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Simulating realistic membrane shapes

CURRENT OPINION IN CELL BIOLOGY (2021)

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Article Biophysics

Lipid-Composition-Mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins

Zack Jarin et al.

Summary: This study reveals the significant roles of protein curvature and lipid clustering in the relaxation of large membrane deformations. Lipid clusters mediate interactions between I-BAR domains and cause the formation of aggregates, leading to more cylindrical protrusions within membrane protrusions compared to irregularly shaped ones.

BIOPHYSICAL JOURNAL (2021)

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Article Biophysics

Diffusion on Membrane Domes, Tubes, and Pearling Structures

Rossana Rojas Molina et al.

Summary: Diffusion is a fundamental mechanism for protein distribution in cell membranes, with membrane geometry playing a crucial role in influencing the diffusive spreading of proteins and molecules. Research shows that membrane necks act as diffusion barriers and there is a quadratic relationship between the diffusive half-time and the averaged mean curvature of the membrane shape.

BIOPHYSICAL JOURNAL (2021)

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Article Biology

Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity

Kristyna Pluhackova et al.

Summary: The study prepared four membrane models of E. coli polar lipid extract to demonstrate the importance of lipid tail complexity in stabilizing membrane properties and laying a solid foundation for future realistic lipid membrane simulation studies.

BMC BIOLOGY (2021)

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Article Microbiology

Simulations of Proposed Mechanisms of FtsZ-Driven Cell Constriction

Lam T. Nguyen et al.

Summary: Bacteria divide by constricting their membranes against turgor pressure, driven by FtsZ filaments. Two predominant models suggest either overlapping filaments forming rings that slide past each other or filaments exerting force on the membrane through conformational changes. Three-dimensional simulations show that mechanisms like depolymerization or treadmilling are needed for sustained constriction by sliding, and a constraint mechanism is required for filament bending to maintain the observed distance between filaments and the membrane.

JOURNAL OF BACTERIOLOGY (2021)

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Article Chemistry, Medicinal

Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus

Martin Sonora et al.

Summary: In short, we have introduced an optimized pipeline for simulating enveloped virus-like particles, which can prepare accurate membrane models within hours and conduct production MD simulations. This pipeline has already shown success in studying the Zika virus.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

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Review Biophysics

Protein-dependent membrane remodeling in mitochondrial morphology and clathrin-mediated endocytosis

Daryna Tarasenko et al.

Summary: Cellular membranes can adopt various shapes to fulfill physiological functions, with membrane morphology closely related to cellular physiology. Membrane trafficking pathways demonstrate the intricate relationship between membrane shape changes and cellular functions. The complex ultrastructure of organelle membranes, such as the mitochondria, can impact cellular health and disease progression.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2021)

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Article Chemistry, Physical

EnCurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations

Semen Yesylevskyy et al.

Summary: The EnCurv method is introduced for maintaining membrane curvature in molecular dynamics simulations, allowing for any desired curvature in a lipid membrane sector bent in a single plane. The method is simple, easy to implement, and scales linearly with system size, while being agnostic to force field, simulation parameters, and membrane composition. The proof of principle implementation is compatible with most modern simulation packages and yields consistent results on model systems.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes

Marc Siggel et al.

Summary: Living cells constantly remodel the shape of their lipid membranes. The Reticulophagy Regulator 1 (RETR1/FAM134B) in the endoplasmic reticulum forms autophagic puncta associated with membrane removal. Molecular dynamics simulations show that FAM134B-RHD clusters induce membrane buds formation in a nucleation process, with kinetics depending on protein concentration and bilayer asymmetry.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2021)

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Article Engineering, Mechanical

Curvature-regulated lipid membrane softening of nano-vesicles

Choon-Peng Chng et al.

Summary: The physico-mechanical properties of nanoscale lipid vesicles play a crucial role in their interaction with biological systems. The interplay between vesicle size and stiffness is essential for understanding their biological functions and optimizing diagnostics and therapeutics. Molecular dynamics simulations reveal that the softening of nano-vesicles is closely related to changes in membrane structure, providing a valuable insight for further exploration in biophysics and biomedical applications of nano-vesicles.

EXTREME MECHANICS LETTERS (2021)

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Article Chemistry, Physical

Membrane morphologies induced by mixtures of arc-shaped particles with opposite curvature

Francesco Bonazzi et al.

Summary: The study investigates the membrane morphologies induced by proteins of different shapes, finding that a small fraction of convex-binding particles can stabilize three-way junctions of membrane tubules. Additionally, when the ratios of concave-binding and convex-binding particles are comparable, lines of particles of the same type and various membrane morphologies with grooves and bulges are observed on the membranes due to these particle lines. The alignment and segregation of the particles are driven by indirect, membrane-mediated interactions.

SOFT MATTER (2021)

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Article Chemistry, Physical

Annexin A4 trimers are recruited by high membrane curvatures in giant plasma membrane vesicles

Christoffer Dam Florentsen et al.

