1
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Hossein A, Beaven AH, Sapp K, Sodt AJ. Softening in Two-Component Lipid Mixtures by Spontaneous Curvature Variance. J Phys Chem B 2024; 128:6317-6326. [PMID: 38889363 DOI: 10.1021/acs.jpcb.3c08117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The bending modulus of a lipid bilayer quantifies its mechanical resistance to curvature. It is typically understood in terms of thickness; e.g., thicker bilayers are usually stiffer. Here, we describe an additional and powerful molecular determinant of stiffness─the variance in the distribution of curvature sensitivity of lipids and lipid conformations. Zwitterionic choline and ethanolamine headgroups of glycerophospholipids dynamically explore inter- and intraspecies interactions, leading to transient clustering. We demonstrate that these clusters couple strongly to negative curvature, exciting undulatory membrane modes and reducing the apparent bending modulus. Three force fields (Martini 2, Martini 3, and all-atom CHARMM C36) each show the effect to a different extent, with the coarse-grained Martini models showing the most clustering and thus the most softening. The theory is a guide to understanding the stiffness of biological membranes with their complex composition, as well as how choices of force field parameterization are translated into mechanical stiffness.
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Affiliation(s)
- Amirali Hossein
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892, United States
| | - Andrew H Beaven
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892, United States
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, Bethesda, Maryland 20892, United States
| | - Kayla Sapp
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892, United States
| | - Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892, United States
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2
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Park S, Rice A, Im W, Pastor RW. Spontaneous curvature generation by peptides in asymmetric bilayers. J Comput Chem 2024; 45:512-522. [PMID: 37991280 PMCID: PMC10922693 DOI: 10.1002/jcc.27261] [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: 07/11/2023] [Revised: 09/30/2023] [Accepted: 11/05/2023] [Indexed: 11/23/2023]
Abstract
Peptides and proteins play crucial roles in membrane remodeling by inducing spontaneous curvature. However, extracting spontaneous curvatures from simulations of asymmetric bilayers is challenging because differential stress (i.e., the difference of the leaflet surface tensions) arising from leaflet area strains can vary substantially among initial conditions. This study investigates peptide-induced spontaneous curvatureδc 0 p in asymmetric bilayers consisting of a single lipid type and a peptide confined to one leaflet;δc 0 p is calculated from the Helfrich equation using the first moment of the lateral pressure tensor and an alternative expression using the differential stress. It is shown that differential stress introduced during initial system generation is effectively relaxed by equilibrating using P21 periodic boundary conditions, which allows lipids to switch leaflets across cell boundaries and equalize their chemical potentials across leaflets. This procedure leads to robust estimates ofδc 0 p for the systems simulated, and is recommended when equality of chemical potentials between the leaflets is a primary consideration.
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Affiliation(s)
- Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Amy Rice
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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3
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Beaven AH, Bikkumalla V, Chon NL, Matthews AE, Lin H, Knight JD, Sodt AJ. Synaptotagmin 7 C2 domains induce membrane curvature stress via electrostatic interactions and the wedge mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575084. [PMID: 38313280 PMCID: PMC10837831 DOI: 10.1101/2024.01.10.575084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Synaptotagmin 7 (Syt-7) is part of the synaptotagmin protein family that regulates exocytotic lipid membrane fusion. Among the family, Syt-7 stands out by its membrane binding strength and stabilization of long-lived membrane fusion pores. Given that Syt-7 vesicles form long-lived fusion pores, we hypothesize that its interactions with the membrane stabilize the specific curvatures, thicknesses, and lipid compositions that support a metastable fusion pore. Using all-atom molecular dynamics simulations and FRET-based assays of Syt-7's membrane-binding C2 domains (C2A and C2B), we found that Syt-7 C2 domains sequester anionic lipids, are sensitive to cholesterol, thin membranes, and generate lipid membrane curvature by two competing, but related mechanisms. First, Syt-7 forms strong electrostatic contacts with the membrane, generating negative curvature stress. Second, Syt-7's calcium binding loops embed in the membrane surface, acting as a wedge to thin the membrane and induce positive curvature stress. These curvature mechanisms are linked by the protein insertion depth as well as the resulting protein tilt. Simplified quantitative models of the curvature-generating mechanisms link simulation observables to their membrane-reshaping effectiveness.
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Affiliation(s)
- Andrew H. Beaven
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD
| | | | - Nara L. Chon
- Department of Chemistry, University of Colorado Denver, Denver, CO
| | | | - Hai Lin
- Department of Chemistry, University of Colorado Denver, Denver, CO
| | | | - Alexander J. Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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4
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Pajtinka P, Vácha R. Amphipathic Helices Can Sense Both Positive and Negative Curvatures of Lipid Membranes. J Phys Chem Lett 2024; 15:175-179. [PMID: 38153203 PMCID: PMC10788957 DOI: 10.1021/acs.jpclett.3c02785] [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: 10/06/2023] [Revised: 12/09/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023]
Abstract
Curvature sensing is an essential ability of biomolecules to preferentially localize to membrane regions of a specific curvature. It has been shown that amphipathic helices (AHs), helical peptides with both hydrophilic and hydrophobic regions, could sense a positive membrane curvature. The origin of this AH sensing has been attributed to their ability to exploit lipid-packing defects that are enhanced in regions of positive curvature. In this study, we revisit an alternative framework where AHs act as sensors of local internal stress within the membrane, suggesting the possibility of an AH sensing a negative membrane curvature. Using molecular dynamics simulations, we gradually tuned the hydrophobicity of AHs, thereby adjusting their insertion depth so that the curvature preference of AHs is switched from positive to negative. This study suggests that highly hydrophobic AHs could preferentially localize proteins to regions of a negative membrane curvature.
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Affiliation(s)
- Peter Pajtinka
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Robert Vácha
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department
of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech
Republic
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5
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Hossein A, Beaven AH, Sapp K, Sodt AJ. Softening in two-component lipid mixtures by spontaneous curvature variance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571323. [PMID: 38168180 PMCID: PMC10760180 DOI: 10.1101/2023.12.12.571323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The bending modulus of a lipid bilayer quantifies its mechanical resistance to curvature. It is typically understood in terms of thickness, e.g., thicker bilayers are stiffer. Here, we describe an additional and powerful molecular determinant of stiffness - the variance in the distribution of curvature sensitivity of lipids and lipid conformations. Zwitterionic choline and ethanolamine head-groups of glycero-phospholipids dynamically explore inter- and intra-species interactions, leading to transient clustering. We demonstrate that these clusters couple strongly to negative curvature, exciting undulatory membrane modes and reducing the apparent bending modulus. Three forcefields (Martini 2, Martini 3, and all-atom CHARMM C36) each show the effect to a different extent, with the coarse-grained Martini models showing the most clustering and thus the most softening. The theory is a guide to understanding the stiffness of biological membranes with their complex composition, as well as how choices of forcefield parameterization are translated into mechanical stiffness.
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Affiliation(s)
- Amirali Hossein
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, United States
| | - Andrew H Beaven
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, United States
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, Bethesda, MD 20892, United States
| | - Kayla Sapp
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, United States
| | - Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, United States
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6
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Rombouts J, Elliott J, Erzberger A. Forceful patterning: theoretical principles of mechanochemical pattern formation. EMBO Rep 2023; 24:e57739. [PMID: 37916772 DOI: 10.15252/embr.202357739] [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: 06/30/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
Biological pattern formation is essential for generating and maintaining spatial structures from the scale of a single cell to tissues and even collections of organisms. Besides biochemical interactions, there is an important role for mechanical and geometrical features in the generation of patterns. We review the theoretical principles underlying different types of mechanochemical pattern formation across spatial scales and levels of biological organization.
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Affiliation(s)
- Jan Rombouts
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jenna Elliott
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Anna Erzberger
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
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7
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Kondrashov OV, Akimov SA. Alteration of Average Thickness of Lipid Bilayer by Membrane-Deforming Inclusions. Biomolecules 2023; 13:1731. [PMID: 38136602 PMCID: PMC10741968 DOI: 10.3390/biom13121731] [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: 11/10/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Thickness of lipid bilayer membranes is a key physical parameter determining membrane permeability and stability with respect to formation of through pores. Most membrane inclusions or impurities like amphipathic peptides, transmembrane peptides, lipid inclusions of a different molecular shape, lipid domains, and protein-lipid domains, locally deform the membrane. The detailed structure of the locally deformed region of the membrane is a kind of "fingerprint" for the inclusion type. However, most experimental methods allow determining only averaged parameters of membranes with incorporated inclusions, thus preventing the direct obtaining of the characteristics of the inclusion. Here we developed a model that allows the obtaining of characteristic parameters of three types of membrane inclusions (amphipathic peptides, transmembrane peptides, monolayer lipid patches) from experimentally observable dependencies of the average thickness of lipid bilayer on the surface concentration of the inclusions. In the case of amphipathic peptides, the model provided the peptide parameters that were in qualitative agreement with the available experimental data.
