1
|
Shih KC, Leriche G, Liu CH, He J, John VT, Fang J, Barker JG, Nagao M, Yang L, Yang J, Nieh MP. Antivesiculation and Complete Unbinding of Tail-Tethered Lipids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1688-1697. [PMID: 38186288 DOI: 10.1021/acs.langmuir.3c02663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
We report the effect of tail-tethering on vesiculation and complete unbinding of bilayered membranes. Amphiphilic molecules of a bolalipid, resembling the tail-tethered molecular structure of archaeal lipids, with two identical zwitterionic phosphatidylcholine headgroups self-assemble into a large flat lamellar membrane, in contrast to the multilamellar vesicles (MLVs) observed in its counterpart, monopolar nontethered zwitterionic lipids. The antivesiculation is confirmed by small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cyro-TEM). With the net charge of zero and higher bending rigidity of the membrane (confirmed by neutron spin echo (NSE) spectroscopy), the current membrane theory would predict that membranes should stack with each other (aka "bind") due to dominant van der Waals attraction, while the outcome of the nonstacking ("unbinding") membrane suggests that the theory needs to include entropic contribution for the nonvesicular structures. This report pioneers an understanding of how the tail-tethering of amphiphiles affects the structure, enabling better control over the final nanoscale morphology.
Collapse
Affiliation(s)
| | - Geoffray Leriche
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | | | - Jibao He
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Vijay T John
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | | | - John G Barker
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Michihiro Nagao
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | | |
Collapse
|
2
|
Poruthoor AJ, Sharma A, Grossfield A. Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics. Biophys J 2023; 122:4144-4159. [PMID: 37742069 PMCID: PMC10645549 DOI: 10.1016/j.bpj.2023.09.012] [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: 03/06/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 09/25/2023] Open
Abstract
Liquid-liquid phase separation inside the cell often results in biological condensates that can critically affect cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the "lipid raft" hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For these reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation-essentially measuring the sign (but not the amplitude) of the free-energy change upon separation-rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from MD simulations.
Collapse
Affiliation(s)
- Ashlin J Poruthoor
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Akshara Sharma
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
| |
Collapse
|
3
|
Poruthoor AJ, Sharma A, Grossfield A. Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526537. [PMID: 36778479 PMCID: PMC9915641 DOI: 10.1101/2023.01.31.526537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Liquid-liquid phase separation (LLPS) inside the cell often results in biological condensates that can critically impact cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the so-called "lipid raft" hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For this reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation - essentially measuring the sign (but not the amplitude) of the free energy change upon separation - rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from molecular dynamics simulations. SIGNIFICANCE Standard molecular dynamics simulations can determine the sign the free energy change upon phase separation, but not the amplitude. We present a new method to determine the phase separation free energy for lipid membranes, based on a enhanced sampling using the weighted ensemble method combined with a novel collective variable, validated using coarse-grained simulations applied to several simple systems. The new method will be valuable as a way to develop models that connect molecular-level structural features to the thermodynamics of phase separation.
Collapse
Affiliation(s)
- Ashlin J. Poruthoor
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642
| | - Akshara Sharma
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642
| |
Collapse
|
4
|
Lin X, Lin K, He S, Zhou Y, Li X, Lin X. Membrane Domain Anti-Registration Induces an Intrinsic Transmembrane Potential. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11621-11627. [PMID: 37563986 DOI: 10.1021/acs.langmuir.3c01137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Plasma membrane segregation into various nanoscale membrane domains is driven by distinct interactions between diverse lipids and proteins. Among them, liquid-ordered (Lo) membrane domains are defined as "lipid rafts" and liquid-disordered (Ld) ones as "lipid non-rafts". Using model membrane systems, both intra-leaflet and inter-leaflet dynamics of these membrane domains are widely studied. Nevertheless, the biological impact of the latter, which is accompanied by membrane domain registration/anti-registration, is far from clear. Hence, in this work, we studied the biological relevance of the membrane domain anti-registration using both all-atom molecular dynamics (MD) simulations and confocal fluorescence microscopy. All-atom MD simulations suggested an intrinsic transmembrane potential for the case of the membrane anti-registration (Lo/Ld). Meanwhile, confocal fluorescence microscopy experiments of HeLa and 293T cell lines indicated that membrane cholesterol depletion could significantly alter the transmembrane potential of cells. Considering differences in the cholesterol content between Lo and Ld membrane domains, our confocal fluorescence microscopy experiments are consistent with our all-atom MD simulations. In short, membrane domain anti-registration induces local membrane asymmetry and, thus, an intrinsic transmembrane potential.
Collapse
Affiliation(s)
- Xiaoqian Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
- Shen Yuan Honors College, Beihang University, Beijing 100191, China
| | - Kaidong Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Shiqi He
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yue Zhou
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xiu Li
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xubo Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| |
Collapse
|
5
|
Li S, Huang F, Xia T, Shi Y, Yue T. Phosphatidylinositol 4,5-Bisphosphate Sensing Lipid Raft via Inter-Leaflet Coupling Regulated by Acyl Chain Length of Sphingomyelin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5995-6005. [PMID: 37086192 DOI: 10.1021/acs.langmuir.2c03492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PIP2) is an important molecule located at the inner leaflet of cell membrane, where it serves as anchoring sites for a cohort of membrane-associated molecules and as a broad-reaching signaling intermediate. The lipid raft is thought as the major platform recruiting proteins for signal transduction and also known to mediate PIP2 accumulation across the membrane. While the significance of this cross-membrane coupling is increasingly appreciated, it remains unclear whether and how PIP2 senses the dynamic change of the ordered lipid domains over the packed hydrophobic core of the bilayer. Herein, by means of molecular dynamic simulation, we reveal that inner PIP2 molecules can sense the outer lipid domain via inter-leaflet coupling, and the coupling manner is dictated by the acyl chain length of sphingomyelin (SM) partitioned to the lipid domain. Shorter SM promotes membrane domain registration, whereby PIP2 accumulates beneath the domain across the membrane. In contrast, the anti-registration is thermodynamically preferred if the lipid domain has longer SM due to the hydrophobic mismatch between the corresponding acyl chains in SM and PIP2. In this case, PIP2 is expelled by the domain with a higher diffusivity. These results provide molecular insights into the regulatory mechanism of correlation between the outer lipid domain and inner PIP2, both of which are critical components for cell signal transduction.
