chemical neighborhoods.
Language	English
Publishing date	2020-12-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0031249
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Article ; Online: Hydration free energies from kernel-based machine learning: Compound-database bias.

Rauer, Clemens / Bereau, Tristan

The Journal of chemical physics

2020 Volume 153, Issue 1, Page(s) 14101

Abstract: We consider the prediction of a basic thermodynamic property-hydration free energies-across a large subset of the chemical space of small organic molecules. Our in silico study is based on computer simulations at the atomistic level with implicit solvent. ...

Abstract	We consider the prediction of a basic thermodynamic property-hydration free energies-across a large subset of the chemical space of small organic molecules. Our in silico study is based on computer simulations at the atomistic level with implicit solvent. We report on a kernel-based machine learning approach that is inspired by recent work in learning electronic properties but differs in key aspects: The representation is averaged over several conformers to account for the statistical ensemble. We also include an atomic-decomposition ansatz, which offers significant added transferability compared to molecular learning. Finally, we explore the existence of severe biases from databases of experimental compounds. By performing a combination of dimensionality reduction and cross-learning models, we show that the rate of learning depends significantly on the breadth and variety of the training dataset. Our study highlights the dangers of fitting machine-learning models to databases of a narrow chemical range.
Language	English
Publishing date	2020-07-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0012230
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