1
|
Brown CM, Marrink SJ. Modeling membranes in situ. Curr Opin Struct Biol 2024; 87:102837. [PMID: 38744147 DOI: 10.1016/j.sbi.2024.102837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Molecular dynamics simulations of cellular membranes have come a long way-from simple model lipid bilayers to multicomponent systems capturing the crowded and complex nature of real cell membranes. In this opinionated minireview, we discuss the current challenge to simulate the dynamics of membranes in their native environment, in situ, with the prospect of reaching the level of whole cells and cell organelles using an integrative modeling framework.
Collapse
Affiliation(s)
- Chelsea M Brown
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands. https://twitter.com/chelseabrowncg
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands. s.j.marrinkrug.nl
| |
Collapse
|
2
|
Doktorova M, Khelashvili G, Brown MF. Efficient calculation of orientation-dependent lipid dynamics from membrane simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.23.542012. [PMID: 37292992 PMCID: PMC10245828 DOI: 10.1101/2023.05.23.542012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular dynamics simulations of lipid membranes have become increasingly impactful in biophysics because they offer atomistic resolution of structural fluctuations in relation to their functional outputs. Yet quantitative characterization of multiscale processes is a formidable challenge due to the distribution of motions that evade analysis of discrete simulation data. Here we investigate the efficient calculation of CH bond relaxation rates from membrane simulations. Widely used computational approaches offer numerical simplicity but fall short of capturing crucial aspects of the orientation dependence of the dynamics. To circumvent this problem, we introduced a robust framework based on liquid crystal theory which considers explicitly the CH bond motions with respect to the director axis (bilayer normal). Analysis of the orientation dependence of the dynamics shows excellent agreement with experiment, illustrating how the ordering potential affects the calculated relaxation rates. Furthermore, a fit-based resampling of the autocorrelation function of the bond fluctuations validates the new approach for low-temporal resolution data. The recovered relaxation rates indicate that at short timescales, both with and without cholesterol, the local motions of CH bonds describe the bilayer microviscosity and resemble liquid hydrocarbons. Our results establish the critical role of the orientational anisotropy in analysis of membrane simulations, explain fundamental aspects of lipid dynamics, and provide guidelines for extracting information that can be compared to experimental data.
Collapse
Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology & Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
- Department of Physics, University of Arizona, Tucson, AZ, USA
- Program in Applied Mathematics, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
3
|
Fábián B, Javanainen M. Diffusion Analyses along Mean and Gaussian-Curved Membranes with CurD. J Phys Chem Lett 2024; 15:3214-3220. [PMID: 38483514 DOI: 10.1021/acs.jpclett.4c00338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Curved cellular membranes are both abundant and functionally relevant. While novel tomography approaches reveal the structural details of curved membranes, their dynamics pose an experimental challenge. Curvature especially affects the diffusion of lipids and macromolecules, yet neither experiments nor continuum models distinguish geometric effects from those caused by curvature-induced changes in membrane properties. Molecular simulations could excel here, yet despite community interest toward curved membranes, tools for their analysis are still lacking. Here, we satisfy this demand by introducing CurD, our novel and openly available implementation of the Vertex-oriented Triangle Propagation algorithm to the study of lipid diffusion along membranes with mean and/or Gaussian curvature. This approach, aided by our highly optimized implementation, computes geodetic distances significantly faster than conventional implementations of path-finding algorithms. Our tool, applied to coarse-grained simulations, allows for the first time the analysis of curvature effects on diffusion at size scales relevant to physiological processes such as endocytosis. Our analyses with different membrane geometries reveal that Gaussian curvature plays a surprisingly small role on lipid motion, whereas mean curvature; i.e., the packing of lipid headgroups largely dictates their mobility.
Collapse
Affiliation(s)
- Balázs Fábián
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16000 Prague 6, Czech Republic
- Institute of Biotechnology, University of Helsinki, FI-00790 Helsinki, Finland
| |
Collapse
|
4
|
Lee TH, Charchar P, Separovic F, Reid GE, Yarovsky I, Aguilar MI. The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes. Chem Sci 2024; 15:3408-3427. [PMID: 38455013 PMCID: PMC10915831 DOI: 10.1039/d3sc04523d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
It is now evident that the cell manipulates lipid composition to regulate different processes such as membrane protein insertion, assembly and function. Moreover, changes in membrane structure and properties, lipid homeostasis during growth and differentiation with associated changes in cell size and shape, and responses to external stress have been related to drug resistance across mammalian species and a range of microorganisms. While it is well known that the biomembrane is a fluid self-assembled nanostructure, the link between the lipid components and the structural properties of the lipid bilayer are not well understood. This perspective aims to address this topic with a view to a more detailed understanding of the factors that regulate bilayer structure and flexibility. We describe a selection of recent studies that address the dynamic nature of bacterial lipid diversity and membrane properties in response to stress conditions. This emerging area has important implications for a broad range of cellular processes and may open new avenues of drug design for selective cell targeting.