Summary: The plasma membrane of eukaryotic cells is a crowded environment with a high diversity of proteins in a complex lipid matrix. The lateral organization of membrane proteins in the plasma membrane is closely related to biological functions such as endocytosis. Annexin A4 (ANXA4), a key player in various biological functions, is involved in plasma membrane repair and is activated by Ca2+ influx. ANXA4 is found to be a sensor of negative membrane curvatures and the trimer structure of ANXA4 generates membrane curvature upon binding, with an affinity for highly curved membrane regions only within a defined curvature window.

SOFT MATTER (2021)

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Article Chemistry, Multidisciplinary

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics

Giacomo Fiorin et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2020)

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Article Biophysics

Spontaneous Curvature, Differential Stress, and Bending Modulus of Asymmetric Lipid Membranes

Amirali Hossein et al.

BIOPHYSICAL JOURNAL (2020)

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Article Biophysics

An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

Christopher T. Lee et al.

BIOPHYSICAL JOURNAL (2020)

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Article Biophysics

Molecular Simulation of Mechanical Properties and Membrane Activities of the ESCRT-III Complexes

Taraknath Mandal et al.

BIOPHYSICAL JOURNAL (2020)

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Article Biochemistry & Molecular Biology

To infect or not to infect: molecular determinants of bacterial outer membrane vesicle internalization by host membranes

Damien Jefferies et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

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Article Multidisciplinary Sciences

Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers

Carsten F. E. Schroer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Review Biochemistry & Molecular Biology

Simulation of subcellular structures

Syma Khalid et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)

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Article Chemistry, Physical

Dual Resolution Membrane Simulations Using Virtual Sites

Yang Liu et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

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Article Multidisciplinary Sciences

Backmapping triangulated surfaces to coarse-grained membrane models

Weria Pezeshkian et al.

NATURE COMMUNICATIONS (2020)

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Article Biology

A molecular view on the escape of lipoplexed DNA from the endosome

Bart M. H. Bruininks et al.

ELIFE (2020)

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Article Biochemistry & Molecular Biology

A helical assembly of human ESCRT-I scaffolds reverse-topology membrane scission

Thomas G. Flower et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

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Article Chemistry, Physical

Capturing Biologically Complex Tissue-Specific Membranes at Different Levels of Compositional Complexity

Helgi I. Ingolfsson et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

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Article Multidisciplinary Sciences

Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models

Mohsen Sadeghi et al.

NATURE COMMUNICATIONS (2020)

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Article Multidisciplinary Sciences

Active particles induce large shape deformations in giant lipid vesicles

Hanumantha Rao Vutukuri et al.

NATURE (2020)

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Article Chemistry, Multidisciplinary

Coarse-Grained Simulations Suggest the Epsin N-Terminal Homology Domain Can Sense Membrane Curvature without Its Terminal Amphipathic Helix

Alexis Belessiotis-Richards et al.

ACS NANO (2020)

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Review Chemistry, Multidisciplinary

Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes

Alison N. Leonard et al.

CHEMICAL REVIEWS (2019)

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Review Chemistry, Multidisciplinary

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

Giray Enkavi et al.

CHEMICAL REVIEWS (2019)

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Article Chemistry, Multidisciplinary

Bilayer Membranes with Frequent Flip-Flops Have Tensionless Leaflets

Markus S. Miettinen et al.

NANO LETTERS (2019)

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Article Multidisciplinary Sciences

Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy

Ramachandra M. Bhaskara et al.

NATURE COMMUNICATIONS (2019)

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Review Chemistry, Multidisciplinary

Reactive molecular dynamics: From small molecules to proteins

Markus Meuwly

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2019)

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Article Chemistry, Physical

MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes

Harsh Bhatia et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

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Article Biochemistry & Molecular Biology

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Abhishek Singharoy et al.

CELL (2019)

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Article Chemistry, Physical

Curvature as a Collective Coordinate in Enhanced Sampling Membrane Simulations

Benjamin Bouvier

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

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Article Multidisciplinary Sciences

Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending

Grzegorz Nawrocki et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Article Multidisciplinary Sciences

Shape transition from elliptical to cylindrical membrane tubes induced by chiral crescent-shaped protein rods

Hiroshi Noguchi

SCIENTIFIC REPORTS (2019)

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Article Multidisciplinary Sciences

Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine

Semen Yesylevskyy et al.

SCIENTIFIC REPORTS (2019)

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Article Multidisciplinary Sciences

Mitochondrial morphology provides a mechanism for energy buffering at synapses

Guadalupe C. Garcia et al.

SCIENTIFIC REPORTS (2019)

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Article Physics, Fluids & Plasmas

Tubulation pattern of membrane vesicles coated with biofilaments

Gaurav Kumar et al.

PHYSICAL REVIEW E (2019)

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Article Chemistry, Physical

Fluctuations and conformational stability of a membrane patch with curvature inducing inclusions

Weria Pezeshkian et al.

