1
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Peyear TA, Andersen OS. Screening for bilayer-active and likely cytotoxic molecules reveals bilayer-mediated regulation of cell function. J Gen Physiol 2023; 155:e202213247. [PMID: 36763053 PMCID: PMC9948646 DOI: 10.1085/jgp.202213247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/06/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023] Open
Abstract
A perennial problem encountered when using small molecules (drugs) to manipulate cell or protein function is to assess whether observed changes in function result from specific interactions with a desired target or from less specific off-target mechanisms. This is important in laboratory research as well as in drug development, where the goal is to identify molecules that are unlikely to be successful therapeutics early in the process, thereby avoiding costly mistakes. We pursued this challenge from the perspective that many bioactive molecules (drugs) are amphiphiles that alter lipid bilayer elastic properties, which may cause indiscriminate changes in membrane protein (and cell) function and, in turn, cytotoxicity. Such drug-induced changes in bilayer properties can be quantified as changes in the monomer↔dimer equilibrium for bilayer-spanning gramicidin channels. Using this approach, we tested whether molecules in the Pathogen Box (a library of 400 drugs and drug-like molecules with confirmed activity against tropical diseases released by Medicines for Malaria Venture to encourage the development of therapies for neglected tropical diseases) are bilayer modifiers. 32% of the molecules in the Pathogen Box were bilayer modifiers, defined as molecules that at 10 µM shifted the monomer↔dimer equilibrium toward the conducting dimers by at least 50%. Correlation analysis of the molecules' reported HepG2 cell cytotoxicity to bilayer-modifying potency, quantified as the shift in the gramicidin monomer↔dimer equilibrium, revealed that molecules producing <25% change in the equilibrium had significantly lower probability of being cytotoxic than molecules producing >50% change. Neither cytotoxicity nor bilayer-modifying potency (quantified as the shift in the gramicidin monomer↔dimer equilibrium) was well predicted by conventional physico-chemical descriptors (hydrophobicity, polar surface area, etc.). We conclude that drug-induced changes in lipid bilayer properties are robust predictors of the likelihood of membrane-mediated off-target effects, including cytotoxicity.
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Affiliation(s)
- Thasin A. Peyear
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences. New York, NY, USA
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
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2
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Tóth Á, Janaszkiewicz A, Crespi V, Di Meo F. On the interplay between lipids and asymmetric dynamics of an NBS degenerate ABC transporter. Commun Biol 2023; 6:149. [PMID: 36737455 PMCID: PMC9898250 DOI: 10.1038/s42003-023-04537-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Multidrug resistance-associated proteins are ABC C-family exporters. They are crucial in pharmacology as they transport various substrates across membranes. However, the role of the degenerate nucleotide-binding site (NBS) remains unclear likewise the interplay with the surrounding lipid environment. Here, we propose a dynamic and structural overview of MRP1 from ca. 110 μs molecular dynamics simulations. ATP binding to NBS1 is likely maintained along several transport cycles. Asymmetric NBD behaviour is ensured by lower signal transduction from NBD1 to the rest of the protein owing to the absence of ball-and-socket conformation between NBD1 and coupling helices. Even though surrounding lipids play an active role in the allosteric communication between the substrate-binding pocket and NBDs, our results suggest that lipid composition has a limited impact, mostly by affecting transport kinetics. We believe that our work can be extended to other degenerate NBS ABC proteins and provide hints for deciphering mechanistic differences among ABC transporters.
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Affiliation(s)
- Ágota Tóth
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Angelika Janaszkiewicz
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Veronica Crespi
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Florent Di Meo
- Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute-Univ. Limoges, 2 rue du Prof. Descottes, 87000 F, Limoges, France.