Collapse
Affiliation(s)
- Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology, Monash University Clayton VIC 3800 Australia
| | - Patrick Charchar
- School of Engineering, RMIT University Melbourne Victoria 3001 Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne VIC 3010 Australia
| | - Gavin E Reid
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne VIC 3010 Australia
- Department of Biochemistry and Pharmacology, University of Melbourne Parkville VIC 3010 Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University Melbourne Victoria 3001 Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University Clayton VIC 3800 Australia
| |
Collapse
|
5
|
Pezeshkian W, Ipsen JH. Mesoscale simulation of biomembranes with FreeDTS. Nat Commun 2024; 15:548. [PMID: 38228588 PMCID: PMC10792169 DOI: 10.1038/s41467-024-44819-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/05/2024] [Indexed: 01/18/2024] Open
Abstract
We present FreeDTS software for performing computational research on biomembranes at the mesoscale. In this software, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included in the software to simulate complex membranes at different conditions such as framed membranes with constant tension, vesicles and high-genus membranes with various fixed volumes or constant pressure differences and applying external forces to membrane regions. Furthermore, the software allows the user to turn off the shape evolution of the membrane and focus solely on the organization of proteins. As a result, we can take realistic membrane shapes obtained from, for example, cryo-electron tomography and backmap them into a finer simulation model. In addition to many biomembrane applications, this software brings us a step closer to simulating realistic biomembranes with molecular resolution. Here we provide several interesting showcases of the power of the software but leave a wide range of potential applications for interested users.
Collapse
Affiliation(s)
- Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark.
| | - John H Ipsen
- MEMPHYS/PhyLife, Department of Physics, Chemistry and Pharmacy (FKF), University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| |
Collapse
|
6
|
van Tilburg MA, Marrink SJ, König M, Grünewald F. Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks. J Chem Theory Comput 2024; 20:212-223. [PMID: 38109481 PMCID: PMC10782443 DOI: 10.1021/acs.jctc.3c00961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023]
Abstract
The process of osmosis, a fundamental phenomenon in life, drives water through a semipermeable membrane in response to a solute concentration gradient across this membrane. In vitro, osmotic shocks are often used to drive shape changes in lipid vesicles, for instance, to study fission events in the context of artificial cells. While experimental techniques provide a macroscopic picture of large-scale membrane remodeling processes, molecular dynamics (MD) simulations are a powerful tool to study membrane deformations at the molecular level. However, simulating an osmotic shock is a time-consuming process due to slow water diffusion across the membrane, making it practically impossible to examine its effects in classic MD simulations. In this article, we present Shocker, a Python-based MD tool for simulating the effects of an osmotic shock by selecting and relocating water particles across a membrane over the course of several pumping cycles. Although this method is primarily aimed at efficiently simulating volume changes in vesicles, it can also handle membrane tubes and double bilayer systems. Additionally, Shocker is force field-independent and compatible with both coarse-grained and all-atom systems. We demonstrate that our tool is applicable to simulate both hypertonic and hypotonic osmotic shocks for a range of vesicular and bilamellar setups, including complex multicomponent systems containing membrane proteins or crowded internal solutions.
Collapse
Affiliation(s)
- Marco
P. A. van Tilburg
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Melanie König
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Fabian Grünewald
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
- Heidelberg
Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| |
Collapse
|
7
|
Golla VK, Boyd KJ, May ER. Curvature sensing lipid dynamics in a mitochondrial inner membrane model. Commun Biol 2024; 7:29. [PMID: 38182788 PMCID: PMC10770132 DOI: 10.1038/s42003-023-05657-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 11/30/2023] [Indexed: 01/07/2024] Open
Abstract
Membrane curvature is essential for many cellular structures and processes, and factors such as leaflet asymmetry, lipid composition, and proteins all play important roles. Cardiolipin is the signature lipid of mitochondrial membranes and is essential for maintaining the highly curved shapes of the inner mitochondrial membrane (IMM) and the spatial arrangement of membrane proteins. In this study, we investigate the partitioning behavior of various lipids present in the IMM using coarse-grained molecular dynamics simulations. This study explores curved bilayer systems containing phosphatidylcholine (PC), phosphatidylethanolamine (PE), and cardiolipin (CDL) in binary and ternary component mixtures. Curvature properties such as mean and Gaussian curvatures, as well as the distribution of lipids into the various curved regions of the cristae models, are quantified. Overall, this work represents an advance beyond previous studies on lipid curvature sensing by simulating these systems in a geometry that has the morphological features and scales of curvature consistent with regions of the IMM. We find that CDL has a stronger preference for accumulating in regions of negative curvature than PE lipids, in agreement with previous results. Furthermore, we find lipid partitioning propensity is dominated by sensitivity to mean curvature, while there is a weaker correlation with Gaussian curvature.