Collapse
Affiliation(s)
- Shixin Li
- College of Bioscience and Biotechnology and Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, Shandong 266580, China
| | - Tie Xia
- Institute for Immunology and Department of Basic Medical Sciences, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Shi
- Institute for Immunology and Department of Basic Medical Sciences, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Microbiology, Immunology & Infectious Disease and Snyder Institute, University of Calgary, Calgary, Alberta 00000, Canada
| | - Tongtao Yue
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, Shandong 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| |
Collapse
|
6
|
Fábián B, Thallmair S, Hummer G. Optimal Bond Constraint Topology for Molecular Dynamics Simulations of Cholesterol. J Chem Theory Comput 2023; 19:1592-1601. [PMID: 36800179 PMCID: PMC10018735 DOI: 10.1021/acs.jctc.2c01032] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
We recently observed artificial temperature gradients in molecular dynamics (MD) simulations of phase-separating ternary lipid mixtures using the Martini 2 force field. We traced this artifact to insufficiently converged bond length constraints with typical time steps and default settings for the linear constraint solver (LINCS). Here, we systematically optimize the constraint scaffold of cholesterol. With massive virtual sites in an equimomental arrangement, we accelerate bond constraint convergence while preserving the original cholesterol force field and dynamics. The optimized model does not induce nonphysical temperature gradients even at relaxed LINCS settings and is at least as fast as the original model at the strict LINCS settings required for proper thermal sampling. We provide a python script to diagnose possible problems with constraint convergence for other molecules and force fields. Equimomental constraint topology optimization can also be used to boost constraint convergence in atomistic MD simulations of molecular systems.
Collapse
Affiliation(s)
- Balázs Fábián
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Sebastian Thallmair
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - 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
| |
Collapse
|
7
|
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
|
8
|
Foley SL, Hossein A, Deserno M. Fluid-gel coexistence in lipid membranes under differential stress. Biophys J 2022; 121:2997-3009. [PMID: 35859420 PMCID: PMC9463654 DOI: 10.1016/j.bpj.2022.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/03/2022] [Accepted: 07/12/2022] [Indexed: 11/21/2022] Open
Abstract
A widely conserved property of many biological lipid bilayers is their asymmetry. In addition to having distinct compositions on its two sides, a membrane can also exhibit different tensions in its two leaflets, a state known as differential stress. Here, we examine how this stress can influence the phase behavior of the constituent lipid monolayers of a single-component membrane. For temperatures sufficiently close to, but still above, the main transition, molecular dynamics simulations show the emergence of finite gel domains within the compressed leaflet. We describe the thermodynamics of this phenomenon by adding two empirical single-leaflet free energies for the fluid-gel transition, each evaluated at its respective asymmetry-dependent lipid density. Finite size effects arising in simulation are included in the theory through a geometry-dependent interfacial term. Our model reproduces the phase coexistence observed in simulation. It could therefore be used to connect the "hidden variable" of differential stress to experimentally observable properties of the main phase transition. These ideas could be generalized to any first-order bilayer phase transition in the presence of asymmetry, including liquid-ordered/liquid-disordered phase separation.
Collapse
Affiliation(s)
- Samuel L Foley
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Amirali Hossein
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania.
| |
Collapse
|
9
|
Li X, Zhou S, Lin X. Molecular View on the Impact of DHA Molecules on the Physical Properties of a Model Cell Membrane. J Chem Inf Model 2022; 62:2421-2431. [PMID: 35513897 DOI: 10.1021/acs.jcim.2c00074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Docosahexaenoic acid (DHA) is a ω-3 polyunsaturated fatty acid, which can be uptaken by cells and is essential for proper neuronal and retinal function. However, the detailed physical impact of DHA molecules on the plasma membrane is still unclear. Hence, in this work, we carried out μs-scale coarse-grained molecular dynamics (MD) simulations to reveal the interactions between DHA molecules and a model cell membrane. As is known, the cell membrane can segregate into liquid-ordered (Lo) and liquid-disordered (Ld) membrane domains due to the differential interactions between lipids and proteins. In order to capture this feature, we adopted the three-component phase-separated lipid membranes and considered both anionic and neutral DHA molecules in the current work. Our results showed that DHA molecules can spontaneously self-assemble into nanoclusters, fuse with lipid membranes, and localize preferably in Ld membrane domains. During the membrane fusion process, DHA molecules can change the intrinsic transmembrane potential of the lipid membrane, and the effects of anionic DHA molecules are much more significant. Besides, the presence of DHA molecules mainly in the Ld membrane domains could regulate the differences in the lipid chain order, membrane thickness, cholesterol preference, and cholesterol flip-flop basically in a concentration-dependent manner, which further promote the stability of the intraleaflet dynamics and inhibit the interleaflet dynamics (or promote membrane domain registration) of the membrane domains. In short, the impact of DHA molecules on the physical properties of a model cell membrane on the molecular level revealed in our work will provide useful insights for understanding the biological functions of DHA molecules.
Collapse
Affiliation(s)
- Xiu Li
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Shiying Zhou
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xubo Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| |
Collapse
|
10
|
Sharma A, Seal A, Iyer SS, Srivastava A. Enthalpic and entropic contributions to interleaflet coupling drive domain registration and antiregistration in biological membrane. Phys Rev E 2022; 105:044408. [PMID: 35590589 DOI: 10.1103/physreve.105.044408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/14/2022] [Indexed: 06/15/2023]
Abstract
Biological membrane is a complex self-assembly of lipids, sterols, and proteins organized as a fluid bilayer of two closely stacked lipid leaflets. Differential molecular interactions among its diverse constituents give rise to heterogeneities in the membrane lateral organization. Under certain conditions, heterogeneities in the two leaflets can be spatially synchronized and exist as registered domains across the bilayer. Several contrasting theories behind mechanisms that induce registration of nanoscale domains have been suggested. Following a recent study showing the effect of position of lipid tail unsaturation on domain registration behavior, we decided to develop an analytical theory to elucidate the driving forces that create and maintain domain registry across leaflets. Towards this, we formulated a Hamiltonian for a stacked lattice system where site variables capture the lipid molecular properties such as the position of unsaturation and various other interactions that could drive phase separation and interleaflet coupling. We solve the Hamiltonian using Monte Carlo simulations and create a complete phase diagram that reports the presence or absence of registered domains as a function of various Hamiltonian parameters. We find that the interleaflet coupling should be described as a competing enthalpic contribution due to interaction of lipid tail termini, primarily due to saturated-saturated interactions, and an interleaflet entropic contribution from overlap of unsaturated tail termini. A higher position of unsaturation is seen to provide weaker interleaflet coupling. Thermodynamically stable nanodomains could also be observed for certain points in the parameter space in our bilayer model, which were further verified by carrying out extended Monte Carlo simulations. These persistent noncoalescing registered nanodomains close to the lower end of the accepted nanodomain size range also point towards a possible "nanoscale" emulsion description of lateral heterogeneities in biological membrane leaflets.