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3
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Alas CD, Haselwandter CA. Dependence of protein-induced lipid bilayer deformations on protein shape. Phys Rev E 2023; 107:024403. [PMID: 36932542 DOI: 10.1103/physreve.107.024403] [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: 08/09/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Membrane proteins typically deform the surrounding lipid bilayer membrane, which can play an important role in the function, regulation, and organization of membrane proteins. Membrane elasticity theory provides a beautiful description of protein-induced lipid bilayer deformations, in which all physical parameters can be directly determined from experiments. While analytic solutions of protein-induced elastic bilayer deformations are most easily developed for proteins with approximately circular cross sections, structural biology has shown that membrane proteins come in a variety of distinct shapes, with often considerable deviations from a circular cross section. We develop here a boundary value method (BVM) that permits the construction of analytic solutions of protein-induced elastic bilayer deformations for protein shapes with arbitrarily large deviations from a circular cross section, for constant as well as variable boundary conditions along the bilayer-protein interface. We apply this BVM to protein-induced lipid bilayer thickness deformations. Our BVM reproduces available analytic solutions for proteins with circular cross section and yields, for proteins with noncircular cross section, excellent agreement with numerical, finite element solutions. On this basis, we formulate a simple analytic approximation of the bilayer thickness deformation energy associated with general protein shapes and show that, for modest deviations from rotational symmetry, this analytic approximation is in good agreement with BVM solutions. Using the BVM, we survey the dependence of protein-induced elastic bilayer thickness deformations on protein shape, and thus explore how the coupling of protein shape and bilayer thickness deformations affects protein oligomerization and transitions in protein conformational state.
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Affiliation(s)
- Carlos D Alas
- Department of Physics and Astronomy and Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
| | - Christoph A Haselwandter
- Department of Physics and Astronomy and Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
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4
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Bakhtiari S, Manshadi MKD, Candas M, Beskok A. Changes in Electrical Capacitance of Cell Membrane Reflect Drug Partitioning-Induced Alterations in Lipid Bilayer. MICROMACHINES 2023; 14:316. [PMID: 36838014 PMCID: PMC9961635 DOI: 10.3390/mi14020316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/06/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
The plasma membrane is a lipid bilayer that establishes the outer boundary of a living cell. The composition of the lipid bilayer influences the membrane's biophysical properties, including fluidity, thickness, permeability, phase behavior, charge, elasticity, and formation of flat sheet or curved structures. Changes in the biophysical properties of the membrane can be occasioned when new entities, such as drug molecules, are partitioned in the bilayer. Therefore, assessing drugs for their effect on the biophysical properties of the lipid bilayer of a cell membrane is critical to understanding specific and non-specific drug action. Previously, we reported a non-invasive technique for real-time characterization of cellular dielectric properties, such as membrane capacitance and cytoplasmic conductivity. In this study, we discuss the potential application of the technique in assessing the biophysical properties of the cell membrane in response to interaction with amiodarone compared to aspirin/acetylsalicylic acid and glucose. Amiodarone is a potent drug used to treat cardiac arrhythmia, but it also exerts various non-specific effects. Compared to aspirin and glucose, we measured a rapid and higher magnitude increase in membrane capacitance on cells under amiodarone treatment. Increased membrane capacitance induced by aspirin and glucose quickly returned to baseline in 15 s, while amiodarone-induced increased capacitance sustained and decreased slowly, approaching baseline or another asymptotic limit in ~2.5 h. Because amiodarone has a strong lipid partitioning property, we reason that drug partitioning alters the lipid bilayer context and subsequently reduces bilayer thickness, leading to an increase in the electrical capacitance of the cell membrane. The presented microfluidic system promises a new approach to assess drug-membrane interactions and delineate specific and non-specific actions of the drug on cells.
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Affiliation(s)
- Shide Bakhtiari
- Mechanical Engineering Department, Southern Methodist University, Dallas, TX 75275, USA
| | | | - Mehmet Candas
- Department of Biological Sciences, University of Texas at Dallas, Dallas, TX 75080, USA
| | - Ali Beskok
- Mechanical Engineering Department, Southern Methodist University, Dallas, TX 75275, USA
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5
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Qin X, Tieleman DP, Liang Q. Effects of Cholesterol and PIP2 on Interactions between Glycophorin A and Band 3 in Lipid Bilayers. Biophys J 2022; 121:2069-2077. [PMID: 35524411 DOI: 10.1016/j.bpj.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/17/2022] [Accepted: 05/02/2022] [Indexed: 11/02/2022] Open
Abstract
In the erythrocyte membrane, the interactions between Glycophorin A (GPA) and Band 3 are associated strongly with the biological function of the membrane and several blood disorders. In this work, using coarse-grained molecular dynamics simulation, we systematically investigate the effects of cholesterol and phosphatidylinositol-4,5-bisphosphate (PIP2) on the interactions of GPA with Band 3 in the model erythrocyte membranes. We examine the dynamics of the interactions of GPA with Band 3 in different lipid bilayers on the microsecond time scale and calculate the binding free energy between GPA and Band 3. The results indicate that cholesterols thermodynamically favor the binding of GPA to Band 3 by increasing the thickness of the lipid bilayer and by producing an effective attraction between the proteins due to the depletion effect. Cholesterols also slow the kinetics of the binding of GPA to Band 3 by reducing the lateral mobility of the lipids and proteins and may influence the binding sites between the proteins. The anionic PIP2 lipids prefer binding to the surface of the proteins through electrostatic attraction between the PIP2 headgroup and the positively charged residues on the protein surface. Ions in the solvent facilitate the PIP2 aggregation which promotes the binding of GPA to Band 3.