Collapse
Affiliation(s)
- Vinaya Kumar Golla
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
- NVIDIA, 2860 County Hwy G4, Santa Clara, CA, 95051, USA
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA.
| |
Collapse
|
8
|
Borges-Araújo L, Borges-Araújo AC, Ozturk TN, Ramirez-Echemendia DP, Fábián B, Carpenter TS, Thallmair S, Barnoud J, Ingólfsson HI, Hummer G, Tieleman DP, Marrink SJ, Souza PCT, Melo MN. Martini 3 Coarse-Grained Force Field for Cholesterol. J Chem Theory Comput 2023; 19:7387-7404. [PMID: 37796943 DOI: 10.1021/acs.jctc.3c00547] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and inclusion of new bead types and sizes. However, the release of the new model resulted in the need to reparameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume, and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving the overall behavior.
Collapse
Affiliation(s)
- Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Ana C Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tugba Nur Ozturk
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Daniel P Ramirez-Echemendia
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Balázs Fábián
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Timothy S Carpenter
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sebastian Thallmair
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - Jonathan Barnoud
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Rúa de Jenaro de la Fuente, 15705 Santiago de Compostela, Spain
| | - Helgi I Ingólfsson
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| |
Collapse
|
9
|
Chaisson EH, Heberle FA, Doktorova M. Building Asymmetric Lipid Bilayers for Molecular Dynamics Simulations: What Methods Exist and How to Choose One? MEMBRANES 2023; 13:629. [PMID: 37504995 PMCID: PMC10384462 DOI: 10.3390/membranes13070629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 07/29/2023]
Abstract
The compositional asymmetry of biological membranes has attracted significant attention over the last decade. Harboring more differences from symmetric membranes than previously appreciated, asymmetric bilayers have proven quite challenging to study with familiar concepts and techniques, leaving many unanswered questions about the reach of the asymmetry effects. One particular area of active research is the computational investigation of composition- and number-asymmetric lipid bilayers with molecular dynamics (MD) simulations. Offering a high level of detail into the organization and properties of the simulated systems, MD has emerged as an indispensable tool in the study of membrane asymmetry. However, the realization that results depend heavily on the protocol used for constructing the asymmetric bilayer models has sparked an ongoing debate about how to choose the most appropriate approach. Here we discuss the underlying source of the discrepant results and review the existing methods for creating asymmetric bilayers for MD simulations. Considering the available data, we argue that each method is well suited for specific applications and hence there is no single best approach. Instead, the choice of a construction protocol-and consequently, its perceived accuracy-must be based primarily on the scientific question that the simulations are designed to address.
Collapse
Affiliation(s)
- Emily H. Chaisson
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37916, USA
| | - Frederick A. Heberle
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37916, USA
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| |
Collapse
|
10
|
Duncan AL, Pezeshkian W. Mesoscale simulations: An indispensable approach to understand biomembranes. Biophys J 2023:S0006-3495(23)00123-6. [PMID: 36809878 DOI: 10.1016/j.bpj.2023.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/10/2022] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
Computer simulation techniques form a versatile tool, a computational microscope, for exploring biological processes. This tool has been particularly effective in exploring different features of biological membranes. In recent years, thanks to elegant multiscale simulation schemes, some fundamental limitations of investigations by distinct simulation techniques have been resolved. As a result, we are now capable of exploring processes spanning multiple scales beyond the capacity of any single technique. In this perspective, we argue that mesoscale simulations require more attention and must be further developed to fill evident gaps in a quest toward simulating and modeling living cell membranes.
Collapse
Affiliation(s)
- Anna L Duncan
- Department of Chemistry, Aarhus University, Aarhus C, Denmark.
| | - Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
11
|
Close, but not too close: a mesoscopic description of (a)symmetry and membrane shaping mechanisms. Emerg Top Life Sci 2023; 7:81-93. [PMID: 36645200 DOI: 10.1042/etls20220078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 01/17/2023]
Abstract
Biomembranes are fundamental to our understanding of the cell, the basic building block of all life. An intriguing aspect of membranes is their ability to assume a variety of shapes, which is crucial for cell function. Here, we review various membrane shaping mechanisms with special focus on the current understanding of how local curvature and local rigidity induced by membrane proteins leads to emerging forces and consequently large-scale membrane deformations. We also argue that describing the interaction of rigid proteins with membranes purely in terms of local membrane curvature is incomplete and that changes in the membrane rigidity moduli must also be considered.
Collapse
|
12
|
Corey RA, Baaden M, Chavent M. A brief history of visualizing membrane systems in molecular dynamics simulations. FRONTIERS IN BIOINFORMATICS 2023; 3:1149744. [PMID: 37213533 PMCID: PMC10196259 DOI: 10.3389/fbinf.2023.1149744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/13/2023] [Indexed: 05/23/2023] Open
Abstract
Understanding lipid dynamics and function, from the level of single, isolated molecules to large assemblies, is more than ever an intensive area of research. The interactions of lipids with other molecules, particularly membrane proteins, are now extensively studied. With advances in the development of force fields for molecular dynamics simulations (MD) and increases in computational resources, the creation of realistic and complex membrane systems is now common. In this perspective, we will review four decades of the history of molecular dynamics simulations applied to membranes and lipids through the prism of molecular graphics.