Collapse
Affiliation(s)
- Akshara Sharma
- Department of Physics, Indian Institute of Science-Bangalore, C. V. Raman Road, Bangalore, Karnataka 560012, India
| | - Aniruddha Seal
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, Khurda, Odisha 752050, India
| | - Sahithya S Iyer
- 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
|
11
|
Lin X, Lin X. Designing amphiphilic Janus nanoparticles with tunable lipid raft affinity via molecular dynamics simulation. Biomater Sci 2021; 9:8249-8258. [PMID: 34757373 DOI: 10.1039/d1bm01364e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to the differential interactions among lipids and proteins, the plasma membrane can segregate into a series of functional nanoscale membrane domains ("lipid rafts"), which are essential in multiple biological processes such as signaling transduction, protein trafficking and endocytosis. On the other hand, Janus nanoparticles (NPs) have shown great promise in various biomedical applications due to their asymmetric characteristics and can integrate different surface properties and thus synergetic functions. Hence, in this work, we aim to design an amphiphilic Janus NP to target and regulate lipid rafts via tuning its surface ligand amphiphilicity using coarse-grained molecular dynamics (MD) simulations. Our μs-scale free coarse-grained MD simulations as well as umbrella sampling free energy calculations indicated that the hydrophobicity of the hydrophobic surface ligands not only determined the lateral membrane partitioning thermodynamics of Janus NPs in phase-separated lipid membranes, but also the difficulty in their insertion into different membrane domains of the lipid membrane. These two factors jointly regulated the lipid raft affinity of Janus NPs. Meanwhile, the hydrophilicity of the hydrophilic surface ligands could affect the insertion ability of Janus NPs. Besides, the ultra-small size could ensure the membrane-bound behavior of Janus NPs without disrupting the overall structure and phase separation kinetics of the lipid membrane. These results may provide valuable insights into the design of functional NPs targeting and controllably regulating lipid rafts.
Collapse
Affiliation(s)
- Xiaoqian Lin
- Institute of Single Cell Engineering, Key Laboratory of Ministry of Education for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China. .,Shen Yuan Honors College, Beihang University, Beijing 100191, China
| | - Xubo Lin
- Institute of Single Cell Engineering, Key Laboratory of Ministry of Education for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.
| |
Collapse
|
12
|
Smith P, Lorenz CD. LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations. J Chem Theory Comput 2021; 17:5907-5919. [PMID: 34450002 DOI: 10.1021/acs.jctc.1c00447] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations are now widely used to study emergent phenomena in lipid membranes with complex compositions. Here, we present LiPyphilic-a fast, fully tested, and easy-to-install Python package for analyzing such simulations. Analysis tools in LiPyphilic include the identification of cholesterol flip-flop events, the classification of local lipid environments, and the degree of interleaflet registration. LiPyphilic is both force field- and resolution-agnostic, and by using the powerful atom selection language of MDAnalysis, it can handle membranes with highly complex compositions. LiPyphilic also offers two on-the-fly trajectory transformations to (i) fix membranes split across periodic boundaries and (ii) perform nojump coordinate unwrapping. Our implementation of nojump unwrapping accounts for fluctuations in the box volume under the NPT ensemble-an issue that most current implementations have overlooked. The full documentation of LiPyphilic, including installation instructions and links to interactive online tutorials, is available at https://lipyphilic.readthedocs.io/en/latest.
Collapse
Affiliation(s)
- Paul Smith
- Department of Physics, King's College London, London WC2R 2LS, U.K
| | | |
Collapse
|
13
|
Lin X, Lin X. Surface ligand rigidity modulates lipid raft affinity of ultra-small hydrophobic nanoparticles: insights from molecular dynamics simulations. NANOSCALE 2021; 13:9825-9833. [PMID: 34032262 DOI: 10.1039/d1nr01563j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Differential preferences between lipids and proteins drive the formation of dynamical nanoscale membrane domains (lipid rafts), which play key roles in the proper functioning of cells. On the other hand, due to the potent physicochemical properties of nanoparticles (NPs), they have been widely used in drug delivery, bio-imaging and regulating various essential biological processes of the cells. Hence, in this work, we aim to design ultra-small hydrophobic NPs with tunable raft affinity, which is supposed to partition into the hydrophobic region of lipid membranes and be able to regulate the dynamics of the lipid raft domains. A series of μs-scale coarse-grained molecular dynamics simulations and umbrella sampling free energy calculations were performed to investigate the role of surface ligand rigidity of ultra-small hydrophobicNPs in their raft affinity. Our results indicated that the preferred localization of NPs can be tuned by adjusting their surface ligand rigidity. Generally, rigid NPs tended to target the raft domain, while soft NPs preferred the interface of the raft and non-raft domains. The free energy analysis further indicated that the surface ligand rigidity of NPs can enhance their targeting to lipid raft domains. Besides, we found that these ultra-small NPs had no significant effects on the phase separation of the lipid membrane although they might cause some local interference to surrounding lipids. These results indicate that the targeting to the lipid raft domain can be achieved by the surface ligand rigidity of NPs, which provides helpful insights for further regulations of lipid raft-mediated biological processes.
Collapse
Affiliation(s)
- Xiaoqian Lin
- Institute of Single Cell Engineering, Key Laboratory of Ministry of Education for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.
| | | |
Collapse
|
14
|
Otosu T, Yamaguchi S. Leaflet-specific Lipid Diffusion Revealed by Fluorescence Lifetime Correlation Analyses. CHEM LETT 2020. [DOI: 10.1246/cl.200539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Takuhiro Otosu
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Shoichi Yamaguchi
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| |
Collapse
|
15
|
Luo Y, Maibaum L. Modulated and spiral surface patterns on deformable lipid vesicles. J Chem Phys 2020; 153:144901. [PMID: 33086800 DOI: 10.1063/5.0020087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We investigate the behavior of two-dimensional systems that exhibit a transition between homogeneous and spatially inhomogeneous phases, which have spherical topology, and whose mechanical properties depend on the local value of the order parameter. One example of such a system is multicomponent lipid bilayer vesicles, which serve as a model to study cellular membranes. Under certain conditions, such bilayers separate into coexisting liquid-ordered and liquid-disordered regions. When arranged into the shape of small vesicles, this phase coexistence can result in spatial patterns that are more complex than the basic two-domain configuration encountered in typical bulk systems. The difference in bending rigidity between the liquid-ordered and liquid-disordered regions couples the shape of the vesicle to the local composition. We show that this interplay gives rise to a rich phase diagram that includes homogeneous, separated, and axisymmetric modulated phases that are divided by regions of spiral patterns in the surface morphology.