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Affiliation(s)
- Xiaoxue Qin
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| | - D Peter Tieleman
- Centre for Molecular Simulations and Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China.
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6
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Gao J, Hou R, Li L, Hu J. Membrane-Mediated Interactions Between Protein Inclusions. Front Mol Biosci 2021; 8:811711. [PMID: 35004858 PMCID: PMC8727768 DOI: 10.3389/fmolb.2021.811711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Integral or peripheral membrane proteins, or protein oligomers often get close to each other on cell membranes and carry out biological tasks in a collective manner. In addition to electrostatic and van der Waals interactions, those proteins also experience membrane-mediated interactions, which may be necessary for their functionality. The membrane-mediated interactions originate from perturbation of lipid membranes by the presence of protein inclusions, and have been the subject of intensive research in membrane biophysics. Here we review both theoretical and numerical studies of such interactions for membrane proteins and for nanoparticles bound to lipid membranes.
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Affiliation(s)
- Jie Gao
- Kuang Yaming Honors School, Nanjing University, Nanjing, China
| | - Ruihan Hou
- Kuang Yaming Honors School, Nanjing University, Nanjing, China
| | - Long Li
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
| | - Jinglei Hu
- Kuang Yaming Honors School, Nanjing University, Nanjing, China
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7
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Khelashvili G, Pillai AN, Lee J, Pandey K, Payne AM, Siegel Z, Cuendet MA, Lewis TR, Arshavsky VY, Broichhagen J, Levitz J, Menon AK. Unusual mode of dimerization of retinitis pigmentosa-associated F220C rhodopsin. Sci Rep 2021; 11:10536. [PMID: 34006992 PMCID: PMC8131606 DOI: 10.1038/s41598-021-90039-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/29/2021] [Indexed: 12/30/2022] Open
Abstract
Mutations in the G protein-coupled receptor (GPCR) rhodopsin are a common cause of autosomal dominant retinitis pigmentosa, a blinding disease. Rhodopsin self-associates in the membrane, and the purified monomeric apo-protein opsin dimerizes in vitro as it transitions from detergent micelles to reconstitute into a lipid bilayer. We previously reported that the retinitis pigmentosa-linked F220C opsin mutant fails to dimerize in vitro, reconstituting as a monomer. Using fluorescence-based assays and molecular dynamics simulations we now report that whereas wild-type and F220C opsin display distinct dimerization propensities in vitro as previously shown, they both dimerize in the plasma membrane of HEK293 cells. Unexpectedly, molecular dynamics simulations show that F220C opsin forms an energetically favored dimer in the membrane when compared with the wild-type protein. The conformation of the F220C dimer is unique, with transmembrane helices 5 and 6 splayed apart, promoting widening of the intracellular vestibule of each protomer and influx of water into the protein interior. FRET experiments with SNAP-tagged wild-type and F220C opsin expressed in HEK293 cells are consistent with this conformational difference. We speculate that the unusual mode of dimerization of F220C opsin in the membrane may have physiological consequences.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA.
- Institute of Computational Biomedicine, Weill Cornell Medical College, New York, NY, 10065, USA.
| | | | - Joon Lee
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kalpana Pandey
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Alexander M Payne
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Zarek Siegel
- Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michel A Cuendet
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Tylor R Lewis
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut Für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA.