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Affiliation(s)
- Oleg V. Kondrashov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
| | - Sergey A. Akimov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
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8
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Punia R, Goel G. Free Energy Surface and Molecular Mechanism of Slow Structural Transitions in Lipid Bilayers. J Chem Theory Comput 2023; 19:8245-8257. [PMID: 37947833 DOI: 10.1021/acs.jctc.3c00856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Lipid membrane remodeling, crucial for many cellular processes, is governed by the coupling of membrane structure and shape fluctuations. Given the importance of the ∼ nm length scale, details of the transition intermediates for conformational change are not fully captured by a continuum-mechanical description. Slow dynamics and the lack of knowledge of reaction coordinates (RCs) for biasing methods pose a challenge for all-atom (AA) simulations. Here, we map system dynamics on Langevin dynamics in a normal mode space determined from an elastic network model representation for the lipid-water Hamiltonian. AA molecular dynamics (MD) simulations are used to determine model parameters, and Langevin dynamics predictions for bilayer structural, mechanical, and dynamic properties are validated against MD simulations and experiments. Transferability to describe the dynamics of a larger lipid bilayer and a heterogeneous membrane-protein system is assessed. A set of generic RCs for pore formation in two tensionless bilayers is obtained by coupling Langevin dynamics to the underlying energy landscape for membrane deformations. Structure evolution is carried out by AA MD, wherein the generic RCs are used in a path metadynamics or an umbrella sampling simulation to determine the thermodynamics of pore formation and its molecular determinants, such as the role of distinct bilayer motions, lipid solvation, and lipid packing.
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Affiliation(s)
- Rajat Punia
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
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9
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Gupta S, Soni J, Kumar A, Mandal T. Origin of the nonlinear structural and mechanical properties in oppositely curved lipid mixtures. J Chem Phys 2023; 159:165102. [PMID: 37873964 DOI: 10.1063/5.0167144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023] Open
Abstract
Structural and mechanical properties of membranes such as thickness, tail order, bending modulus and curvature energetics play crucial role in controlling various cellular functions that depend on the local lipid organization and membrane reshaping. While behavior of these biophysical properties are well understood in single component membranes, very little is known about how do they change in the mixed lipid membranes. Often various properties of the mixed lipid bilayers are assumed to change linearly with the mole fractions of the constituent lipids which, however, is true for "ideal" mixing only. In this study, using molecular dynamics simulations, we show that structural and mechanical properties of binary lipid mixture change nonlinearly with the lipid mole fractions, and the strength of the nonlinearity depends on two factors - spontaneous curvature difference and locally inhomogeneous interactions between the lipid components.
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Affiliation(s)
- Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jatin Soni
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Awneesh Kumar
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
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10
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Paul S, Audhya A, Cui Q. Molecular mechanism of GTP binding- and dimerization-induced enhancement of Sar1-mediated membrane remodeling. Proc Natl Acad Sci U S A 2023; 120:e2212513120. [PMID: 36780528 PMCID: PMC9974494 DOI: 10.1073/pnas.2212513120] [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: 07/20/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
The Sar1 GTPase initiates coat protein II (COPII)-mediated protein transport by generating membrane curvature at subdomains on the endoplasmic reticulum, where it is activated by the guanine nucleotide exchange factor (GEF) Sec12. Crystal structures of GDP- and GTP-bound forms of Sar1 suggest that it undergoes a conformational switch in which GTP binding enhances the exposure of an amino-terminal amphipathic helix necessary for efficient membrane penetration. However, key residues in the amino terminus were not resolved in crystal structures, and experimental studies have suggested that the amino terminus of Sar1 is solvent-exposed in the absence of a membrane, even in the GDP-bound state. Therefore, the molecular mechanism by which GTP binding activates the membrane-remodeling activity of Sar1 remains unclear. Using atomistic molecular dynamics simulations, we compare the membrane-binding and curvature generation activities of Sar1 in its GDP- and GTP-bound states. We show that in the GTP-bound state, Sar1 inserts into the membrane with its complete (residues 1 to 23) amphipathic amino-terminal helix, while Sar1-GDP binds to the membrane only through its first 12 residues. Such differential membrane-binding modes translate into significant differences in the protein volume inserted into the membrane. As a result, Sar1-GTP generates positive membrane curvature 10 to 20 times higher than Sar1-GDP. Dimerization of the GTP-bound form of Sar1 further amplifies curvature generation. Taken together, our results present a detailed molecular mechanism for how the nucleotide-bound state of Sar1 regulates its membrane-binding and remodeling activities in a concentration-dependent manner, paving the way toward a better understanding COPII-mediated membrane transport.
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Affiliation(s)
- Sanjoy Paul
- Department of Chemistry, Boston University, Boston, MA02215
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA02215
- Departments of Physics, Boston University, Boston, MA02215
- Departments of Biomedical Engineering, Boston University, Boston, MA02215
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11
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Kalutskii MA, Galimzyanov TR, Pinigin KV. Determination of elastic parameters of lipid membranes from simulation under varied external pressure. Phys Rev E 2023; 107:024414. [PMID: 36932616 DOI: 10.1103/physreve.107.024414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Many cellular processes such as endocytosis, exocytosis, and vesicle trafficking involve membrane deformations, which can be analyzed in the framework of the elastic theories of lipid membranes. These models operate with phenomenological elastic parameters. A connection between these parameters and the internal structure of lipid membranes can be provided by three-dimensional (3D) elastic theories. Considering a membrane as a 3D layer, Campelo et al. [F. Campelo et al., Adv. Colloid Interface Sci. 208, 25 (2014)10.1016/j.cis.2014.01.018] developed a theoretical basis for the calculation of elastic parameters. In this work we generalize and improve this approach by considering a more general condition of global incompressibility instead of local incompressibility. Crucially, we find an important correction to the theory of Campelo et al., which if not taken into account leads to a significant miscalculation of elastic parameters. With the total volume conservation taken into account, we derive an expression for the local Poisson's ratio, which determines how the local volume changes upon stretching and permits a more precise determination of elastic parameters. Also, we substantially simplify the procedure by calculating the derivatives of the moments of the local tension with respect to stretching instead of calculating the local stretching modulus. We obtain a relation between the Gaussian curvature modulus as a function of stretching and the bending modulus, showing that these two elastic parameters are not independent, as was previously assumed. The proposed algorithm is applied to membranes composed of pure dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and their mixture. The following elastic parameters of these systems are obtained: the monolayer bending and stretching moduli, spontaneous curvature, neutral surface position, and local Poisson's ratio. It is shown that the bending modulus of the DPPC/DOPC mixture follows a more complex trend than predicted by the classical Reuss averaging, which is often employed in theoretical frameworks.
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Affiliation(s)
- Maksim A Kalutskii
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, Moscow 119071, Russia
- Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology "MISiS," 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Timur R Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, Moscow 119071, Russia
- Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology "MISiS," 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Konstantin V Pinigin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, Moscow 119071, Russia
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12
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Kozlov MM, Taraska JW. Generation of nanoscopic membrane curvature for membrane trafficking. Nat Rev Mol Cell Biol 2023; 24:63-78. [PMID: 35918535 DOI: 10.1038/s41580-022-00511-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
Curved membranes are key features of intracellular organelles, and their generation involves dynamic protein complexes. Here we describe the fundamental mechanisms such as the hydrophobic insertion, scaffolding and crowding mechanisms these proteins use to produce membrane curvatures and complex shapes required to form intracellular organelles and vesicular structures involved in endocytosis and secretion. For each mechanism, we discuss its cellular functions as well as the underlying physical principles and the specific membrane properties required for the mechanism to be feasible. We propose that the integration of individual mechanisms into a highly controlled, robust process of curvature generation often relies on the assembly of proteins into coats. How cells unify and organize the curvature-generating factors at the nanoscale is presented for three ubiquitous coats central for membrane trafficking in eukaryotes: clathrin-coated pits, caveolae, and COPI and COPII coats. The emerging theme is that these coats arrange and coordinate curvature-generating factors in time and space to dynamically shape membranes to accomplish membrane trafficking within cells.
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Affiliation(s)
- Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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13
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Semeraro EF, Pajtinka P, Marx L, Kabelka I, Leber R, Lohner K, Vácha R, Pabst G. Magainin 2 and PGLa in bacterial membrane mimics IV: Membrane curvature and partitioning. Biophys J 2022; 121:4689-4701. [PMID: 36258677 PMCID: PMC9748257 DOI: 10.1016/j.bpj.2022.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 12/15/2022] Open
Abstract
We previously reported that the synergistically enhanced antimicrobial activity of magainin 2 (MG2a) and PGLa is related to membrane adhesion and fusion. Here, we demonstrate that equimolar mixtures of MG2a and L18W-PGLa induce positive monolayer curvature stress and sense, at the same time, positive mean and Gaussian bilayer curvatures already at low amounts of bound peptide. The combination of both abilities-membrane curvature sensing and inducing-is most likely the base for the synergistically enhanced peptide activity. In addition, our coarse-grained simulations suggest that fusion stalks are promoted by decreasing the free-energy barrier for their formation rather than by stabilizing their shape. We also interrogated peptide partitioning as a function of lipid and peptide concentration using tryptophan fluorescence spectroscopy and peptide-induced leakage of dyes from lipid vesicles. In agreement with a previous report, we find increased membrane partitioning of L18W-PGLa in the presence of MG2a. However, this effect does not prevail to lipid concentrations higher than 1 mM, above which all peptides associate with the lipid bilayers. This implies that synergistic effects of MG2a and L18W-PGLa in previously reported experiments with lipid concentrations >1 mM are due to peptide-induced membrane remodeling and not their specific membrane partitioning.