Collapse
Affiliation(s)
- Yongtian Luo
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| |
Collapse
|
16
|
Dorrell MW, Beaven AH, Sodt AJ. A combined molecular/continuum-modeling approach to predict the small-angle neutron scattering of curved membranes. Chem Phys Lipids 2020; 233:104983. [PMID: 33035544 DOI: 10.1016/j.chemphyslip.2020.104983] [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: 06/17/2020] [Revised: 09/20/2020] [Accepted: 09/28/2020] [Indexed: 11/16/2022]
Abstract
This paper develops a framework to compute the small-angle neutron scattering (SANS) from highly curved, dynamically fluctuating, and potentially inhomogeneous membranes. This method is needed to compute the scattering from nanometer-scale membrane domains that couple to curvature, as predicted by molecular modeling. The detailed neutron scattering length density of a small planar bilayer patch is readily available via molecular dynamics simulation. A mathematical, mechanical transformation of the planar scattering length density is developed to predict the scattering from curved bilayers. By simulating a fluctuating, curved, surface-continuum model, long time- and length-scales can be reached while, with the aid of the planar-to-curved transformation, the molecular features of the scattering length density can be retained. A test case for the method is developed by constructing a coarse-grained lipid vesicle following a protocol designed to relieve both the osmotic stress inside the vesicle and the lipid-number stress between the leaflets. A question was whether the hybrid model would be able to replicate the scattering from the highly deformed inner and outer leaflets of the small vesicle. Matching the scattering of the full (molecular vesicle) and hybrid (continuum vesicle) models indicated that the inner and outer leaflets of the full vesicle were expanded laterally, consistent with previous simulations of the Martini forcefield that showed thinning in small vesicles. The vesicle structure is inconsistent with a zero-tension leaflet deformed by a single set of elastic parameters, and the results show that this is evident in the scattering. The method can be applied to translate observations of any molecular model's neutron scattering length densities from small patches to large length and timescales.
Collapse
Affiliation(s)
- Mitchell W Dorrell
- Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, USA; Department of Physics and Astronomy, University of Delaware, Newark, DE, USA
| | - Andrew H Beaven
- Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, USA
| | - Alexander J Sodt
- Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, USA.
| |
Collapse
|
17
|
Direct imaging of liquid domains in membranes by cryo-electron tomography. Proc Natl Acad Sci U S A 2020; 117:19713-19719. [PMID: 32759217 DOI: 10.1073/pnas.2002245117] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Images of micrometer-scale domains in lipid bilayers have provided the gold standard of model-free evidence to understand the domains' shapes, sizes, and distributions. Corresponding techniques to directly and quantitatively assess smaller (nanoscale and submicron) liquid domains have been limited. Researchers commonly seek to correlate activities of membrane proteins with attributes of the domains in which they reside; doing so hinges on identification and characterization of membrane domains. Although some features of membrane domains can be probed by indirect methods, these methods are often constrained by the limitation that data must be analyzed in the context of models that require multiple assumptions or parameters. Here, we address this challenge by developing and testing two methods of identifying submicron domains in biomimetic membranes. Both methods leverage cryo-electron tomograms of ternary membranes under vitrified, hydrated conditions. The first method is optimized for probe-free applications: Domains are directly distinguished from the surrounding membrane by their thickness. This technique quantitatively and accurately measures area fractions of domains, in excellent agreement with known phase diagrams. The second method is optimized for applications in which a single label is deployed for imaging membranes by both high-resolution cryo-electron tomography and diffraction-limited optical microscopy. For this method, we test a panel of probes, find that a trimeric mCherry label performs best, and specify criteria for developing future high-performance, dual-use probes. These developments have led to direct and quantitative imaging of submicron membrane domains in vitrified, hydrated vesicles.
Collapse
|
18
|
Paulowski L, Donoghue A, Nehls C, Groth S, Koistinen M, Hagge SO, Böhling A, Winterhalter M, Gutsmann T. The Beauty of Asymmetric Membranes: Reconstitution of the Outer Membrane of Gram-Negative Bacteria. Front Cell Dev Biol 2020; 8:586. [PMID: 32766244 PMCID: PMC7381204 DOI: 10.3389/fcell.2020.00586] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/16/2020] [Indexed: 11/23/2022] Open
Abstract
The architecture of the lipid matrix of the outer membrane of Gram-negative bacteria is extremely asymmetric: Whereas the inner leaflet is composed of a phospholipid mixture, the outer leaflet is built up by glycolipids. For most Gram-negative species, these glycolipids are lipopolysaccharides (LPS), for a few species, however, glycosphingolipids. We demonstrate experimental approaches for the reconstitution of these asymmetric membranes as (i) solid supported membranes prepared by the Langmuir-Blodgett technique, (ii) planar lipid bilayers prepared by the Montal-Mueller technique, and (iii) giant unilamellar vesicles (GUVs) prepared by the phase transfer method. The asymmetric GUVs (aGUVs) composed of LPS on one leaflet are shown for the first time. They are characterized with respect to their phase behavior, flip-flop of lipids and their usability to investigate the interaction with membrane active peptides or proteins. For the antimicrobial peptide LL-32 and for the bacterial porin OmpF the specificity of the interaction with asymmetric membranes is shown. The three reconstitution systems are compared with respect to their usability to investigate domain formation and interactions with peptides and proteins.
Collapse
Affiliation(s)
- Laura Paulowski
- Division of Biophysics, Priority Research Area Infection, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- Division of Diagnostic Mycobacteriology, Priority Research Area Infection, National Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Annemarie Donoghue
- Division of Biophysics, Priority Research Area Infection, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- Department of Life Sciences & Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Christian Nehls
- Division of Biophysics, Priority Research Area Infection, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Sabrina Groth
- Division of Biophysics, Priority Research Area Infection, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Max Koistinen
- Division of Biophysics, Priority Research Area Infection, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Sven O. Hagge
- Division of Biophysics, Priority Research Area Infection, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Arne Böhling
- Division of Biophysics, Priority Research Area Infection, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Mathias Winterhalter
- Department of Life Sciences & Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Thomas Gutsmann
- Division of Biophysics, Priority Research Area Infection, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| |
Collapse
|
19
|
Mostofian B, Johnson QR, Smith JC, Cheng X. Carotenoids promote lateral packing and condensation of lipid membranes. Phys Chem Chem Phys 2020; 22:12281-12293. [PMID: 32432296 DOI: 10.1039/d0cp01031f] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Carotenoids are pigment molecules that protect biomembranes against degradation and may be involved in the formation of functional bacterial membrane microdomains. Little is known on whether different types of carotenoids have different effects on the membrane or if there is any concentration dependence of these effects. In this work, we present results from molecular dynamics simulations of phospholipid bilayers containing different amounts of either β-carotene or zeaxanthin. Both β-carotene and zeaxanthin show the ability to laterally condense the membrane lipids and reduce their inter-leaflet interactions. With increasing concentrations, both carotenoids increase the bilayer thickness and rigidity. The results reveal that carotenoids have similar effects to cholesterol on regulating the behavior of fluid-phase membranes, suggesting that they could function as sterol substitutes and confirming their potential role in the formation of functional membrane domains.