Collapse
Affiliation(s)
- R. A. Corey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - M. Baaden
- Centre Nationale de la Recherche Scientifique, Laboratoire de Biochimie Théorique, Université Paris Cité, Paris, France
| | - M. Chavent
- Institut de Pharmacologie et Biologie Structurale, CNRS, Université de Toulouse, Toulouse, France
- *Correspondence: M. Chavent,
| |
Collapse
|
13
|
Nieto F, Garrido F, Dinamarca S, Cebrian I, Mayorga LS. Kinetics of antigen cross-presentation assessed experimentally and by a model of the complete endomembrane system. Cell Immunol 2022; 382:104636. [PMID: 36399818 DOI: 10.1016/j.cellimm.2022.104636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/08/2022]
Abstract
Dendritic cells (DCs) have a specialized endomembrane system capable of presenting exogenous antigens in the context of MHC class I (MHC-I) molecules. This process, named cross-presentation, is crucial to activate CD8+ T lymphocytes and initiate cytotoxic immune responses. In this report, we present an Agent-Based Model in combination with Ordinary Differential Equations with enough complexity to reproduce cross-presentation. The model embraces the secretory and endocytic pathways, in connection with the plasma membrane, the endoplasmic reticulum, and the cytosol. Key molecules required for cross-presentation were included as cargoes. In the simulations, the kinetics of MHC-I uptake and recycling, and cross-presentation accurately reproduced experimental values. The model proved to be a suitable tool to elaborate hypotheses and design experiments. In particular, the model predictions and the experimental results obtained indicate that the rate-limiting step in cross-presentation of soluble ovalbumin is MHC-I loading after proteasomal processing of the antigenic protein.
Collapse
Affiliation(s)
- Franco Nieto
- Instituto de Histología y Embriología de Mendoza (IHEM) - Universidad Nacional de Cuyo - CONICET, Mendoza 5500, Argentina
| | - Facundo Garrido
- Instituto de Histología y Embriología de Mendoza (IHEM) - Universidad Nacional de Cuyo - CONICET, Mendoza 5500, Argentina
| | - Sofía Dinamarca
- Instituto de Histología y Embriología de Mendoza (IHEM) - Universidad Nacional de Cuyo - CONICET, Mendoza 5500, Argentina
| | - Ignacio Cebrian
- Instituto de Histología y Embriología de Mendoza (IHEM) - Universidad Nacional de Cuyo - CONICET, Mendoza 5500, Argentina.
| | - Luis S Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM) - Universidad Nacional de Cuyo - CONICET, Mendoza 5500, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza 5500, Argentina.
| |
Collapse
|
14
|
Kumar G, Duggisetty SC, Srivastava A. A Review of Mechanics-Based Mesoscopic Membrane Remodeling Methods: Capturing Both the Physics and the Chemical Diversity. J Membr Biol 2022; 255:757-777. [PMID: 36197492 DOI: 10.1007/s00232-022-00268-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/29/2022] [Indexed: 12/24/2022]
Abstract
Specialized classes of proteins, working together in a tightly orchestrated manner, induce and maintain highly curved cellular and organelles membrane morphology. Due to the various experimental constraints, including the resolution limits of imaging techniques, it is non-trivial to accurately elucidate interactions among the various components involved in membrane deformation. The spatial and temporal scales of the systems also make it formidable to investigate them using simulations with molecular details. Interestingly, mechanics-based mesoscopic models have been used with great success in recapitulating the membrane deformations observed in experiments. In this review, we collate together and discuss the various mechanics-based mesoscopic models for protein-mediated membrane deformation studies. In particular, we provide an elaborate description of a mesoscopic model where the membrane is modeled as a triangulated sheet and proteins are represented as either nematics or filaments. This representation allows us to explore the various aspects of protein-protein and protein-membrane interactions as well as examine the underlying mechanistic pathways for emergent behavior such as curvature-mediated protein localization and membrane deformation. We also put forward current efforts in the field towards back-mapping these mesoscopic models to finer-grained particle-based models-a framework that could be used to explore how molecular interactions propagate to physical scales and vice-versa. We end the review with an integrative-modeling-based road map where experimental imaging micrograph and biochemical data are combined with mesoscopic and molecular simulations methods in a theoretically consistent manner to faithfully recapitulate the multiple length and time scales in the membrane remodeling processes.
Collapse
Affiliation(s)
- Gaurav Kumar
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, C. V. Raman Road, Bangalore, Karnataka, 560012, India
| | - Satya Chaithanya Duggisetty
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, C. V. Raman Road, Bangalore, Karnataka, 560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, C. V. Raman Road, Bangalore, Karnataka, 560012, India.
| |
Collapse
|
15
|
De Franceschi N, Pezeshkian W, Fragasso A, Bruininks BMH, Tsai S, Marrink SJ, Dekker C. Synthetic Membrane Shaper for Controlled Liposome Deformation. ACS NANO 2022; 17:966-978. [PMID: 36441529 PMCID: PMC9878720 DOI: 10.1021/acsnano.2c06125] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
Shape defines the structure and function of cellular membranes. In cell division, the cell membrane deforms into a "dumbbell" shape, while organelles such as the autophagosome exhibit "stomatocyte" shapes. Bottom-up in vitro reconstitution of protein machineries that stabilize or resolve the membrane necks in such deformed liposome structures is of considerable interest to characterize their function. Here we develop a DNA-nanotechnology-based approach that we call the synthetic membrane shaper (SMS), where cholesterol-linked DNA structures attach to the liposome membrane to reproducibly generate high yields of stomatocytes and dumbbells. In silico simulations confirm the shape-stabilizing role of the SMS. We show that the SMS is fully compatible with protein reconstitution by assembling bacterial divisome proteins (DynaminA, FtsZ:ZipA) at the catenoidal neck of these membrane structures. The SMS approach provides a general tool for studying protein binding to complex membrane geometries that will greatly benefit synthetic cell research.