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Affiliation(s)
- Enrico F Semeraro
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria
| | - Peter Pajtinka
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lisa Marx
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria
| | - Ivo Kabelka
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Regina Leber
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria
| | - Karl Lohner
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria.
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14
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Jiménez-Munguía I, Beaven AH, Blank PS, Sodt AJ, Zimmerberg J. Interferon-induced transmembrane protein 3 (IFITM3) and its antiviral activity. Curr Opin Struct Biol 2022; 77:102467. [PMID: 36306674 DOI: 10.1016/j.sbi.2022.102467] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/05/2022] [Accepted: 08/15/2022] [Indexed: 01/30/2023]
Abstract
Infections caused by enveloped viruses require fusion with cellular membranes for viral genome entry. Viral entry occurs following an interaction of viral and cellular membranes allowing the formation of fusion pores, by which the virus accesses the cytoplasm. Here, we focus on interferon-induced transmembrane protein 3 (IFITM3) and its antiviral activity. IFITM3 is predicted to block or stall viral fusion at an intermediate state, causing viral propagation to fail. After introducing IFITM3, we describe the generalized lipid membrane fusion pathway and how it can be stalled, particularly with respect to IFITM3, and current questions regarding IFITM3's topology, with specific emphasis on IFITM3's amphipathic α-helix (AAH) 59V-68M, which is necessary for the antiviral activity. We report new hydrophobicity and hydrophobic moment calculations for this peptide and a variety of active site peptides from known membrane-remodeling proteins. Finally, we discuss the effects of posttranslational modifications and localization, how IFITM3's AAH may block viral fusion, and possible ramifications of membrane composition.
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Affiliation(s)
- I Jiménez-Munguía
- Section on Integrative Biophysics Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), MD, USA
| | - A H Beaven
- Unit on Membrane Chemical Physics Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH) MD, USA; Postdoctoral Research Associate Program, National Institute of General Medical Sciences National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - P S Blank
- Section on Integrative Biophysics Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), MD, USA
| | - A J Sodt
- Unit on Membrane Chemical Physics Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH) MD, USA.
| | - J Zimmerberg
- Section on Integrative Biophysics Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), MD, USA.
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15
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Pinigin KV. Determination of Elastic Parameters of Lipid Membranes with Molecular Dynamics: A Review of Approaches and Theoretical Aspects. MEMBRANES 2022; 12:membranes12111149. [PMID: 36422141 PMCID: PMC9692374 DOI: 10.3390/membranes12111149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 05/12/2023]
Abstract
Lipid membranes are abundant in living organisms, where they constitute a surrounding shell for cells and their organelles. There are many circumstances in which the deformations of lipid membranes are involved in living cells: fusion and fission, membrane-mediated interaction between membrane inclusions, lipid-protein interaction, formation of pores, etc. In all of these cases, elastic parameters of lipid membranes are important for the description of membrane deformations, as these parameters determine energy barriers and characteristic times of membrane-involved phenomena. Since the development of molecular dynamics (MD), a variety of in silico methods have been proposed for the determination of elastic parameters of simulated lipid membranes. These MD methods allow for the consideration of details unattainable in experimental techniques and represent a distinct scientific field, which is rapidly developing. This work provides a review of these MD approaches with a focus on theoretical aspects. Two main challenges are identified: (i) the ambiguity in the transition from the continuum description of elastic theories to the discrete representation of MD simulations, and (ii) the determination of intrinsic elastic parameters of lipid mixtures, which is complicated due to the composition-curvature coupling effect.
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Affiliation(s)
- Konstantin V Pinigin
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
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16
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Rahman K, Datta SA, Beaven AH, Jolley AA, Sodt AJ, Compton AA. Cholesterol Binds the Amphipathic Helix of IFITM3 and Regulates Antiviral Activity. J Mol Biol 2022; 434:167759. [PMID: 35872070 PMCID: PMC9342930 DOI: 10.1016/j.jmb.2022.167759] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 02/05/2023]
Abstract
The interferon-induced transmembrane (IFITM) proteins broadly inhibit the entry of diverse pathogenic viruses, including Influenza A virus (IAV), Zika virus, HIV-1, and SARS coronaviruses by inhibiting virus-cell membrane fusion. IFITM3 was previously shown to disrupt cholesterol trafficking, but the functional relationship between IFITM3 and cholesterol remains unclear. We previously showed that inhibition of IAV entry by IFITM3 is associated with its ability to promote cellular membrane rigidity, and these activities are functionally linked by a shared requirement for the amphipathic helix (AH) found in the intramembrane domain (IMD) of IFITM3. Furthermore, it has been shown that the AH of IFITM3 alters lipid membranes in vitro in a cholesterol-dependent manner. Therefore, we aimed to elucidate the relationship between IFITM3 and cholesterol in more detail. Using a fluorescence-based in vitro binding assay, we found that a peptide derived from the AH of IFITM3 directly interacted with the cholesterol analog, NBD-cholesterol, while other regions of the IFITM3 IMD did not, and native cholesterol competed with this interaction. In addition, recombinant full-length IFITM3 protein also exhibited NBD-cholesterol binding activity. Importantly, previously characterized mutations within the AH of IFITM3 that strongly inhibit antiviral function (F63Q and F67Q) disrupted AH structure in solution, inhibited cholesterol binding in vitro, and restricted bilayer insertion in silico. Our data suggest that direct interactions with cholesterol may contribute to the inhibition of membrane fusion pore formation by IFITM3. These findings may facilitate the design of therapeutic peptides for use in broad-spectrum antiviral therapy.
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Affiliation(s)
- Kazi Rahman
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States
| | - Siddhartha A.K. Datta
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States
| | - Andrew H. Beaven
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, United States,National Institute of General Medical Sciences, Bethesda, MD 20892, United States
| | - Abigail A. Jolley
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States
| | - Alexander J. Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, United States
| | - Alex A. Compton
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States,Corresponding author
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17
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Lessen HJ, Sapp KC, Beaven AH, Ashkar R, Sodt AJ. Molecular mechanisms of spontaneous curvature and softening in complex lipid bilayer mixtures. Biophys J 2022; 121:3188-3199. [PMID: 35927953 PMCID: PMC9463698 DOI: 10.1016/j.bpj.2022.07.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/01/2022] [Accepted: 07/28/2022] [Indexed: 11/21/2022] Open
Abstract
Membrane reshaping is an essential biological process. The chemical composition of lipid membranes determines their mechanical properties and thus the energetics of their shape. Hundreds of distinct lipid species make up native bilayers, and this diversity complicates efforts to uncover what compositional factors drive membrane stability in cells. Simplifying assumptions, therefore, are used to generate quantitative predictions of bilayer dynamics based on lipid composition. One assumption commonly used is that "per lipid" mechanical properties are both additive and constant-that they are an intrinsic property of lipids independent of the surrounding composition. Related to this is the assumption that lipid bulkiness, or "shape," determines its curvature preference, independently of context. In this study, all-atom molecular dynamics simulations on three separate multilipid systems were used to explicitly test these assumptions, applying methodology recently developed to isolate properties of single lipids or nanometer-scale patches of lipids. The curvature preference experienced by populations of lipid conformations were inferred from their redistribution on a dynamically fluctuating bilayer. Representative populations were extracted by both structural similarity and semi-automated hidden Markov model analysis. The curvature preferences of lipid dimers were then determined and compared with an additive model that combines the monomer curvature preference of both the individual lipids. In all three systems, we identified conformational subpopulations of lipid dimers that showed non-additive curvature preference, in each case mediated by a special chemical interaction (e.g., hydrogen bonding). Our study highlights the importance of specific chemical interactions between lipids in multicomponent bilayers and the impact of interactions on bilayer stiffness. We identify two mechanisms of bilayer softening: diffusional softening, driven by the dynamic coupling between lipid distributions and membrane undulations, and conformational softening, driven by the inter-conversion between distinct dimeric conformations.
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Affiliation(s)
- Henry J Lessen
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Kayla C Sapp
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Andrew H Beaven
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland; Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, Virginia; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia
| | - Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
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18
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Zhang L, Wang Y, Dong Y, Pant A, Liu Y, Masserman L, Xu Y, McLaughlin RN, Bai J. The endophilin curvature-sensitive motif requires electrostatic guidance to recycle synaptic vesicles in vivo. Dev Cell 2022; 57:750-766.e5. [PMID: 35303431 PMCID: PMC8969179 DOI: 10.1016/j.devcel.2022.02.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/21/2022] [Accepted: 02/22/2022] [Indexed: 12/29/2022]
Abstract
Curvature-sensing mechanisms assist proteins in executing particular actions on various membrane organelles. Here, we investigate the functional specificity of curvature-sensing amphipathic motifs in Caenorhabditis elegans through the study of endophilin, an endocytic protein for synaptic vesicle recycling. We generate chimeric endophilin proteins by replacing the endophilin amphipathic motif H0 with other curvature-sensing amphipathic motifs. We find that the role of amphipathic motifs cannot simply be extrapolated from the identity of their parental proteins. For example, the amphipathic motif of the nuclear pore complex protein NUP133 functionally replaces the synaptic role of endophilin H0. Interestingly, non-functional endophilin chimeras have similar defects-producing fewer synaptic vesicles but more endosomes-and this indicates that the curvature-sensing motifs in these chimeras have a common deficiency for reforming synaptic vesicles. Finally, we convert non-functional endophilin chimeras into functional proteins by changing the cationic property of amphipathic motifs, successfully reprogramming the functional specificity of curvature-sensing motifs in vivo.