Collapse
Affiliation(s)
- Barmak Mostofian
- Center for Molecular Biophysics, Oak Ridge National Lab, Oak Ridge, TN 37830, USA.
| | | | | | | |
Collapse
|
20
|
Bolmatov D, Soloviov D, Zhernenkov M, Zav'yalov D, Mamontov E, Suvorov A, Cai YQ, Katsaras J. Molecular Picture of the Transient Nature of Lipid Rafts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4887-4896. [PMID: 32259453 DOI: 10.1021/acs.langmuir.0c00125] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In biological membranes, lipid rafts are now thought to be transient and nanoscopic. However, the mechanism responsible for these nanoscopic assemblies remains poorly understood, even in the case of model membranes. As a result, it has proven extremely challenging to probe the physicochemical properties of lipid rafts at the molecular level. Here, we use all-atom molecular dynamics (MD) simulations and inelastic X-ray scattering (IXS), an intrinsically nanoscale technique, to directly probe the energy transfer and collective short-wavelength dynamics (phonons) of biologically relevant model membranes. We show that the nanoscale propagation of stress in lipid rafts takes place in the form of collective motions made up of longitudinal (compression waves) and transverse (shear waves) molecular vibrations. Importantly, we provide a molecular picture for the so-called van der Waals mediated "force from lipid" [Anishkin, A. et al. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 7898], a key parameter for the ionic channel mechano-transduction and the mechanism for the lipid transfer of molecular level stress [Aponte-Santamarı́a, C. et al. J. Am. Chem. Soc. 2017, 139, 13588]. Specifically, we describe how lipid rafts are formed and maintained through the propagation of molecular stress, lipid raft rattling dynamics, and a relaxation process. Eventually, the rafts dissipate through the self-diffusion of lipids making up the rafts. We also show that the molecular stress and viscoelastic properties of transient lipid rafts can be modulated through the use of hydrophobic biomolecules such as melatonin and tryptophan. Ultimately, the herein proposed mechanism describing the molecular interactions for the formation and dissolution of lipid rafts may offer insights as to how lipid rafts enable biological function.
Collapse
Affiliation(s)
- Dima Bolmatov
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Dmytro Soloviov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia
- Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Kyiv 03680, Ukraine
| | - Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | | | - Eugene Mamontov
- Spectroscopy Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Alexey Suvorov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - John Katsaras
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
| |
Collapse
|
21
|
Ou L, Corradi V, Tieleman DP, Liang Q. Atomistic Simulations on Interactions between Amphiphilic Janus Nanoparticles and Lipid Bilayers: Effects of Lipid Ordering and Leaflet Asymmetry. J Phys Chem B 2020; 124:4466-4475. [DOI: 10.1021/acs.jpcb.9b11989] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luping Ou
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| | - Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| |
Collapse
|
22
|
Saitov A, Akimov SA, Galimzyanov TR, Glasnov T, Pohl P. Ordered Lipid Domains Assemble via Concerted Recruitment of Constituents from Both Membrane Leaflets. PHYSICAL REVIEW LETTERS 2020; 124:108102. [PMID: 32216409 PMCID: PMC7115998 DOI: 10.1103/physrevlett.124.108102] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 02/26/2020] [Indexed: 06/10/2023]
Abstract
Lipid rafts serve as anchoring platforms for membrane proteins. Thus far they escaped direct observation by light microscopy due to their small size. Here we used differently colored dyes as reporters for the registration of both ordered and disordered lipids from the two leaves of a freestanding bilayer. Photoswitchable lipids dissolved or reformed the domains. Measurements of domain mobility indicated the presence of 120 nm wide ordered and 40 nm wide disordered domains. These sizes are in line with the predicted roles of line tension and membrane undulation as driving forces for alignment.
Collapse
Affiliation(s)
- Ali Saitov
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstraße 40, Linz 4020, Austria
| | - Sergey A Akimov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy prospekt, Moscow 119071, Russia
| | - Timur R Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy prospekt, Moscow 119071, Russia
| | - Toma Glasnov
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010 Graz, Austria
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstraße 40, Linz 4020, Austria
| |
Collapse
|
23
|
Gu RX, Baoukina S, Tieleman DP. Phase Separation in Atomistic Simulations of Model Membranes. J Am Chem Soc 2020; 142:2844-2856. [DOI: 10.1021/jacs.9b11057] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ruo-Xu Gu
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
| | - Svetlana Baoukina
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
| |
Collapse
|
24
|
Rajagopal N, Irudayanathan FJ, Nangia S. Computational Nanoscopy of Tight Junctions at the Blood-Brain Barrier Interface. Int J Mol Sci 2019; 20:E5583. [PMID: 31717316 PMCID: PMC6888702 DOI: 10.3390/ijms20225583] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022] Open
Abstract
The selectivity of the blood-brain barrier (BBB) is primarily maintained by tight junctions (TJs), which act as gatekeepers of the paracellular space by blocking blood-borne toxins, drugs, and pathogens from entering the brain. The BBB presents a significant challenge in designing neurotherapeutics, so a comprehensive understanding of the TJ architecture can aid in the design of novel therapeutics. Unraveling the intricacies of TJs with conventional experimental techniques alone is challenging, but recently developed computational tools can provide a valuable molecular-level understanding of TJ architecture. We employed the computational methods toolkit to investigate claudin-5, a highly expressed TJ protein at the BBB interface. Our approach started with the prediction of claudin-5 structure, evaluation of stable dimer conformations and nanoscale assemblies, followed by the impact of lipid environments, and posttranslational modifications on these claudin-5 assemblies. These led to the study of TJ pores and barriers and finally understanding of ion and small molecule transport through the TJs. Some of these in silico, molecular-level findings, will need to be corroborated by future experiments. The resulting understanding can be advantageous towards the eventual goal of drug delivery across the BBB. This review provides key insights gleaned from a series of state-of-the-art nanoscale simulations (or computational nanoscopy studies) performed on the TJ architecture.