Collapse
Affiliation(s)
- Nicola De Franceschi
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Weria Pezeshkian
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AGGroningen, The Netherlands
- The
Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, 17DK-2100Copenhagen, Denmark
| | - Alessio Fragasso
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Bart M. H. Bruininks
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AGGroningen, The Netherlands
| | - Sean Tsai
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AGGroningen, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| |
Collapse
|
16
|
Bottacchiari M, Gallo M, Bussoletti M, Casciola CM. Activation energy and force fields during topological transitions of fluid lipid vesicles. COMMUNICATIONS PHYSICS 2022; 5:283. [PMID: 36405503 PMCID: PMC9660165 DOI: 10.1038/s42005-022-01055-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Topological transitions of fluid lipid membranes are fundamental processes for cell life. For example, they are required for endo- and exocytosis or to enable neurotransmitters to cross the neural synapses. Here, inspired by the idea that fusion and fission proteins could have evolved in Nature in order to carry out a minimal work expenditure, we evaluate the minimal free energy pathway for the transition between two spherical large unilamellar vesicles and a dumbbell-shaped one. To address the problem, we propose and successfully use a Ginzburg-Landau type of free energy, which allows us to uniquely describe without interruption the whole, full-scale topological change. We also compute the force fields needed to overcome the involved energy barriers. The obtained forces are in excellent agreement, in terms of intensity, scale, and spatial localization with experimental data on typical fission protein systems, whereas they suggest the presence of additional features in fusion proteins.
Collapse
Affiliation(s)
- Matteo Bottacchiari
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
| | - Mirko Gallo
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
- Present Address: School of Architecture, Technology and Engineering, University of Brighton, Brighton, United Kingdom
| | - Marco Bussoletti
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
| | - Carlo Massimo Casciola
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
| |
Collapse
|
17
|
Larsen AH. Molecular Dynamics Simulations of Curved Lipid Membranes. Int J Mol Sci 2022; 23:ijms23158098. [PMID: 35897670 PMCID: PMC9331392 DOI: 10.3390/ijms23158098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma membrane to the highly curved membranes of organelles, vesicles, and membrane protrusions. These curvatures are generated and sustained by curvature-inducing proteins, peptides, and lipids, and describing these mechanisms is an important scientific challenge. In addition to that, some molecules can sense membrane curvature and thereby be trafficked to specific locations. The description of curvature sensing is another fundamental challenge. Curved lipid membranes and their interplay with membrane-associated proteins can be investigated with molecular dynamics (MD) simulations. Various methods for simulating curved membranes with MD are discussed here, including tools for setting up simulation of vesicles and methods for sustaining membrane curvature. The latter are divided into methods that exploit scaffolding virtual beads, methods that use curvature-inducing molecules, and methods applying virtual forces. The variety of simulation tools allow researcher to closely match the conditions of experimental studies of membrane curvatures.
Collapse
|
18
|
Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| |
Collapse
|
19
|
Larsen A, John L, Sansom M, Corey R. Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us? Biosci Rep 2022; 42:BSR20211406. [PMID: 35297484 PMCID: PMC9008707 DOI: 10.1042/bsr20211406] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding domains are typically solved in a soluble form, sometimes with a lipid or lipid headgroup at the binding site. To provide a detailed molecular view of PMP interactions with the membrane, computational methods such as molecular dynamics (MD) simulations can be applied. Here, we outline recent attempts to characterise these binding interactions, focusing on both intracellular proteins, such as phosphatidylinositol phosphate (PIP)-binding domains, and extracellular proteins such as glycolipid-binding bacterial exotoxins. We compare methods used to identify and analyse lipid-binding sites from simulation data and highlight recent work characterising the energetics of these interactions using free energy calculations. We describe how improvements in methodologies and computing power will help MD simulations to continue to contribute to this field in the future.