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Affiliation(s)
- Lin Zhang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yu Wang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, P.R. China; Fudan University, Shanghai 200433, P.R. China
| | - Yongming Dong
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Aaradhya Pant
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yan Liu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Laura Masserman
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ye Xu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Jihong Bai
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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19
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Fu Y, Zeno WF, Stachowiak JC, Johnson ME. A continuum membrane model can predict curvature sensing by helix insertion. SOFT MATTER 2021; 17:10649-10663. [PMID: 34792524 PMCID: PMC8877990 DOI: 10.1039/d1sm01333e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein domains, such as ENTH (epsin N-terminal homology) and BAR (bin/amphiphysin/rvs), contain amphipathic helices that drive preferential binding to curved membranes. However, predicting how the physical parameters of these domains control this 'curvature sensing' behavior is challenging due to the local membrane deformations generated by the nanoscopic helix on the surface of a large sphere. We here use a deformable continuum model that accounts for the physical properties of the membrane and the helix insertion to predict curvature sensing behavior, with direct validation against multiple experimental datasets. We show that the insertion can be modeled as a local change to the membrane's spontaneous curvature, cins0, producing excellent agreement with the energetics extracted from experiments on ENTH binding to vesicles and cylinders, and of ArfGAP helices to vesicles. For small vesicles with high curvature, the insertion lowers the membrane energy by relieving strain on a membrane that is far from its preferred curvature of zero. For larger vesicles, however, the insertion has the inverse effect, de-stabilizing the membrane by introducing more strain. We formulate here an empirical expression that accurately captures numerically calculated membrane energies as a function of both basic membrane properties (bending modulus κ and radius R) as well as stresses applied by the inserted helix (cins0 and area Ains). We therefore predict how these physical parameters will alter the energetics of helix binding to curved vesicles, which is an essential step in understanding their localization dynamics during membrane remodeling processes.
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Affiliation(s)
- Yiben Fu
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, USA.
| | - Wade F Zeno
- Mork Family Department of Chemical Engineering and Materials Science, The University of Southern California, Los Angeles, California, 90089, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Margaret E Johnson
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, USA.
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20
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Study of Resveratrol's Interaction with Planar Lipid Models: Insights into Its Location in Lipid Bilayers. MEMBRANES 2021; 11:membranes11020132. [PMID: 33672841 PMCID: PMC7918209 DOI: 10.3390/membranes11020132] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/16/2023]
Abstract
Resveratrol, a polyphenolic molecule found in edible fruits and vegetables, shows a wide range of beneficial effects on human health, including anti-microbial, anti-inflammatory, anti-cancer, and anti-aging properties. Due to its poor water solubility and high liposome-water partition coefficient, the biomembrane seems to be the main target of resveratrol, although the mode of interaction with membrane lipids and its location within the cell membrane are still unclear. In this study, using electrophysiological measurements, we study the interaction of resveratrol with planar lipid membranes (PLMs) of different composition. We found that resveratrol incorporates into palmitoyl-oleoyl-phosphatidylcholine (POPC) and POPC:Ch PLMs and forms conductive units unlike those found in dioleoyl-phosphatidylserine (DOPS):dioleoyl-phosphatidylethanolamine (DOPE) PLMs. The variation of the biophysical parameters of PLMs in the presence of resveratrol provides information on its location within a lipid double layer, thus contributing to an understanding of its mechanism of action.
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21
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Spangler EJ, Olinger AD, Kumar PBS, Laradji M. Binding, unbinding and aggregation of crescent-shaped nanoparticles on nanoscale tubular membranes. SOFT MATTER 2021; 17:1016-1027. [PMID: 33284936 DOI: 10.1039/d0sm01642j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Using molecular dynamics simulations of a coarse-grained implicit solvent model, we investigate the binding of crescent-shaped nanoparticles (NPs) on tubular lipid membranes. The NPs adhere to the membrane through their concave side. We found that the binding/unbinding transition is first-order, with the threshold binding energy being higher than the unbinding threshold, and the energy barrier between the bound and unbound states at the transition that increases with increasing the NP's arclength Lnp or curvature mismatch μ = Rc/Rnp, where Rc and Rnp are the radii of curvature of the tubular membrane and the NP, respectively. Furthermore, we found that the threshold binding energy increases with increasing either Lnp or μ. NPs with curvature larger than that of the tubule (μ > 1) lie perpendicularly to the tubule's axis. However, for μ smaller than a specific arclength-dependent mismatch μ*, the NPs are tilted with respect to the tubule's axis, with the tilt angle that increases with decreasing μ. We also investigated the self-assembly of the NPs on the tubule at relatively weak adhesion strength and found that for μ > 1 and high values of Lnp, the NPs self-assemble into linear chains, and lie side-by-side. For μ < μ* and high Lnp, the NPs also self-assemble into chains, while being tilted with respect to the tubule's axis.
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Affiliation(s)
- Eric J Spangler
- Department of Biomedical Engineering and Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA
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22
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Downing R, Volpe Bossa G, May S. Saddle-curvature instability of lipid bilayer induced by amphipathic peptides: a molecular model. SOFT MATTER 2020; 16:5032-5043. [PMID: 32452495 DOI: 10.1039/d0sm00499e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Amphipathic peptides that partition into lipid bilayers affect the curvature elastic properties of their host. Some of these peptides are able to shift the Gaussian modulus to positive values, thus triggering an instability with respect to the formation of saddle curvatures. To characterize the generic aspects of the underlying mechanism, we employ a molecular lipid model that accounts for the interfacial tension between the polar and apolar regions of the membrane, for interactions between the lipid headgroups, and for the energy to stretch or compress the hydrocarbon chains. Peptides are modeled as cylinders that partition into the host membrane in a parallel orientation where they diminish the space available to the lipid headgroups and chains. The penetration depth into the membrane is determined by the angular size of the peptide's hydrophilic region. We demonstrate that only peptides with a small angular size of their hydrophilic region have an intrinsic tendency to render the Gaussian modulus more positive, and we identify conditions at which the Gaussian modulus adopts a positive sign upon increasing the peptide concentration. Our model allows us to also incorporate electrostatic interactions between cationic peptides and anionic lipids on the level of the linear Debye-Hückel model. We show that electrostatic interactions tend to shift the Gaussian modulus toward more positive values. Steric and electrostatic lipid-peptide interactions jointly decrease the effective interaction strength in the headgroup region of the host membrane thus suggesting a generic mechanisms of how certain amphipathic peptides are able to induce the formation of saddle curvatures.
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Affiliation(s)
- Rachel Downing
- Department of Physics, North Dakota State University, Fargo North Dakota 58108-6050, USA
| | - Guilherme Volpe Bossa
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil.
| | - Sylvio May
- Department of Physics, North Dakota State University, Fargo North Dakota 58108-6050, USA
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23
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Furlan AL, Laurin Y, Botcazon C, Rodríguez-Moraga N, Rippa S, Deleu M, Lins L, Sarazin C, Buchoux S. Contributions and Limitations of Biophysical Approaches to Study of the Interactions between Amphiphilic Molecules and the Plant Plasma Membrane. PLANTS 2020; 9:plants9050648. [PMID: 32443858 PMCID: PMC7285231 DOI: 10.3390/plants9050648] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 12/20/2022]
Abstract
Some amphiphilic molecules are able to interact with the lipid matrix of plant plasma membranes and trigger the immune response in plants. This original mode of perception is not yet fully understood and biophysical approaches could help to obtain molecular insights. In this review, we focus on such membrane-interacting molecules, and present biophysically grounded methods that are used and are particularly interesting in the investigation of this mode of perception. Rather than going into overly technical details, the aim of this review was to provide to readers with a plant biochemistry background a good overview of how biophysics can help to study molecular interactions between bioactive amphiphilic molecules and plant lipid membranes. In particular, we present the biomimetic membrane models typically used, solid-state nuclear magnetic resonance, molecular modeling, and fluorescence approaches, because they are especially suitable for this field of research. For each technique, we provide a brief description, a few case studies, and the inherent limitations, so non-specialists can gain a good grasp on how they could extend their toolbox and/or could apply new techniques to study amphiphilic bioactive compound and lipid interactions.
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Affiliation(s)
- Aurélien L. Furlan
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Yoann Laurin
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Camille Botcazon
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Technologie de Compiègne, 60200 Compiègne, France;
| | - Nely Rodríguez-Moraga
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Sonia Rippa
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Technologie de Compiègne, 60200 Compiègne, France;
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, TERRA Research Center, Université de Liège, B5030 Gembloux, Belgium; (A.L.F.); (Y.L.); (M.D.); (L.L.)
| | - Catherine Sarazin
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
| | - Sébastien Buchoux
- Unité de Génie Enzymatique et Cellulaire, UMR 7025 CNRS/UPJV/UTC, Université de Picardie Jules Verne, 80039 Amiens, France; (C.B.); (N.R.-M.); (C.S.)