Collapse
Affiliation(s)
| | | | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
| |
Collapse
|
25
|
Zhang S, Lin X. Lipid Acyl Chain cis Double Bond Position Modulates Membrane Domain Registration/Anti-Registration. J Am Chem Soc 2019; 141:15884-15890. [DOI: 10.1021/jacs.9b06977] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Siya Zhang
- Institute of Nanotechnology for Single Cell Analysis (INSCA), Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China
- State Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Peking Union Medical College and Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Xubo Lin
- Institute of Nanotechnology for Single Cell Analysis (INSCA), Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| |
Collapse
|
26
|
Role of Transmembrane Proteins for Phase Separation and Domain Registration in Asymmetric Lipid Bilayers. Biomolecules 2019; 9:biom9080303. [PMID: 31349669 PMCID: PMC6723173 DOI: 10.3390/biom9080303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 02/05/2023] Open
Abstract
It is well known that the formation and spatial correlation of lipid domains in the two apposed leaflets of a bilayer are influenced by weak lipid–lipid interactions across the bilayer’s midplane. Transmembrane proteins span through both leaflets and thus offer an alternative domain coupling mechanism. Using a mean-field approximation of a simple bilayer-type lattice model, with two two-dimensional lattices stacked one on top of the other, we explore the role of this “structural” inter-leaflet coupling for the ability of a lipid membrane to phase separate and form spatially correlated domains. We present calculated phase diagrams for various effective lipid–lipid and lipid–protein interaction strengths in membranes that contain a binary lipid mixture in each leaflet plus a small amount of added transmembrane proteins. The influence of the transmembrane nature of the proteins is assessed by a comparison with “peripheral” proteins, which result from the separation of one single integral protein into two independent units that are no longer structurally connected across the bilayer. We demonstrate that the ability of membrane-spanning proteins to facilitate domain formation requires sufficiently strong lipid–protein interactions. Weak lipid–protein interactions generally tend to inhibit phase separation in a similar manner for transmembrane as for peripheral proteins.
Collapse
|
27
|
Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 410] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
Collapse
Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| |
Collapse
|
28
|
Weiner MD, Feigenson GW. Molecular Dynamics Simulations Reveal Leaflet Coupling in Compositionally Asymmetric Phase-Separated Lipid Membranes. J Phys Chem B 2019; 123:3968-3975. [PMID: 31009218 DOI: 10.1021/acs.jpcb.9b03488] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The eukaryotic plasma membrane has an asymmetric distribution of its component lipids. Rafts that result from liquid-liquid phase separation are a feature of its exoplasmic leaflet, but how these exoplasmic leaflet domains are coupled to the cytoplasmic leaflet is not understood. These rafts can be studied in model membranes of three-component mixtures that produce coexisting liquid ordered (Lo) and liquid disordered (Ld) domains. We conducted all-atom molecular dynamics simulations of compositionally asymmetric lipid bilayers that reflect a more realistic model of the plasma membrane. One leaflet contained phase-separated domains with phosphatidylcholine and cholesterol, representing the exoplasmic leaflet, whereas the other contained phosphatidylethanolamine, phosphatidylserine, and cholesterol, which are the predominant components of the cytoplasmic leaflet. Inspired by findings of domain alignment across the two leaflets in compositionally symmetric model membranes, we examined the coupling between the two leaflets to see how the single-phase cytoplasmic leaflet would respond to phase separation in the other leaflet and if information could be communicated across the membrane. We found the region of the single-phase leaflet apposing the Lo domain to be slightly more ordered and thicker than the region apposing the Ld domain. The region across from the Lo domain is somewhat enriched in cholesterol and significantly depleted of polyunsaturated lipids.
Collapse
|
29
|
Hu J, Lou Y, Wu F. Improved Intracellular Delivery of Polyarginine Peptides with Cargoes. J Phys Chem B 2019; 123:2636-2644. [PMID: 30830784 DOI: 10.1021/acs.jpcb.8b10483] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complementary to endocytosis, cell-penetrating peptides (CPPs) at high concentrations can penetrate the cell membrane in a direct way, which further makes CPPs popular candidates for delivering therapeutic or diagnostic agents. Although featured as rapid uptake, the translocation efficiency and potential toxicity of the direct penetration are usually affected by cargoes, which is still unclear. Here, using coarse-grained molecular dynamics simulations, we show that the polyarginine (R8) peptides penetrate the membrane through a water pore in the membrane, and the transmembrane efficiency is improved by conjugating to small nanoparticles (NPs) with proper linkers. It can be attributed to both the extension of the lifetime of the water pore by the NPs and outward diffusion of negative lipids in the asymmetry membrane, which induces the surrounding R8-NP conjugates to the water pore before it is closed. The translocation efficiency is closely related to the length of the linkers, and it gets the maximum value when the length of the linkers is around half of the membrane thickness. Overlong linkers not only decrease the transmembrane efficiency because of the blockage of NPs in the water pore but may also cause cytotoxicity because of the unclosed water pore. The results provide insights into the internalization of CPPs and facilitate the design of CPP and drug conjugates with high efficiency and low toxicity.
Collapse
Affiliation(s)
- Juanmei Hu
- Key Laboratory of Optical Field Manipulation & Center for Optoelectronics Materials and Devices of Zhejiang Province, Department of Physics , Zhejiang Sci-Tech University , Hangzhou 310018 , China
| | - Yimin Lou
- Key Laboratory of Optical Field Manipulation & Center for Optoelectronics Materials and Devices of Zhejiang Province, Department of Physics , Zhejiang Sci-Tech University , Hangzhou 310018 , China
| | - Fengmin Wu
- Key Laboratory of Optical Field Manipulation & Center for Optoelectronics Materials and Devices of Zhejiang Province, Department of Physics , Zhejiang Sci-Tech University , Hangzhou 310018 , China
| |
Collapse
|
30
|
Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
Collapse
Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
| |
Collapse
|
31
|
Oh Y, Sung BJ. Facilitated and Non-Gaussian Diffusion of Cholesterol in Liquid Ordered Phase Bilayers Depends on the Flip-Flop and Spatial Arrangement of Cholesterol. J Phys Chem Lett 2018; 9:6529-6535. [PMID: 30346769 DOI: 10.1021/acs.jpclett.8b02982] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The diffusion of cholesterol in biological membranes is critical to cellular processes such as the formation of cholesterol-enriched domains. The cholesterol diffusion may be complicated especially when cholesterol flip-flops and/or stays at the membrane center. Understanding the diffusion mechanism of cholesterol at a molecular level should be, therefore, a topic of interest. We perform molecular dynamics simulations up to 100 μs for lipid bilayers with various concentrations of cholesterol. We find that cholesterol diffusion in the liquid ordered phase depends on whether it is within leaflets or at the bilayer center, is non-Gaussian for several microseconds, and is enhanced significantly compared to that of lipids. Cholesterol at the bilayer center diffuses fast, while cholesterol in the hydrocarbon region with upright orientation diffuses relatively slowly. Such position-dependent dynamics of cholesterol leads to facilitated and non-Gaussian diffusion.