SOFT MATTER (2019)

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Article Biochemistry & Molecular Biology

A Multi-Scale Approach to Membrane Remodeling Processes

Weria Pezeshkian et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2019)

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Article Chemistry, Physical

Detachment of a fluid membrane from a substrate and vesiculation

Hiroshi Noguchi

SOFT MATTER (2019)

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Article Biochemistry & Molecular Biology

Organizing membrane-curving proteins: the emerging dynamical picture

Mijo Simunovic et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)

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Article Physiology

Mitochondrial ATP synthase dimers spontaneously associate due to a long-range membrane-induced force

Claudio Anselmi et al.

JOURNAL OF GENERAL PHYSIOLOGY (2018)

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Review Physics, Applied

The 2018 biomembrane curvature and remodeling roadmap

Patricia Bassereau et al.

JOURNAL OF PHYSICS D-APPLIED PHYSICS (2018)

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Review Physics, Condensed Matter

Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales

N. Ramakrishnan et al.

JOURNAL OF PHYSICS-CONDENSED MATTER (2018)

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Article Chemistry, Multidisciplinary

Curvature-Mediated Assembly of Janus Nanoparticles on Membrane Vesicles

Amir Houshang Bahrami et al.

NANO LETTERS (2018)

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Article Multidisciplinary Sciences

The glycolipid GM1 reshapes asymmetric biomembranes and giant vesicles by curvature generation

Raktim Dasgupta et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

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Article Multidisciplinary Sciences

How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins

Matthieu Chavent et al.

NATURE COMMUNICATIONS (2018)

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Article Biology

Acyl chain asymmetry and polyunsaturation of brain phospho ipids facilitate membrane vesiculation without leakage

Marco M. Manni et al.

ELIFE (2018)

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Article Biophysics

Accurate In Silico Modeling of Asymmetric Bilayers Based on Biophysical Principles

Milka Doktorova et al.

BIOPHYSICAL JOURNAL (2018)

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Review Multidisciplinary Sciences

Biophysical experiments and biomolecular simulations: A perfect match?

Sandro Bottaro et al.

SCIENCE (2018)

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Article Chemistry, Physical

BUMPy: A Model-Independent Tool for Constructing Lipid Bilayers of Varying Curvature and Composition

Kevin J. Boyd et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

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Article Biology

The role of scaffold reshaping and disassembly in dynamin driven membrane fission

Martina Pannuzzo et al.

ELIFE (2018)

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Article Multidisciplinary Sciences

Curvature-Induced Sorting of Lipids in Plasma Membrane Tethers

Svetlana Baoukina et al.

ADVANCED THEORY AND SIMULATIONS (2018)

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Article Chemistry, Physical

It Is Complicated: Curvature, Diffusion, and Lipid Sorting within the Two Membranes of Escherichia coli

Pin-Chia Hsu et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2017)

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Article Physics, Condensed Matter

Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations

Ricardo de Oliveira dos Santos Soares et al.

JOURNAL OF PHYSICS-CONDENSED MATTER (2017)

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Article Chemistry, Multidisciplinary

t-SNARE Transmembrane Domain Clustering Modulates Lipid Organization and Membrane Curvature

Satyan Sharma et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

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Article Multidisciplinary Sciences

Golgi apparatus self-organizes into the characteristic shape via postmitotic reassembly dynamics

Masashi Tachikawa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

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Article Nanoscience & Nanotechnology

The influence of solid scaffolds on flat and curved lipid membranes

D. H. de Jong et al.

AIP ADVANCES (2017)

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Article Multidisciplinary Sciences

Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes

Anna L. Duncan et al.

SCIENTIFIC REPORTS (2017)

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Article Biochemistry & Molecular Biology

Computational virology: From the inside out

Tyler Reddy et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2016)

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Article Physics, Multidisciplinary

Nonadditive Compositional Curvature Energetics of Lipid Bilayers

A. J. Sodt et al.

PHYSICAL REVIEW LETTERS (2016)

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Article Chemistry, Physical

Membrane invagination induced by Shiga toxin B-subunit: from molecular structure to tube formation

W. Pezeshkian et al.

SOFT MATTER (2016)

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Article Biochemistry & Molecular Biology

Pushing the Envelope: Dengue Viral Membrane Coaxed into Shape by Molecular Simulations

Jan K. Marzinek et al.

STRUCTURE (2016)

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Article Biochemical Research Methods

The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube Formation

Julian Weichsel et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

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Article Chemistry, Physical

Organelle morphogenesis by active membrane remodeling

N. Ramakrishnan et al.

SOFT MATTER (2015)

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Article Biochemical Research Methods

Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers

Heidi Koldso et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

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Article Physics, Multidisciplinary

Curvature-Dependent Elastic Properties of Liquid-Ordered Domains Result in Inverted Domain Sorting on Uniaxially Compressed Vesicles

H. Jelger Risselada et al.

PHYSICAL REVIEW LETTERS (2011)

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