- Correspondence: ; Tel.: +33-(0)3-2282-7473
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24
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Pinigin KV, Kondrashov OV, Jiménez-Munguía I, Alexandrova VV, Batishchev OV, Galimzyanov TR, Akimov SA. Elastic deformations mediate interaction of the raft boundary with membrane inclusions leading to their effective lateral sorting. Sci Rep 2020; 10:4087. [PMID: 32139760 PMCID: PMC7058020 DOI: 10.1038/s41598-020-61110-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/18/2020] [Indexed: 02/06/2023] Open
Abstract
Liquid-ordered lipid domains represent a lateral inhomogeneity in cellular membranes. These domains have elastic and physicochemical properties different from those of the surrounding membrane. In particular, their thickness exceeds that of the disordered membrane. Thus, elastic deformations arise at the domain boundary in order to compensate for the thickness mismatch. In equilibrium, the deformations lead to an incomplete register of monolayer ordered domains: the elastic energy is minimal if domains in opposing monolayers lie on the top of each other, and their boundaries are laterally shifted by about 3 nm. This configuration introduces a region, composed of one ordered and one disordered monolayers, with an intermediate bilayer thickness. Besides, a jump in a local monolayer curvature takes place in this intermediate region, concentrating here most of the elastic stress. This region can participate in a lateral sorting of membrane inclusions by offering them an optimal bilayer thickness and local curvature conditions. In the present study, we consider the sorting of deformable lipid inclusions, undeformable peripheral and deeply incorporated peptide inclusions, and undeformable transmembrane inclusions of different molecular geometry. With rare exceptions, all types of inclusions have an affinity to the ordered domain boundary as compared to the bulk phases. The optimal lateral distribution of inclusions allows relaxing the elastic stress at the boundary of domains.
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Affiliation(s)
- Konstantin V Pinigin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow, 119071, Russia
| | - Oleg V Kondrashov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow, 119071, Russia
| | - Irene Jiménez-Munguía
- National University of Science and Technology "MISiS", 4 Leninskiy prospect, Moscow, 119049, Russia
| | | | - Oleg V Batishchev
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow, 119071, Russia
| | - Timur R Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow, 119071, Russia
| | - Sergey A Akimov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow, 119071, Russia.
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25
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Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations. Sci Rep 2019; 9:14557. [PMID: 31601944 PMCID: PMC6787258 DOI: 10.1038/s41598-019-51202-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/24/2019] [Indexed: 01/04/2023] Open
Abstract
F-Bin/Amphiphysin/Rvs (F-BAR) domain proteins play essential roles in biological processes that involve membrane remodelling, such as endocytosis and exocytosis. It has been shown that such proteins transform the lipid membrane into tubes. Notably, Pacsin1 from the Pacsin/Syndapin subfamily has the ability to transform the membrane into various morphologies: striated tubes, featureless wide and thin tubes, and pearling vesicles. The molecular mechanism of this interesting ability remains elusive. In this study, we performed all-atom (AA) and coarse-grained (CG) molecular dynamics simulations to investigate the curvature induction and sensing mechanisms of Pacsin1 on a membrane. From AA simulations, we show that Pacsin1 has internal structural flexibility. In CG simulations with parameters tuned from the AA simulations, spontaneous assembly of two Pacsin1 dimers through lateral interaction is observed. Based on the complex structure, we show that the regularly assembled Pacsin1 dimers bend a tensionless membrane. We also show that a single Pacsin1 dimer senses the membrane curvature, binding to a buckled membrane with a preferred curvature. These results provide molecular insights into polymorphic membrane remodelling.
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26
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Nepal B, Leveritt J, Lazaridis T. Membrane Curvature Sensing by Amphipathic Helices: Insights from Implicit Membrane Modeling. Biophys J 2019; 114:2128-2141. [PMID: 29742406 DOI: 10.1016/j.bpj.2018.03.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/24/2018] [Accepted: 03/14/2018] [Indexed: 01/09/2023] Open
Abstract
Sensing and generation of lipid membrane curvature, mediated by the binding of specific proteins onto the membrane surface, play crucial roles in cell biology. A number of mechanisms have been proposed, but the molecular understanding of these processes is incomplete. All-atom molecular dynamics simulations have offered valuable insights but are extremely demanding computationally. Implicit membrane simulations could provide a viable alternative, but current models apply only to planar membranes. In this work, the implicit membrane model 1 is extended to spherical and tubular membranes. The geometric change from planar to curved shapes is straightforward but insufficient for capturing the full curvature effect, which includes changes in lipid packing. Here, these packing effects are taken into account via the lateral pressure profile. The extended implicit membrane model 1 is tested on the wild-types and mutants of the antimicrobial peptide magainin, the ALPS motif of arfgap1, α-synuclein, and an ENTH domain. In these systems, the model is in qualitative agreement with experiments. We confirm that favorable electrostatic interactions tend to weaken curvature sensitivity in the presence of strong hydrophobic interactions but may actually have a positive effect when those are weak. We also find that binding to vesicles is more favorable than binding to tubes of the same diameter and that the long helix of α-synuclein tends to orient along the axis of tubes, whereas shorter helices tend to orient perpendicular to it. Adoption of a specific orientation could provide a mechanism for coupling protein oligomerization to tubule formation.
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Affiliation(s)
- Binod Nepal
- Department of Chemistry, City College of New York, New York, New York
| | - John Leveritt
- Department of Chemistry, Newman University, Wichita, Kansas
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, New York, New York; Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York.
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27
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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.
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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.
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28
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Rhys NH, Duffy IB, Sowden CL, Lorenz CD, McLain SE. On the hydration of DOPE in solution. J Chem Phys 2019; 150:115104. [PMID: 30902020 DOI: 10.1063/1.5085736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The atomic-scale hydration structure around the 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) headgroup in a chloroform/water solution has been investigated using neutron diffraction enhanced by isotopic substitution and NMR, coupled with empirical potential structure refinement and molecular dynamics simulations. The results obtained show the preferential binding sites for water molecules on the DOPE headgroups, with the most predominant interactions being with the ammonium and phosphate groups. Interestingly, the level of hydration, as well as the association of DOPE molecules, varies according to the simulation method used. The results here suggest the presence of a tight water network around these lipid headgroups that could affect the permeability of the membrane for lipid-mediated diffusion.
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Affiliation(s)
- Natasha H Rhys
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Imogen B Duffy
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Christopher L Sowden
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Christian D Lorenz
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Sylvia E McLain
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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29
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Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chem Rev 2019; 119:6227-6269. [DOI: 10.1021/acs.chemrev.8b00384] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Alagumuthu M, Dahiya D, Singh Nigam P. Phospholipid—the dynamic structure between living and non-living world; a much obligatory supramolecule for present and future. AIMS MOLECULAR SCIENCE 2019. [DOI: 10.3934/molsci.2019.1.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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31
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Directed Supramolecular Organization of N-BAR Proteins through Regulation of H0 Membrane Immersion Depth. Sci Rep 2018; 8:16383. [PMID: 30401832 PMCID: PMC6219572 DOI: 10.1038/s41598-018-34273-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/11/2018] [Indexed: 11/12/2022] Open
Abstract
Many membrane remodeling events rely on the ability of curvature-generating N-BAR membrane proteins to organize into distinctive supramolecular configurations. Experiments have revealed a conformational switch in N-BAR proteins resulting in vesicular or tubular membrane shapes, with shallow membrane immersion of the H0 amphipathic helices of N-BAR proteins on vesicles but deep H0 immersion on tubes. We develop here a minimal elastic model of the local thinning of the lipid bilayer resulting from H0 immersion. Our model predicts that the observed conformational switch in N-BAR proteins produces a corresponding switch in the bilayer-mediated N-BAR interactions due to the H0 helices. In agreement with experiments, we find that bilayer-mediated H0 interactions oppose N-BAR multimerization for the shallow H0 membrane immersion depths measured on vesicles, but promote self-assembly of supramolecular N-BAR chains for the increased H0 membrane immersion depths measured on tubes. Finally, we consider the possibility that bilayer-mediated H0 interactions might contribute to the concerted structural reorganization of N-BAR proteins suggested by experiments. Our results indicate that the membrane immersion depth of amphipathic protein helices may provide a general molecular control parameter for membrane organization.
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32
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Shi Y, Wan M, Fu L, Zhang S, Wang S, Gao L, Fang W. Peptide-Lipid Interaction Sites Affect Vesicles' Responses to Antimicrobial Peptides. Biophys J 2018; 115:1518-1529. [PMID: 30268538 DOI: 10.1016/j.bpj.2018.08.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/22/2018] [Accepted: 08/30/2018] [Indexed: 11/25/2022] Open
Abstract
This article presents coarse-grained molecular dynamics simulations of pore-forming antimicrobial peptide melittin and its interactions with vesicles composed of a mixture of zwitterionic and anionic phospholipids. Besides creating holes in the membrane, the adsorption of melittin also induces vesicle budding, which can develop into vesiculation at high peptide concentrations, as well as vesicle invagination, which can eventually result in a corrugated membrane surface. These rich morphology changes are mediated by the curvature of the vesicles and the peptide concentration. Highly curved vesicles favor the recruitment of melittins with a higher density of binding sites. The peptides mainly penetrate into the membrane surface in monomers via hydrophobic interaction. Lowly curved vesicles recruit melittins with a low density of binding sites. Surplus peptides are prone to form oligomers and shallowly adsorb on the surface of membrane via electrostatic interaction. The penetration of monomers induces membrane pore formation and positive membrane curvature, which promote vesicle budding. The adsorption of oligomers induces negative membrane curvature, which promotes vesicle invagination. This work demonstrates that antimicrobial peptides adopt multiple actions to destroy bacterial membranes.