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8
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Dielectric Spectroscopy Based Detection of Specific and Nonspecific Cellular Mechanisms. SENSORS 2021; 21:s21093177. [PMID: 34063599 PMCID: PMC8124793 DOI: 10.3390/s21093177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/14/2022]
Abstract
Using radiofrequency dielectric spectroscopy, we have investigated the impact of the interaction between a G protein-coupled receptor (GPCR), the sterile2 α-factor receptor protein (Ste2), and its cognate agonist ligand, the α-factor pheromone, on the dielectric properties of the plasma membrane in living yeast cells (Saccharomyces cerevisiae). The dielectric properties of a cell suspension containing a saturating concentration of α-factor were measured over the frequency range 40Hz–110 MHz and compared to the behavior of a similarly prepared suspension of cells in the absence of α-factor. A spherical three-shell model was used to determine the electrical phase parameters for the yeast cells in both types of suspensions. The relative permittivity of the plasma membrane showed a significant increase after exposure to α-factor (by 0.06 ± 0.05). The equivalent experiment performed on yeast cells lacking the ability to express Ste2 showed no change in plasma membrane permittivity. Interestingly, a large change also occurred to the electrical properties of the cellular interior after the addition of α-factor to the cell suspending medium, whether or not the cells were expressing Ste2. We present a number of different complementary experiments performed on the yeast to support these dielectric data and interpret the results in terms of specific cellular reactions to the presence of α-factor.
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9
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Study of the Interaction of a Novel Semi-Synthetic Peptide with Model Lipid Membranes. MEMBRANES 2020; 10:membranes10100294. [PMID: 33086635 PMCID: PMC7603383 DOI: 10.3390/membranes10100294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 12/31/2022]
Abstract
Most linear peptides directly interact with membranes, but the mechanisms of interaction are far from being completely understood. Here, we present an investigation of the membrane interactions of a designed peptide containing a non-natural, synthetic amino acid. We selected a nonapeptide that is reported to interact with phospholipid membranes, ALYLAIRKR, abbreviated as ALY. We designed a modified peptide (azoALY) by substituting the tyrosine residue of ALY with an antimicrobial azobenzene-bearing amino acid. Both of the peptides were examined for their ability to interact with model membranes, assessing the penetration of phospholipid monolayers, and leakage across the bilayer of large unilamellar vesicles (LUVs) and giant unilamellar vesicles (GUVs). The latter was performed in a microfluidic device in order to study the kinetics of leakage of entrapped calcein from the vesicles at the single vesicle level. Both types of vesicles were prepared from a 9:1 (mol/mol) mixture of POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho(1′-rac-glycerol). Calcein leakage from the vesicles was more pronounced at a low concentration in the case of azoALY than for ALY. Increased vesicle membrane disturbance in the presence of azoALY was also evident from an enzymatic assay with LUVs and entrapped horseradish peroxidase. Molecular dynamics simulations of ALY and azoALY in an anionic POPC/POPG model bilayer showed that ALY peptide only interacts with the lipid head groups. In contrast, azoALY penetrates the hydrophobic core of the bilayers causing a stronger membrane perturbation as compared to ALY, in qualitative agreement with the experimental results from the leakage assays.
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10
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Schachter I, Allolio C, Khelashvili G, Harries D. Confinement in Nanodiscs Anisotropically Modifies Lipid Bilayer Elastic Properties. J Phys Chem B 2020; 124:7166-7175. [PMID: 32697588 PMCID: PMC7526989 DOI: 10.1021/acs.jpcb.0c03374] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
Lipid
nanodiscs are small synthetic lipid bilayer structures that
are stabilized in solution by special circumscribing (or scaffolding)
proteins or polymers. Because they create native-like environments
for transmembrane proteins, lipid nanodiscs have become a powerful
tool for structural determination of this class of systems when combined
with cryo-electron microscopy or nuclear magnetic resonance. The elastic
properties of lipid bilayers determine how the lipid environment responds
to membrane protein perturbations, and how the lipid in turn modifies
the conformational state of the embedded protein. However, despite
the abundant use of nanodiscs in determining membrane protein structure,
the elastic material properties of even pure lipid nanodiscs (i.e.,
without embedded proteins) have not yet been quantitatively investigated.