Collapse
Affiliation(s)
| | - Laura H. John
- Department of Biochemistry, University of Oxford, Oxford, U.K
| | | | - Robin A. Corey
- Department of Biochemistry, University of Oxford, Oxford, U.K
| |
Collapse
|
20
|
Migliore R, Biver T, Barone G, Sgarlata C. Quantitative Analysis of the Interactions of Metal Complexes and Amphiphilic Systems: Calorimetric, Spectroscopic and Theoretical Aspects. Biomolecules 2022; 12:biom12030408. [PMID: 35327600 PMCID: PMC8946196 DOI: 10.3390/biom12030408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 01/27/2023] Open
Abstract
Metals and metal-based compounds have many implications in biological systems. They are involved in cellular functions, employed in the formation of metal-based drugs and present as pollutants in aqueous systems, with toxic effects for living organisms. Amphiphilic molecules also play important roles in the above bio-related fields as models of membranes, nanocarriers for drug delivery and bioremediating agents. Despite the interest in complex systems involving both metal species and surfactant aggregates, there is still insufficient knowledge regarding the quantitative aspects at the basis of their binding interactions, which are crucial for extensive comprehension of their behavior in solution. Only a few papers have reported quantitative analyses of the thermodynamic, kinetic, speciation and binding features of metal-based compounds and amphiphilic aggregates, and no literature review has yet addressed the quantitative study of these complexes. Here, we summarize and critically discuss the recent contributions to the quantitative investigation of the interactions of metal-based systems with assemblies made of amphiphilic molecules by calorimetric, spectrophotometric and computational techniques, emphasizing the unique picture and parameters that such an analytical approach may provide, to support a deep understanding and beneficial use of these systems for several applications.
Collapse
Affiliation(s)
- Rossella Migliore
- Institute of Biomolecular Chemistry, National Research Council, Via Paolo Gaifami 18, 95126 Catania, Italy;
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy;
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Edificio 17, 90128 Palermo, Italy;
| | - Carmelo Sgarlata
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
- Correspondence:
| |
Collapse
|
21
|
Rems L, Tang X, Zhao F, Pérez-Conesa S, Testa I, Delemotte L. Identification of electroporation sites in the complex lipid organization of the plasma membrane. eLife 2022; 11:e74773. [PMID: 35195069 PMCID: PMC8912918 DOI: 10.7554/elife.74773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon termed electroporation is already utilized in many rapidly developing applications in medicine including gene therapy, cancer treatment, and treatment of cardiac arrhythmias. However, the molecular mechanisms of electroporation are not yet sufficiently well understood; in particular, it is unclear where exactly pores form in the complex organization of the plasma membrane. In this study, we combine coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis to identify how formation of pores depends on the local lipid organization. We show that pores do not form homogeneously across the membrane, but colocalize with domains that have specific features, the most important being high density of polyunsaturated lipids. We further show that knowing the lipid organization is sufficient to reliably predict poration sites with machine learning. Additionally, by analysing poration kinetics with Bayesian survival analysis we show that poration does not depend solely on local lipid arrangement, but also on membrane mechanical properties and the polarity of the electric field. Finally, we discuss how the combination of atomistic and coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis can guide the design of future experiments and help us to develop an accurate description of plasma membrane electroporation on the whole-cell level. Achieving this will allow us to shift the optimization of electroporation applications from blind trial-and-error approaches to mechanistic-driven design.
Collapse
Affiliation(s)
- Lea Rems
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Ljubljana, Faculty of Electrical EngineeringLjubljanaSlovenia
| | - Xinru Tang
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Chinese Academy of SciencesBeijingChina
| | - Fangwei Zhao
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Chinese Academy of SciencesBeijingChina
| | - Sergio Pérez-Conesa
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
| | - Ilaria Testa
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
| |
Collapse
|
22
|
Shillcock JC, Thomas DB, Beaumont JR, Bragg GM, Vousden ML, Brown AD. Coupling Bulk Phase Separation of Disordered Proteins to Membrane Domain Formation in Molecular Simulations on a Bespoke Compute Fabric. MEMBRANES 2021; 12:membranes12010017. [PMID: 35054543 PMCID: PMC8779898 DOI: 10.3390/membranes12010017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 05/28/2023]
Abstract
Phospholipid membranes surround the cell and its internal organelles, and their multicomponent nature allows the formation of domains that are important in cellular signalling, the immune system, and bacterial infection. Cytoplasmic compartments are also created by the phase separation of intrinsically disordered proteins into biomolecular condensates. The ubiquity of lipid membranes and protein condensates raises the question of how three-dimensional droplets might interact with two-dimensional domains, and whether this coupling has physiological or pathological importance. Here, we explore the equilibrium morphologies of a dilute phase of a model disordered protein interacting with an ideal-mixing, two-component lipid membrane using coarse-grained molecular simulations. We find that the proteins can wet the membrane with and without domain formation, and form phase separated droplets bound to membrane domains. Results from much larger simulations performed on a novel non-von-Neumann compute architecture called POETS, which greatly accelerates their execution compared to conventional hardware, confirm the observations. Reducing the wall clock time for such simulations requires new architectures and computational techniques. We demonstrate here an inter-disciplinary approach that uses real-world biophysical questions to drive the development of new computing hardware and simulation algorithms.