Collapse
Affiliation(s)
- Younghoon Oh
- Department of Chemistry and Research Institute for Basic Science , Sogang University , Seoul 04107 , Republic of Korea
| | - Bong June Sung
- Department of Chemistry and Research Institute for Basic Science , Sogang University , Seoul 04107 , Republic of Korea
| |
Collapse
|
32
|
Pantelopulos GA, Straub JE. Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation. Biophys J 2018; 115:2167-2178. [PMID: 30414630 DOI: 10.1016/j.bpj.2018.10.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 10/11/2018] [Accepted: 10/16/2018] [Indexed: 01/06/2023] Open
Abstract
Cholesterol is essential to the formation of phase-separated lipid domains in membranes. Lipid domains can exist in different thermodynamic phases depending on the molecular composition and play significant roles in determining structure and function of membrane proteins. We investigate the role of cholesterol in the structure and dynamics of ternary lipid mixtures displaying phase separation using molecular dynamics simulations, employing a physiologically relevant span of cholesterol concentration. We find that cholesterol can induce formation of three regimes of phase behavior: 1) miscible liquid-disordered bulk, 2) phase-separated, domain-registered coexistence of liquid-disordered and liquid-ordered domains, and 3) phase-separated, domain-antiregistered coexistence of liquid-disordered and newly identified nanoscopic gel domains composed of cholesterol threads we name "cholesterolic gel" domains. These findings are validated and discussed in the context of current experimental knowledge, models of cholesterol spatial distributions, and models of ternary lipid-mixture phase separation.
Collapse
Affiliation(s)
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts.
| |
Collapse
|
33
|
Effects of Passive Phospholipid Flip-Flop and Asymmetric External Fields on Bilayer Phase Equilibria. Biophys J 2018; 115:1956-1965. [PMID: 30393103 DOI: 10.1016/j.bpj.2018.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/21/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
Compositional asymmetry between the leaflets of bilayer membranes modifies their phase behavior and is thought to influence other important features such as mechanical properties and protein activity. We address here how phase behavior is affected by passive phospholipid flip-flop, such that the compositional asymmetry is not fixed. We predict transitions from "pre-flip-flop" behavior to a restricted set of phase equilibria that can persist in the presence of passive flip-flop. Surprisingly, such states are not necessarily symmetric. We further account for external symmetry breaking, such as a preferential substrate interaction, and show how this can stabilize strongly asymmetric equilibrium states. Our theory explains several experimental observations of flip-flop-mediated changes in phase behavior and shows how domain formation and compositional asymmetry can be controlled in concert, by manipulating passive flip-flop rates and applying external fields.
Collapse
|
34
|
Thallmair S, Ingólfsson HI, Marrink SJ. Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models. J Phys Chem Lett 2018; 9:5527-5533. [PMID: 30192549 PMCID: PMC6151656 DOI: 10.1021/acs.jpclett.8b01877] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/07/2018] [Indexed: 05/25/2023]
Abstract
The plasma membrane is a highly complex multicomponent system that is central to the functioning of cells. Cholesterol, a key lipid component of the plasma membrane, promotes the formation of nanodomains. These nanodomains are often correlated across the two membrane leaflets, but the underlying physical mechanism remains unclear. Using coarse-grained molecular dynamics simulations, we investigate the influence of cholesterol flip-flop on membrane properties, in particular, the interleaflet coupling of cholesterol-enriched domains. We show that the cholesterol density correlation between the leaflets of an average mammalian plasma membrane is significantly reduced by suppressing interleaflet cholesterol population. Our results suggest an amplifying role of cholesterol in signal transduction across the leaflets.
Collapse
Affiliation(s)
- Sebastian Thallmair
- Groningen
Biomolecular Sciences and Biotechnology Institute and The Zernike
Institute for Advanced Material, University
of Groningen, Nijenborgh
7, 9747 AG Groningen, Netherlands
| | - Helgi I. Ingólfsson
- Groningen
Biomolecular Sciences and Biotechnology Institute and The Zernike
Institute for Advanced Material, University
of Groningen, Nijenborgh
7, 9747 AG Groningen, Netherlands
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, 94550 California, United States
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and The Zernike
Institute for Advanced Material, University
of Groningen, Nijenborgh
7, 9747 AG Groningen, Netherlands
| |
Collapse
|
35
|
Weiner MD, Feigenson GW. Presence and Role of Midplane Cholesterol in Lipid Bilayers Containing Registered or Antiregistered Phase Domains. J Phys Chem B 2018; 122:8193-8200. [DOI: 10.1021/acs.jpcb.8b03949] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
36
|
Yang K, Yang R, Tian X, He K, Filbrun SL, Fang N, Ma Y, Yuan B. Partitioning of nanoscale particles on a heterogeneous multicomponent lipid bilayer. Phys Chem Chem Phys 2018; 20:28241-28248. [DOI: 10.1039/c8cp05710a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Partitioning of nanoparticles into different lipid phases of a cell membrane is regulated by the physical properties of both the membrane and nanoparticles.
Collapse
Affiliation(s)
- Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology
- Soochow University
- Suzhou
- P. R. China
- Jiangsu Key Laboratory of Thin Films
| | - Ran Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology
- Soochow University
- Suzhou
- P. R. China
| | - Xiaodong Tian
- Department of Thoracic Surgery
- Chinese PLA General Hospital
- Beijing
- P. R. China
| | - Kejie He
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology
- Soochow University
- Suzhou
- P. R. China
| | | | - Ning Fang
- Department of Chemistry
- Georgia State University
- Atlanta
- USA
| | - Yuqiang Ma
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology
- Soochow University
- Suzhou
- P. R. China
- National Laboratory of Solid State Microstructures and Department of Physics
| | - Bing Yuan
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology
- Soochow University
- Suzhou
- P. R. China
- Jiangsu Key Laboratory of Thin Films
| |
Collapse
|
37
|
Duncan AL, Reddy T, Koldsø H, Hélie J, Fowler PW, Chavent M, Sansom MSP. Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes. Sci Rep 2017; 7:16647. [PMID: 29192147 PMCID: PMC5709381 DOI: 10.1038/s41598-017-16865-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/15/2017] [Indexed: 01/07/2023] Open
Abstract
Cell membranes are crowded and complex environments. To investigate the effect of protein-lipid interactions on dynamic organization in mammalian cell membranes, we have performed coarse-grained molecular dynamics simulations containing >100 copies of an inwardly rectifying potassium (Kir) channel which forms specific interactions with the regulatory lipid phosphatidylinositol 4,5-bisphosphate (PIP2). The tendency of protein molecules to cluster has the effect of organizing the membrane into dynamic compartments. At the same time, the diversity of lipids present has a marked effect on the clustering behavior of ion channels. Sub-diffusion of proteins and lipids is observed. Protein crowding alters the sub-diffusive behavior of proteins and lipids such as PIP2 which interact tightly with Kir channels. Protein crowding also affects bilayer properties, such as membrane undulations and bending rigidity, in a PIP2-dependent manner. This interplay between the diffusion and the dynamic organization of Kir channels may have important implications for channel function.