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Affiliation(s)
- Yu Shi
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Mingwei Wan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Lei Fu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Shan Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Shiyuan Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Lianghui Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China.
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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33
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Woodward X, Stimpson EE, Kelly CV. Single-lipid tracking on nanoscale membrane buds: The effects of curvature on lipid diffusion and sorting. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2064-2075. [PMID: 29856992 DOI: 10.1016/j.bbamem.2018.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/30/2018] [Accepted: 05/19/2018] [Indexed: 01/25/2023]
Abstract
Nanoscale membrane curvature in cells is critical for endocytosis/exocytosis and membrane trafficking. However, the biophysical ramifications of nanoscale membrane curvature on the behavior of lipids remain poorly understood. Here, we created an experimental model system of membrane curvature at a physiologically-relevant scale and obtained nanoscopic information on single-lipid distributions and dynamics. Supported lipid bilayers were created over 50 and 70 nm radius nanoparticles to create membrane buds. Single-molecule localization microscopy was performed with diverse mixtures of fluorescent and non-fluorescent lipids. Variations in lipid acyl tales length, saturation, head-group, and fluorescent labeling strategy were tested while maintaining a single fluid lipid phase throughout the membrane. Monte Carlo simulations were used to fit our experimental results and quantify the effects of curvature on the lipid diffusion and sorting. Whereas varying the composition of the non-fluorescent lipids yielded minimal changes to the curvature effects, the labeling strategy of the fluorescent lipids yielded highly varying effects of curvature. Most conditions yield single-population Brownian diffusion throughout the membrane; however, curvature-induced lipid sorting, slowing, and aggregation were observed in some conditions. Head-group labeled lipids such as DPPE-Texas Red and POPE-Rhodamine diffused >2.4× slower on the curved vs. the planar membranes; tail-labeled lipids such as NBD-PPC, TopFluor-PPC, and TopFluor-PIP2, as well as DiIC12 and DiIC18 displayed no significant changes in diffusion due to the membrane curvature. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
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Affiliation(s)
- Xinxin Woodward
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States
| | - Eric E Stimpson
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States
| | - Christopher V Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, United States.
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34
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Sych T, Mély Y, Römer W. Lipid self-assembly and lectin-induced reorganization of the plasma membrane. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170117. [PMID: 29632269 PMCID: PMC5904303 DOI: 10.1098/rstb.2017.0117] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2018] [Indexed: 01/10/2023] Open
Abstract
The plasma membrane represents an outstanding example of self-organization in biology. It plays a vital role in protecting the integrity of the cell interior and regulates meticulously the import and export of diverse substances. Its major building blocks are proteins and lipids, which self-assemble to a fluid lipid bilayer driven mainly by hydrophobic forces. Even if the plasma membrane appears-globally speaking-homogeneous at physiological temperatures, the existence of specialized nano- to micrometre-sized domains of raft-type character within cellular and synthetic membrane systems has been reported. It is hypothesized that these domains are the origin of a plethora of cellular processes, such as signalling or vesicular trafficking. This review intends to highlight the driving forces of lipid self-assembly into a bilayer membrane and the formation of small, transient domains within the plasma membrane. The mechanisms of self-assembly depend on several factors, such as the lipid composition of the membrane and the geometry of lipids. Moreover, the dynamics and organization of glycosphingolipids into nanometre-sized clusters will be discussed, also in the context of multivalent lectins, which cluster several glycosphingolipid receptor molecules and thus create an asymmetric stress between the two membrane leaflets, leading to tubular plasma membrane invaginations.This article is part of the theme issue 'Self-organization in cell biology'.
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Affiliation(s)
- Taras Sych
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technology (FIT), Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch Cedex, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch Cedex, France
| | - Winfried Römer
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technology (FIT), Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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35
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Beaven AH, Sodt AJ, Pastor RW, Koeppe RE, Andersen OS, Im W. Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes. J Chem Theory Comput 2017; 13:5054-5064. [PMID: 28870079 DOI: 10.1021/acs.jctc.7b00400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Previous experiments have shown that the lifetime of a gramicidin A dimer channel (which forms from two nonconducting monomers) in a lipid bilayer is modulated by mutations of the tryptophan (Trp) residues at the bilayer-water interface. We explore this further using extensive molecular dynamics simulations of various gA dimer and monomer mutants at the Trp positions in phosphatidylcholine bilayers with different tail lengths. gA interactions with the surrounding bilayer are strongly modulated by mutating these Trp residues. There are three principal effects: eliminating residue hydrogen bonding ability (i.e., reducing the channel-monolayer coupling strength) reduces the extent of the bilayer deformation caused by the assembled dimeric channel; a residue's size and geometry affects its orientation, leading to different hydrogen bonding partners; and increasing a residue's hydrophobicity increases the depth of gA monomer insertion relative to the bilayer center, thereby increasing the lipid bending frustration.
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Affiliation(s)
- Andrew H Beaven
- Department of Chemistry, The University of Kansas , Lawrence, Kansas 66045, United States
| | | | | | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College , New York, New York 10065, United States
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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36
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Mikucki M, Zhou YC. CURVATURE-DRIVEN MOLECULAR FLOW ON MEMBRANE SURFACE. SIAM JOURNAL ON APPLIED MATHEMATICS 2017; 77:1587-1605. [PMID: 29056778 PMCID: PMC5650120 DOI: 10.1137/16m1076551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This work presents a mathematical model for the localization of multiple species of diffusion molecules on membrane surfaces. Morphological change of bilayer membrane in vivo is generally modulated by proteins. Most of these modulations are associated with the localization of related proteins in the crowded lipid environments. We start with the energetic description of the distributions of molecules on curved membrane surface, and define the spontaneous curvature of bilayer membrane as a function of the molecule concentrations on membrane surfaces. A drift-diffusion equation governs the gradient flow of the surface molecule concentrations. We recast the energetic formulation and the related governing equations by using an Eulerian phase field description to define membrane morphology. Computational simulations with the proposed mathematical model and related numerical techniques predict (i) the molecular localization on static membrane surfaces at locations with preferred mean curvatures, and (ii) the generation of preferred mean curvature which in turn drives the molecular localization.
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Affiliation(s)
- Michael Mikucki
- Department of Applied Mathematics & Statistics, Colorado School of Mines, Golden, Colorado, 80401-1887
| | - Y C Zhou
- Department of Mathematics, Colorado State University, Fort Collins, Colorado, 80523-1874
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37
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Soares TA, Vanni S, Milano G, Cascella M. Toward Chemically Resolved Computer Simulations of Dynamics and Remodeling of Biological Membranes. J Phys Chem Lett 2017; 8:3586-3594. [PMID: 28707901 DOI: 10.1021/acs.jpclett.7b00493] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cellular membranes are fundamental constituents of living organisms. Apart from defining the boundaries of the cells, they are involved in a wide range of biological functions, associated with both their structural and the dynamical properties. Biomembranes can undergo large-scale transformations when subject to specific environmental changes, including gel-liquid phase transitions, change of aggregation structure, formation of microtubules, or rupture into vesicles. All of these processes are dependent on a delicate interplay between intermolecular forces, molecular crowding, and entropy, and their understanding requires approaches that are able to capture and rationalize the details of all of the involved interactions. Molecular dynamics-based computational models at atom-level resolution are, in principle, the best way to perform such investigations. Unfortunately, the relevant spatial and time dimensionalities involved in membrane remodeling phenomena would require computational costs that are today unaffordable on a routinely basis. Such hurdles can be removed by coarse-graining the representations of the individual molecular components of the systems. This procedure anyway reduces the possibility of describing the chemical variations in the lipid mixtures composing biological membranes. New hybrid particle field multiscale approaches offer today a promising alternative to the more traditional particle-based simulations methods. By combining chemically distinguishable molecular representations with mesoscale-based computationally affordable potentials, they appear as one of the most promising ways to keep an accurate description of the chemical complexity of biological membranes and, at the same time, cover the required scales to describe remodeling events.
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Affiliation(s)
- Thereza A Soares
- Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária , Recife PE 50740-560, Brazil
| | - Stefano Vanni
- Department of Biology, University of Fribourg , 1700 Fribourg, Switzerland
| | - Giuseppe Milano
- Dipartimento di Chimica e Biologia, Università di Salerno , Via Giovanni Paolo II, 132, I-84084 Fisciano, Italy
| | - Michele Cascella
- Department of Chemistry and Centre for Theoretical and Computational Chemistry (CTCC) , Sem Saelands vei 26, 0371 Oslo, Norway
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38
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Sodt AJ, Beaven AH, Andersen OS, Im W, Pastor RW. Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model. Biophys J 2017; 112:1198-1213. [PMID: 28355547 DOI: 10.1016/j.bpj.2017.01.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/11/2017] [Accepted: 01/30/2017] [Indexed: 12/20/2022] Open
Abstract
To change conformation, a protein must deform the surrounding bilayer. In this work, a three-dimensional continuum elastic model for gramicidin A in a lipid bilayer is shown to describe the sensitivity to thickness, curvature stress, and the mechanical properties of the lipid bilayer. A method is demonstrated to extract the gramicidin-lipid boundary condition from all-atom simulations that can be used in the three-dimensional continuum model. The boundary condition affects the deformation dramatically, potentially much more than typical variations in the material stiffness do as lipid composition is changed. Moreover, it directly controls the sensitivity to curvature stress. The curvature stress and hydrophobic surfaces of the all-atom and continuum models are found to be in excellent agreement. The continuum model is applied to estimate the enrichment of hydrophobically matched lipids near the channel in a mixture, and the results agree with single-channel experiments and extended molecular dynamics simulations from the companion article by Beaven et al. in this issue of Biophysical Journal.