Collapse
Affiliation(s)
- Julian C. Shillcock
- Blue Brain Project and Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - David B. Thomas
- Department of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK; (D.B.T.); (G.M.B.); (M.L.V.); (A.D.B.)
| | - Jonathan R. Beaumont
- Department of Electronic Engineering, Imperial College London, London SW7 2AZ, UK;
| | - Graeme M. Bragg
- Department of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK; (D.B.T.); (G.M.B.); (M.L.V.); (A.D.B.)
| | - Mark L. Vousden
- Department of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK; (D.B.T.); (G.M.B.); (M.L.V.); (A.D.B.)
| | - Andrew D. Brown
- Department of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK; (D.B.T.); (G.M.B.); (M.L.V.); (A.D.B.)
| |
Collapse
|
23
|
Sawade K, Peter C. Multiscale simulations of protein and membrane systems. Curr Opin Struct Biol 2021; 72:203-208. [PMID: 34953308 DOI: 10.1016/j.sbi.2021.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/01/2021] [Accepted: 11/10/2021] [Indexed: 02/07/2023]
Abstract
Classical multiscale simulations are perfectly suited to investigate biological soft matter systems. Owing to the bridging between microscopically realistic and lower-resolution models or the integration of a hierarchy of subsystems, one gets access to biologically relevant system sizes and timescales. In recent years, increasingly complex systems and processes have come into focus such as multidomain proteins, phase separation processes in biopolymer solutions, multicomponent biomembranes, or multiprotein complexes up to entire viruses. The review shows factors that have contributed to this progress - from improved models to machine-learning-based analysis and scale-bridging methods.
Collapse
Affiliation(s)
- Kevin Sawade
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78 457, Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78 457, Konstanz, Germany.
| |
Collapse
|
24
|
Sun Y, Deng Z, Jiang X, Yuan B, Yang K. Interactions between polymyxin B and various bacterial membrane mimics: A molecular dynamics study. Colloids Surf B Biointerfaces 2021; 211:112288. [PMID: 34942463 DOI: 10.1016/j.colsurfb.2021.112288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/21/2021] [Accepted: 12/11/2021] [Indexed: 11/17/2022]
Abstract
Polymyxin B (PMB) is clinically used as a last-line therapy against life-threatening Gram-negative "superbugs". However, thorough understanding of the membrane actions of PMB at a molecular level is still lacking. In this work, a variety of bacterial membrane mimics with varying lipid compositions were built, and their interactions with PMB were systematically investigated using coarse-grained molecular dynamics simulation. PMB demonstrated characteristic preference to specific lipid species during its interaction with different membrane systems, such as the rough mutant lipipolysacchrides (Re LPS) preference in an outer membrane (OM) or the cardiolipin and POPG affinity in an inner membrane (IM). As a result of the lipid-specific actions, complicated membrane interaction states of PMB were observed, including adsorption on the OM surface. In contrast, for the IM or a mutative OM containing "impurity lipids" like POPE, POPG or lipid A, it could insert into the membrane via its acyl chain. Such actions of PMB influence the structure and lipid mobility of the membrane. In particular, the OM-bound PMB breaks the synchronous movement of Re LPS molecules in the outer leaflet and makes them diffuse more randomly, while its insertion into IM blocks the phospholipid diffusion and makes the membrane more homogeneous in the trajectory space. Our results provide insight into the action mechanism of PMB at a membrane level and a foundation for developing novel and safer polymyxin strategies for better clinical use.
Collapse
Affiliation(s)
- Yuliang Sun
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China
| | - Zhixiong Deng
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, Shandong, China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan 523808, Guangdong, China.
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China.
| |
Collapse
|
25
|
Fabrication of Adsorbed Fe(III) and Structurally Doped Fe(III) in Montmorillonite/TiO2 Composite for Photocatalytic Degradation of Phenol. MINERALS 2021. [DOI: 10.3390/min11121381] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Fe(III)-doped montmorillonite (Mt)/TiO2 composites were fabricated by adding Fe(III) during or after the aging of TiO2/Ti(OH)4 sol–gel in Mt, named as xFe-Mt/(1 − x)Fe-TiO2 and Fe/Mt/TiO2, respectively. In the xFe-Mt/(1 − x)Fe-TiO2, Fe(III) cations were expected to be located in the structure of TiO2, in the Mt, and in the interface between them, while Fe(III) ions are physically adsorbed on the surfaces of the composites in the Fe/Mt/TiO2. The narrower energy bandgap (Eg) lower photo-luminescence intensity were observed for the composites compared with TiO2. Better photocatalytic performance for phenol degradation was observed in the Fe/Mt/TiO2. The 94.6% phenol degradation was due to greater charge generation and migration capacity, which was confirmed by photocurrent measurements and electrochemical impedance spectroscopy (EIS). The results of the energy-resolved distribution of electron traps (ERDT) suggested that the Fe/Mt/TiO2 possessed a larger amorphous rutile phase content in direct contact with crystal anatase than that of the xFe-Mt/(1 − x)Fe-TiO2. This component is the fraction that is mainly responsible for the photocatalytic phenol degradation by the composites. As for the xFe-Mt/(1 − x)Fe-TiO2, the active rutile phase was followed by isolated amorphous phases which had larger (Eg) and which did not act as a photocatalyst. Thus, the physically adsorbed Fe(III) enhanced light adsorption and avoided charge recombination, resulting in improved photocatalytic performance. The mechanism of the photocatalytic reaction with the Fe(III)-doped Mt/TiO2 composite was proposed.