A major hurdle is due to the inherently nonlocal treatment of the
elastic properties of lipid systems implemented by most existing methods,
both experimental and computational. In addition, these methods are
best suited for very large “infinite” size lipidic assemblies,
or ones that contain periodicity, in the case of simulations. We have
previously described a computational analysis of molecular dynamics
simulations designed to overcome these limitations, so it allows quantification
of the bending rigidity (KC) and tilt
modulus (κt) on a local scale even for finite, nonperiodic
systems, such as lipid nanodiscs. Here we use this computational approach
to extract values of KC and κt for a set of lipid nanodisc systems that vary in size and
lipid composition. We find that the material properties of lipid nanodiscs
are different from those of infinite bilayers of corresponding lipid
composition, highlighting the effect of nanodisc confinement. Nanodiscs
tend to show higher stiffness than their corresponding macroscopic
bilayers, and moreover, their material properties vary spatially within
them. For small-size MSP1 nanodiscs, the stiffness decreases radially,
from a value that is larger in their center than the moduli of the
corresponding bilayers by a factor of ∼2–3. The larger
nanodiscs (MSP1E3D1 and MSP2N2) show milder spatial changes of moduli
that are composition dependent and can be maximal in the center or
at some distance from it. These trends in moduli correlate with spatially
varying structural properties, including the area per lipid and the
nanodisc thickness. Finally, as has previously been reported, nanodiscs
tend to show deformations from perfectly flat circular geometries
to varying degrees, depending on size and lipid composition. The modulations
of lipid elastic properties that we find should be carefully considered
when making structural and functional inferences concerning embedded
proteins.
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Affiliation(s)
- Itay Schachter
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Christoph Allolio
- Institute of Mathematics, Faculty of Mathematics and Physics, Charles University, Prague 18674, Czech Republic
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States.,Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
| | - Daniel Harries
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
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11
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Khelashvili G, Cheng X, Falzone ME, Doktorova M, Accardi A, Weinstein H. Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins. J Comput Chem 2020; 41:538-551. [PMID: 31750558 PMCID: PMC7261202 DOI: 10.1002/jcc.26105] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/04/2019] [Accepted: 10/17/2019] [Indexed: 12/21/2022]
Abstract
Recent discoveries about functional mechanisms of proteins in the TMEM16 family of phospholipid scramblases have illuminated the dual role of the membrane as both the substrate and a mechanistically responsive environment in the wide range of physiological processes and genetic disorders in which they are implicated. This is highlighted in the review of recent findings from our collaborative investigations of molecular mechanisms of TMEM16 scramblases that emerged from iterative functional, structural, and computational experimentation. In the context of this review, we present new MD simulations and trajectory analyses motivated by the fact that new structural information about the TMEM16 scramblases is emerging from cryo-EM determinations in lipid nanodiscs. Because the functional environment of these proteins in in vivo and in in vitro is closer to flat membranes, we studied comparatively the responses of the membrane to the TMEM16 proteins in flat membranes and nanodiscs. We find that bilayer shapes in the nanodiscs are very different from those observed in the flat membrane systems, but the function-related slanting of the membrane observed at the nhTMEM16 boundary with the protein is similar in the nanodiscs and in the flat bilayers. This changes, however, in the bilayer composed of longer-tail lipids, which is thicker near the phospholipid translocation pathway, which may reflect an enhanced tendency of the long tails to penetrate the pathway and create, as shown previously, a nonconductive environment. These findings support the correspondence between the mechanistic involvement of the lipid environment in the flat membranes, and the nanodiscs. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, 10065
- Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York, 10065
| | - Xiaolu Cheng
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, 10065
| | - Maria E Falzone
- Department of Biochemistry, Weill Cornell Medical College of Cornell University, New York, New York, 10065
| | - Milka Doktorova
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, 77030
| | - Alessio Accardi
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, 10065
- Department of Biochemistry, Weill Cornell Medical College of Cornell University, New York, New York, 10065
- Department of Anesthesiology, Weill Cornell Medical College of Cornell University, New York, New York, 10065
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, 10065
- Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York, 10065
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12
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Zhou W, Fiorin G, Anselmi C, Karimi-Varzaneh HA, Poblete H, Forrest LR, Faraldo-Gómez JD. Large-scale state-dependent membrane remodeling by a transporter protein. eLife 2019; 8:50576. [PMID: 31855177 PMCID: PMC6957315 DOI: 10.7554/elife.50576] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/17/2019] [Indexed: 12/22/2022] Open
Abstract
That channels and transporters can influence the membrane morphology is increasingly recognized. Less appreciated is that the extent and free-energy cost of these deformations likely varies among different functional states of a protein, and thus, that they might contribute significantly to defining its mechanism. We consider the trimeric Na+-aspartate symporter GltPh, a homolog of an important class of neurotransmitter transporters, whose mechanism entails one of the most drastic structural changes known. Molecular simulations indicate that when the protomers become inward-facing, they cause deep, long-ranged, and yet mutually-independent membrane deformations. Using a novel simulation methodology, we estimate that the free-energy cost of this membrane perturbation is in the order of 6–7 kcal/mol per protomer. Compensating free-energy contributions within the protein or its environment must thus stabilize this inward-facing conformation for the transporter to function. We discuss these striking results in the context of existing experimental observations for this and other transporters.