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Affiliation(s)
- Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| | - Andrew H Beaven
- Department of Chemistry, The University of Kansas, Lawrence, Kansas
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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39
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Kim S, Patel DS, Park S, Slusky J, Klauda JB, Widmalm G, Im W. Bilayer Properties of Lipid A from Various Gram-Negative Bacteria. Biophys J 2017; 111:1750-1760. [PMID: 27760361 DOI: 10.1016/j.bpj.2016.09.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/19/2016] [Accepted: 09/06/2016] [Indexed: 01/05/2023] Open
Abstract
Lipid A is the lipid anchor of a lipopolysaccharide in the outer leaflet of the outer membrane of Gram-negative bacteria. In general, lipid A consists of two phosphorylated N-acetyl glucosamine and several acyl chains that are directly linked to the two sugars. Depending on the bacterial species and environments, the acyl chain number and length vary, and lipid A can be chemically modified with phosphoethanolamine, aminoarabinose, or glycine residues, which are key to bacterial pathogenesis. In this work, homogeneous lipid bilayers of 21 distinct lipid A types from 12 bacterial species are modeled and simulated to investigate the differences and similarities of their membrane properties. In addition, different neutralizing ion types (Ca2+, K+, and Na+) are considered to examine the ion's influence on the membrane properties. The trajectory analysis shows that (1) the area per lipid is mostly correlated to the acyl chain number, and the area per lipid increases as a function of the acyl chain number; (2) the hydrophobic thickness is mainly determined by the average acyl chain length with slight dependence on the acyl chain number, and the hydrophobic thickness generally increases with the average acyl chain length; (3) a good correlation is observed among the area per lipid, hydrophobic thickness, and acyl chain order; and (4) although the influence of neutralizing ion types on the area per lipid and hydrophobic thickness is minimal, Ca2+ stays longer on the membrane surface than K+ or Na+, consequently leading to lower lateral diffusion and a higher compressibility modulus, which agrees well with available experiments.
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Affiliation(s)
- Seonghoon Kim
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Dhilon S Patel
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Soohyung Park
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Joanna Slusky
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland, College Park, Maryland
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania.
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40
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Bacle A, Gautier R, Jackson CL, Fuchs PFJ, Vanni S. Interdigitation between Triglycerides and Lipids Modulates Surface Properties of Lipid Droplets. Biophys J 2017; 112:1417-1430. [PMID: 28402884 DOI: 10.1016/j.bpj.2017.02.032] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/07/2017] [Accepted: 02/23/2017] [Indexed: 12/12/2022] Open
Abstract
Intracellular lipid droplets (LDs) are the main cellular site of metabolic energy storage. Their structure is unique inside the cell, with a core of esterified fatty acids and sterols, mainly triglycerides and sterol esters, surrounded by a single monolayer of phospholipids. Numerous peripheral proteins, including several that were previously associated with intracellular compartments surrounded by a lipid bilayer, have been recently shown to target the surface of LDs, but how they are able to selectively target this organelle remains largely unknown. Here, we use atomistic and coarse-grained molecular dynamics simulations to investigate the molecular properties of the LD surface and to characterize how it differs from that of a lipid bilayer. Our data suggest that although several surface properties are remarkably similar between the two structures, key differences originate from the interdigitation between surface phospholipids and core neutral lipids that occurs in LDs. This property is extremely sensitive to membrane undulations, unlike in lipid bilayers, and it strongly affects both lipid-packing defects and the lateral pressure profile. We observed a marked change in overall surface properties for surface tensions >10 mN/m, indicative of a bimodal behavior. Our simulations provide a comprehensive molecular characterization of the unique surface properties of LDs and suggest how the molecular properties of the surface lipid monolayer can be modulated by the underlying neutral lipids.
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Affiliation(s)
- Amélie Bacle
- Institut Jacques Monod, UMR 7592, CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Romain Gautier
- Université Cote d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France
| | - Catherine L Jackson
- Institut Jacques Monod, UMR 7592, CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Patrick F J Fuchs
- Institut Jacques Monod, UMR 7592, CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.
| | - Stefano Vanni
- Université Cote d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France.
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41
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Chen Z, Zhu C, Kuo CJ, Robustelli J, Baumgart T. The N-Terminal Amphipathic Helix of Endophilin Does Not Contribute to Its Molecular Curvature Generation Capacity. J Am Chem Soc 2016; 138:14616-14622. [PMID: 27755867 PMCID: PMC5562367 DOI: 10.1021/jacs.6b06820] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-BAR proteins such as endophilin are thought to bend lipid membranes via scaffolding (the molding of membranes through the crescent protein shape) and membrane insertion (also called wedging) of amphipathic helices. However, the contributions from these distinct mechanisms to membrane curvature generation and sensing have remained controversial. Here we quantitatively demonstrate that the amphipathic N-terminal H0 helix of endophilin is important for recruiting this protein to the membrane, but does not contribute significantly to its intrinsic membrane curvature generation capacity. These observations elevate the importance of the scaffolding mechanism, rather than H0 insertion, for the membrane curvature generation by N-BAR domains. Furthermore, consistent with the thermodynamically required coupling between curvature generation and sensing, we observed that the H0-truncated N-BAR domain is capable of sensing membrane curvature. Overall, our contribution clarifies an important mechanistic controversy in the function of N-BAR domain proteins.
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Affiliation(s)
- Zhiming Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Chen Zhu
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Curtis J. Kuo
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Jaclyn Robustelli
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
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42
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Gómez-Llobregat J, Elías-Wolff F, Lindén M. Anisotropic Membrane Curvature Sensing by Amphipathic Peptides. Biophys J 2016; 110:197-204. [PMID: 26745422 DOI: 10.1016/j.bpj.2015.11.3512] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/29/2015] [Accepted: 11/11/2015] [Indexed: 12/29/2022] Open
Abstract
Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodeling cell membranes. However, the molecular driving forces behind these processes are not well understood. Here, we describe an approach to study curvature sensing by simulating the interactions of single molecules with a buckled lipid bilayer. We analyze three amphipathic antimicrobial peptides, a class of membrane-associated molecules that specifically target and destabilize bacterial membranes, and find qualitatively different sensing characteristics that would be difficult to resolve with other methods. Our findings provide evidence for direction-dependent curvature sensing mechanisms in amphipathic peptides and challenge existing theories of hydrophobic insertion. The buckling approach is generally applicable to a wide range of curvature-sensing molecules, and our results provide strong motivation to develop new experimental methods to track position and orientation of membrane proteins.
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Affiliation(s)
- Jordi Gómez-Llobregat
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Federico Elías-Wolff
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Martin Lindén
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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43
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West A, Brummel BE, Braun AR, Rhoades E, Sachs JN. Membrane remodeling and mechanics: Experiments and simulations of α-Synuclein. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:1594-609. [PMID: 26972046 PMCID: PMC5081225 DOI: 10.1016/j.bbamem.2016.03.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/05/2016] [Accepted: 03/07/2016] [Indexed: 01/24/2023]
Abstract
We review experimental and simulation approaches that have been used to determine curvature generation and remodeling of lipid bilayers by membrane-bending proteins. Particular emphasis is placed on the complementary approaches used to study α-Synuclein (αSyn), a major protein involved in Parkinson's disease (PD). Recent cellular and biophysical experiments have shown that the protein 1) deforms the native structure of mitochondrial and model membranes; and 2) inhibits vesicular fusion. Today's advanced experimental and computational technology has made it possible to quantify these protein-induced changes in membrane shape and material properties. Collectively, experiments, theory and multi-scale simulation techniques have established the key physical determinants of membrane remodeling and rigidity: protein binding energy, protein partition depth, protein density, and membrane tension. Despite the exciting and significant progress made in recent years in these areas, challenges remain in connecting biophysical insights to the cellular processes that lead to disease. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Ana West
- Department of Biomedical Engineering, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA
| | - Benjamin E Brummel
- Department of Biomedical Engineering, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA
| | - Anthony R Braun
- Department of Neuroscience, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, 231 S 34th St., Philadelphia, PA 19104, USA
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA.