Collapse
Affiliation(s)
- Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Tyler Reddy
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- T-6, MS K710, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- D. E. Shaw Research, 120 W 45th St., New York, NY, 10036, USA
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Semmle, Blue Boar Court, 9 Alfred St, Oxford, OX1 4EH, UK
| | - Philip W Fowler
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- IPBS-CNRS, Toulouse, Midi-Pyrénées, France
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| |
Collapse
|
38
|
Haataja MP. Lipid Domain Co-localization Induced by Membrane Undulations. Biophys J 2017; 112:655-662. [PMID: 28256225 DOI: 10.1016/j.bpj.2016.12.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/11/2016] [Accepted: 12/19/2016] [Indexed: 12/28/2022] Open
Abstract
Multicomponent lipid bilayer membranes display rich phase transition and associated compositional lipid domain formation behavior. When both leaflets of the bilayer contain domains, they are often found co-localized across the leaflets, implying the presence of a thermodynamic interleaflet coupling. In this work, it is demonstrated that fluctuation-induced interactions between domains embedded within opposing membrane leaflets provide a robust means to co-localize the domains. In particular, it is shown via a combination of a mode-counting argument, a perturbative calculation, and a non-perturbative treatment of a special case, that spatial variations in membrane bending rigidity associated with lipid domains embedded within the background phase always lead to an attractive interleaflet coupling with a magnitude of ∼0.01kBT/nm2 in simple model membrane systems. Finally, it is demonstrated that the fluctuation-induced coupling is very robust against membrane tension and substrate interactions.
Collapse
Affiliation(s)
- Mikko P Haataja
- Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey.
| |
Collapse
|
39
|
Belička M, Weitzer A, Pabst G. High-resolution structure of coexisting nanoscopic and microscopic lipid domains. SOFT MATTER 2017; 13:1823-1833. [PMID: 28170020 DOI: 10.1039/c6sm02727j] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We studied coexisting micro- and nanoscopic liquid-ordered/liquid-disordered domains in fully hydrated multilamellar vesicles using small-angle X-ray scattering. Large domains exhibited long-range out-of-plane positional correlations of like domains, consistent with previous reports. In contrast, such correlations were absent in nanoscopic domains. Advancing a global analysis of the in situ data allowed us to gain a deep insight into the structural and elastic properties of the coexisting domains, including the partitioning of cholesterol in each domain. In agreement with a previous report, we found that the thickness mismatch between ordered and disordered domains decreased for nanoscopic domains. At the same time, we found also the lipid packing mismatch to be decreased for nano-domains, mainly due to the liquid-disordered domains becoming more densely packed when decreasing their size.
Collapse
Affiliation(s)
- Michal Belička
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Humboldtstr. 50/III, A-8010 Graz, Austria. and BioTechMed-Graz, A-8010 Graz, Austria
| | - Anna Weitzer
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Humboldtstr. 50/III, A-8010 Graz, Austria. and BioTechMed-Graz, A-8010 Graz, Austria
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Humboldtstr. 50/III, A-8010 Graz, Austria. and BioTechMed-Graz, A-8010 Graz, Austria
| |
Collapse
|
40
|
Fujimoto T, Parmryd I. Interleaflet Coupling, Pinning, and Leaflet Asymmetry-Major Players in Plasma Membrane Nanodomain Formation. Front Cell Dev Biol 2017; 4:155. [PMID: 28119914 PMCID: PMC5222840 DOI: 10.3389/fcell.2016.00155] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/27/2016] [Indexed: 01/26/2023] Open
Abstract
The plasma membrane has a highly asymmetric distribution of lipids and contains dynamic nanodomains many of which are liquid entities surrounded by a second, slightly different, liquid environment. Contributing to the dynamics is a continuous repartitioning of components between the two types of liquids and transient links between lipids and proteins, both to extracellular matrix and cytoplasmic components, that temporarily pin membrane constituents. This make plasma membrane nanodomains exceptionally challenging to study and much of what is known about membrane domains has been deduced from studies on model membranes at equilibrium. However, living cells are by definition not at equilibrium and lipids are distributed asymmetrically with inositol phospholipids, phosphatidylethanolamines and phosphatidylserines confined mostly to the inner leaflet and glyco- and sphingolipids to the outer leaflet. Moreover, each phospholipid group encompasses a wealth of species with different acyl chain combinations whose lateral distribution is heterogeneous. It is becoming increasingly clear that asymmetry and pinning play important roles in plasma membrane nanodomain formation and coupling between the two lipid monolayers. How asymmetry, pinning, and interdigitation contribute to the plasma membrane organization is only beginning to be unraveled and here we discuss their roles and interdependence.
Collapse
Affiliation(s)
- Toyoshi Fujimoto
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine Nagoya, Japan
| | - Ingela Parmryd
- Science for Life Laboratory, Medical Cell Biology, Uppsala University Uppsala, Sweden
| |
Collapse
|
41
|
Fujimoto T, Parmryd I. Interleaflet Coupling, Pinning, and Leaflet Asymmetry-Major Players in Plasma Membrane Nanodomain Formation. Front Cell Dev Biol 2016. [PMID: 28119914 DOI: 10.3389/fcell.2016.0015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
The plasma membrane has a highly asymmetric distribution of lipids and contains dynamic nanodomains many of which are liquid entities surrounded by a second, slightly different, liquid environment. Contributing to the dynamics is a continuous repartitioning of components between the two types of liquids and transient links between lipids and proteins, both to extracellular matrix and cytoplasmic components, that temporarily pin membrane constituents. This make plasma membrane nanodomains exceptionally challenging to study and much of what is known about membrane domains has been deduced from studies on model membranes at equilibrium. However, living cells are by definition not at equilibrium and lipids are distributed asymmetrically with inositol phospholipids, phosphatidylethanolamines and phosphatidylserines confined mostly to the inner leaflet and glyco- and sphingolipids to the outer leaflet. Moreover, each phospholipid group encompasses a wealth of species with different acyl chain combinations whose lateral distribution is heterogeneous. It is becoming increasingly clear that asymmetry and pinning play important roles in plasma membrane nanodomain formation and coupling between the two lipid monolayers. How asymmetry, pinning, and interdigitation contribute to the plasma membrane organization is only beginning to be unraveled and here we discuss their roles and interdependence.
Collapse
Affiliation(s)
- Toyoshi Fujimoto
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine Nagoya, Japan
| | - Ingela Parmryd
- Science for Life Laboratory, Medical Cell Biology, Uppsala University Uppsala, Sweden
| |
Collapse
|