Collapse
|
26
|
Langmuir Monolayer Techniques for the Investigation of Model Bacterial Membranes and Antibiotic Biodegradation Mechanisms. MEMBRANES 2021; 11:membranes11090707. [PMID: 34564524 PMCID: PMC8471293 DOI: 10.3390/membranes11090707] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022]
Abstract
The amounts of antibiotics of anthropogenic origin released and accumulated in the environment are known to have a negative impact on local communities of microorganisms, which leads to disturbances in the course of the biodegradation process and to growing antimicrobial resistance. This mini-review covers up-to-date information regarding problems related to the omnipresence of antibiotics and their consequences for the world of bacteria. In order to understand the interaction of antibiotics with bacterial membranes, it is necessary to explain their interaction mechanism at the molecular level. Such molecular-level interactions can be probed with Langmuir monolayers representing the cell membrane. This mini-review describes monolayer experiments undertaken to investigate the impact of selected antibiotics on components of biomembranes, with particular emphasis on the role and content of individual phospholipids and lipopolysaccharides (LPS). It is shown that the Langmuir technique may provide information about the interactions between antibiotics and lipids at the mixed film surface (π–A isotherm) and about the penetration of the active substances into the phospholipid monolayer model membranes (relaxation of the monolayer). Effects induced by antibiotics on the bacterial membrane may be correlated with their bactericidal activity, which may be vital for the selection of appropriate bacterial consortia that would ensure a high degradation efficiency of pharmaceuticals in the environment.
Collapse
|
27
|
Scott HL, Kennison KB, Enoki TA, Doktorova M, Kinnun JJ, Heberle FA, Katsaras J. Model Membrane Systems Used to Study Plasma Membrane Lipid Asymmetry. Symmetry (Basel) 2021; 13. [PMID: 35498375 PMCID: PMC9053528 DOI: 10.3390/sym13081356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
It is well known that the lipid distribution in the bilayer leaflets of mammalian plasma membranes (PMs) is not symmetric. Despite this, model membrane studies have largely relied on chemically symmetric model membranes for the study of lipid–lipid and lipid–protein interactions. This is primarily due to the difficulty in preparing stable, asymmetric model membranes that are amenable to biophysical studies. However, in the last 20 years, efforts have been made in producing more biologically faithful model membranes. Here, we review several recently developed experimental and computational techniques for the robust generation of asymmetric model membranes and highlight a new and particularly promising technique to study membrane asymmetry.
Collapse
Affiliation(s)
- Haden L. Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - Kristen B. Kennison
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - Thais A. Enoki
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - Jacob J. Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - Frederick A. Heberle
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| | - John Katsaras
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (H.L.S.); (K.B.K.); (T.A.E.); (M.D.); (J.J.K.); (F.A.H.); (J.K.)
| |
Collapse
|
28
|
Klumperman J, Pucadyil T. Understanding membrane traffic from molecular ensemble, energetics, and the cell biology of participant components. Curr Opin Cell Biol 2021; 71:iii-vi. [PMID: 34219001 PMCID: PMC8248565 DOI: 10.1016/j.ceb.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Judith Klumperman
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 1oo, 3584CX Utrecht, the Netherlands.
| | - Thomas Pucadyil
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411007, Maharasthra, India.
| |
Collapse
|
29
|
Pezeshkian W, Shillcock JC, Ipsen JH. Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell. Toxins (Basel) 2021; 13:toxins13070449. [PMID: 34203472 PMCID: PMC8309782 DOI: 10.3390/toxins13070449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 01/13/2023] Open
Abstract
Many bacteria secrete toxic protein complexes that modify and disrupt essential processes in the infected cell that can lead to cell death. To conduct their action, these toxins often need to cross the cell membrane and reach a specific substrate inside the cell. The investigation of these protein complexes is essential not only for understanding their biological functions but also for the rational design of targeted drug delivery vehicles that must navigate across the cell membrane to deliver their therapeutic payload. Despite the immense advances in experimental techniques, the investigations of the toxin entry mechanism have remained challenging. Computer simulations are robust complementary tools that allow for the exploration of biological processes in exceptional detail. In this review, we first highlight the strength of computational methods, with a special focus on all-atom molecular dynamics, coarse-grained, and mesoscopic models, for exploring different stages of the toxin protein entry mechanism. We then summarize recent developments that are significantly advancing our understanding, notably of the glycolipid–lectin (GL-Lect) endocytosis of bacterial Shiga and cholera toxins. The methods discussed here are also applicable to the design of membrane-penetrating nanoparticles and the study of the phenomenon of protein phase separation at the surface of the membrane. Finally, we discuss other likely routes for future development.
Collapse
Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9712 Groningen, The Netherlands
- Correspondence:
| | - Julian C. Shillcock
- Blue Brain Project, Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
| | - John H. Ipsen
- MEMPHYS/PhyLife, Department of Physics, Chemistry and Pharmacy (FKF), University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark;
| |
Collapse
|