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44
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Argudo D, Bethel NP, Marcoline FV, Grabe M. Continuum descriptions of membranes and their interaction with proteins: Towards chemically accurate models. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:1619-34. [PMID: 26853937 PMCID: PMC4877259 DOI: 10.1016/j.bbamem.2016.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 01/30/2016] [Accepted: 02/01/2016] [Indexed: 01/21/2023]
Abstract
Biological membranes deform in response to resident proteins leading to a coupling between membrane shape and protein localization. Additionally, the membrane influences the function of membrane proteins. Here we review contributions to this field from continuum elastic membrane models focusing on the class of models that couple the protein to the membrane. While it has been argued that continuum models cannot reproduce the distortions observed in fully-atomistic molecular dynamics simulations, we suggest that this failure can be overcome by using chemically accurate representations of the protein. We outline our recent advances along these lines with our hybrid continuum-atomistic model, and we show the model is in excellent agreement with fully-atomistic simulations of the nhTMEM16 lipid scramblase. We believe that the speed and accuracy of continuum-atomistic methodologies will make it possible to simulate large scale, slow biological processes, such as membrane morphological changes, that are currently beyond the scope of other computational approaches. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- David Argudo
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States
| | - Neville P Bethel
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States
| | - Frank V Marcoline
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States.
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45
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Park S, Beaven AH, Klauda JB, Im W. How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets? J Chem Theory Comput 2016; 11:3466-77. [PMID: 26575780 PMCID: PMC4685941 DOI: 10.1021/acs.jctc.5b00232] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Difficulties in estimating the correct
number of lipids in each
leaflet of complex bilayer membrane simulation systems make it inevitable
to introduce a mismatch in lipid packing (i.e., area per lipid) and
thus alter the lateral pressure of each leaflet. To investigate potential
impacts of such mismatch on simulation results, we performed molecular
dynamics simulations of saturated and monounsaturated lipid bilayers
with and without gramicidin A or WALP23 at various mismatches by adjusting
the number of lipids in the lower leaflet from no mismatch to a 25%
reduction compared to that in the upper leaflet. All simulations were
stable under the constant pressure barostat, but the mismatch induces
asymmetric lipid packing between the leaflets, so that the upper leaflet
becomes more ordered, and the lower leaflet becomes less ordered.
The mismatch impacts on various bilayer properties are mild up to
5–10% mismatch, and bilayers with fully saturated chains appear
to be more prone to these impacts than those with unsaturated tails.
The nonvanishing leaflet surface tensions and the free energy derivatives
with respect to the bilayer curvature indicate that the bilayer would
be energetically unstable in the presence of mismatch. We propose
a quantitative criterion for allowable mismatch based on the energetics
derived from a continuum elastic model, which grows as a square root
of the number of the lipids in the system. On the basis of this criterion,
we infer that the area per lipid mismatch up to 5% would be tolerable
in various membrane simulations of reasonable all-atom system sizes
(40–160 lipids per leaflet).
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Affiliation(s)
| | | | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland , College Park, Maryland 20742, United States
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46
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Zhang L, Rajendram M, Weibel DB, Yethiraj A, Cui Q. Ionic Hydrogen Bonds and Lipid Packing Defects Determine the Binding Orientation and Insertion Depth of RecA on Multicomponent Lipid Bilayers. J Phys Chem B 2016; 120:8424-37. [PMID: 27095675 DOI: 10.1021/acs.jpcb.6b02164] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We describe a computational and experimental approach for probing the binding properties of the RecA protein at the surface of anionic membranes. Fluorescence measurements indicate that RecA behaves differently when bound to phosphatidylglycerol (PG)- and cardiolipin (CL)-containing liposomes. We use a multistage computational protocol that integrates an implicit membrane/solvent model, the highly mobile mimetic membrane model, and the full atomistic membrane model to study how different anionic lipids perturb RecA binding to the membrane. With anionic lipids studied here, the binding interface involves three key regions: the N-terminal helix, the DNA binding loop L2, and the M-M7 region. The nature of binding involves both electrostatic interactions between cationic protein residues and lipid polar/charged groups and insertion of hydrophobic residues. The L2 loop contributes more to membrane insertion than the N-terminal helix. More subtle aspects of RecA-membrane interaction are influenced by specific properties of anionic lipids. Ionic hydrogen bonds between the carboxylate group in phosphatidylserine and several lysine residues in the C-terminal region of RecA stabilize the parallel (∥) binding orientation, which is not locally stable on PG- and CL-containing membranes despite similarity in the overall charge density. Lipid packing defects, which are more prevalent in the presence of conical lipids, are observed to enhance the insertion depth of hydrophobic motifs. The computational finding that RecA binds in a similar orientation to PG- and CL-containing membranes is consistent with the fact that PG alone is sufficient to induce RecA polar localization, although CL might be more effective because of its tighter binding to RecA. The different fluorescence behaviors of RecA upon binding to PG- and CL-containing liposomes is likely due to the different structures and flexibility of the C-terminal region of RecA when it binds to different anionic phospholipids.
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Affiliation(s)
- Leili Zhang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Manohary Rajendram
- Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Douglas B Weibel
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.,Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States.,Department of Biomedical Engineering, University of Wisconsin-Madison , 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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47
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Braun AR, Sachs JN. α-Synuclein Reduces Tension and Increases Undulations in Simulations of Small Unilamellar Vesicles. Biophys J 2016; 108:1848-51. [PMID: 25902424 DOI: 10.1016/j.bpj.2015.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/23/2015] [Accepted: 03/10/2015] [Indexed: 01/21/2023] Open
Abstract
Using coarse-grained molecular dynamics simulations we have explored the effect of α-Synuclein (αSyn) on the structural and mechanical properties of small unilamellar vesicles in the fluid-phase. The study is motivated by observations that a high density of membrane-bound αSyn inhibits the fusion of synthetic small unilamellar vesicles. By combining three-dimensional pressure tensor calculations with our recently developed spherical harmonics fluctuation analysis approach, we show a reduction in membrane surface tension and increased membrane undulations when αSyn is bound to the vesicle's outer leaflet at a 200:1 L/P. The protein effects these changes by decreasing the negative pressure in the headgroup region of the outer leaflet and increasing the positive pressure throughout the hydrocarbon core.
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Affiliation(s)
- Anthony R Braun
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota.
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48
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Lyman E, Sodt AJ. Amphipathic Helices-Wedge? Or Nae Nae? Biophys J 2016; 110:1-2. [PMID: 26745402 DOI: 10.1016/j.bpj.2015.11.3513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 11/26/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022] Open
Affiliation(s)
- Edward Lyman
- Department of Physics and Astronomy and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware.
| | - Alexander J Sodt
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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49
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Smrt ST, Lorieau JL. Membrane Fusion and Infection of the Influenza Hemagglutinin. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 966:37-54. [PMID: 27966108 DOI: 10.1007/5584_2016_174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The influenza virus is a major health concern associated with an estimated 5000 to 30,000 deaths every year (Reed et al. 2015) and a significant economic impact with the development of treatments, vaccinations and research (Molinari et al. 2007). The entirety of the influenza genome is comprised of only eleven coding genes. An enormous degree of variation in non-conserved regions leads to significant challenges in the development of inclusive inhibitors for treatment. The fusion peptide domain of the influenza A hemagglutinin (HA) is a promising candidate for treatment since it is one of the most highly conserved sequences in the influenza genome (Heiny et al. 2007), and it is vital to the viral life cycle. Hemagglutinin is a class I viral fusion protein that catalyzes the membrane fusion process during cellular entry and infection. Impediment of the hemagglutinin's function, either through incomplete post-translational processing (Klenk et al. 1975; Lazarowitz and Choppin 1975) or through mutations (Cross et al. 2001), leads to non-infective virus particles. This review will investigate current research on the role of hemagglutinin in the virus life cycle, its structural biology and mechanism as well as the central role of the hemagglutinin fusion peptide (HAfp) to influenza membrane fusion and infection.
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Affiliation(s)
- Sean T Smrt
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Justin L Lorieau
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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50
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Ding W, Palaiokostas M, Wang W, Orsi M. Effects of Lipid Composition on Bilayer Membranes Quantified by All-Atom Molecular Dynamics. J Phys Chem B 2015; 119:15263-74. [PMID: 26560961 DOI: 10.1021/acs.jpcb.5b06604] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological bilayer membranes typically contain varying amounts of lamellar and nonlamellar lipids. Lamellar lipids, such as dioleoylphosphatidylcholine (DOPC), are defined by their tendency to form the lamellar phase, ubiquitous in biology. Nonlamellar lipids, such as dioleoylphosphatidylethanolamine (DOPE), prefer instead to form nonlamellar phases, which are mostly nonbiological. However, nonlamellar lipids mix with lamellar lipids in biomembrane structures that remain overall lamellar. Importantly, changes in the lamellar vs nonlamellar lipid composition are believed to affect membrane function and modulate membrane proteins. In this work, we employ atomistic molecular dynamics simulations to quantify how a range of bilayer properties are altered by variations in the lamellar vs nonlamellar lipid composition. Specifically, we simulate five DOPC/DOPE bilayers at mixing ratios of 1/0, 3/1, 1/1, 1/3, and 0/1. We examine properties including lipid area and bilayer thickness, as well as the transmembrane profiles of electron density, lateral pressure, electric field, and dipole potential. While the bilayer structure is only marginally altered by lipid composition changes, dramatic effects are observed for the lateral pressure, electric field, and dipole potential profiles. Possible implications for membrane function are discussed.
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Affiliation(s)
- Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
| | - Wen Wang
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
| | - Mario Orsi
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London, E1 4NS, U.K
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