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Affiliation(s)
- Wenchang Zhou
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Giacomo Fiorin
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Claudio Anselmi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Hossein Ali Karimi-Varzaneh
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Horacio Poblete
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States.,Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
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13
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Park S, Yeom MS, Andersen OS, Pastor RW, Im W. Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation between Binary Bilayers. J Chem Theory Comput 2019; 15:6491-6503. [PMID: 31560853 PMCID: PMC7076909 DOI: 10.1021/acs.jctc.9b00815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using a recently developed binary bilayer system (BBS) consisting of two patches of laterally contacting bilayers, umbrella sampling molecular dynamics (MD) simulations were performed for quantitative characterization of protein-lipid interactions. The BBS is composed of 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) with an embedded model membrane protein, a gramicidin A (gA) channel. The calculated free energy difference for the transfer of a gA channel from DLPC (hydrophobic thickness ≈ 21.5 Å) to DMPC (hydrophobic thickness ≈ 25.5 Å) bilayers, ΔG(DLPC → DMPC), is -2.2 ± 0.7 kcal/mol. This value appears at odds with the traditional view that the hydrophobic length of the gA channel is ∼22 Å. To understand this discrepancy, we first note that recent MD simulations by different groups have shown that lipid bilayer thickness profiles in the vicinity of a gA channel differ qualitatively from the deformation profile predicted from continuum elastic bilayer models. Our MD simulations at low and high gA:lipid molar ratios and different membrane compositions indicate that the gA channel's effective hydrophobic length is ∼26 Å. Using this effective hydrophobic length, ΔG(DLPC → DMPC) determined here is in excellent agreement with predictions based on continuum elastic models (-3.0 to -2.2 kcal/mol) where the bilayer deformation energy is approximated as a harmonic function of the mismatch between the channel's effective hydrophobic length and the hydrophobic thickness of the bilayer. The free energy profile for gA in the BBS includes a barrier at the interface between the two bilayers which can be attributed to the line tension at the interface between two bilayers with different hydrophobic thicknesses. This observation implies that translation of a peptide between two different regions of a cell membrane (such as between the liquid ordered and disordered phases) may include effects of a barrier at the interface in addition to the relative free energies of the species far from the interface. The BBS allows for direct transfer free energy calculations between bilayers without a need of a reference medium, such as bulk water, and thus provides an efficient simulation protocol for the quantitative characterization of protein-lipid interactions at all-atom resolution.
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Affiliation(s)
- Soohyung Park
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information , Daejeon , Korea
| | - Olaf S Andersen
- Department of Physiology and Biophysics , Weill Cornell Medicine , New York , New York 10065 , United States
| | - Richard W Pastor
- 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 Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States.,School of Computational Sciences , Korea Institute for Advanced Study , Seoul 02455 , Republic of Korea
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14
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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15
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Kapoor R, Peyear TA, Koeppe RE, Andersen OS. Antidepressants are modifiers of lipid bilayer properties. J Gen Physiol 2019; 151:342-356. [PMID: 30796095 PMCID: PMC6400527 DOI: 10.1085/jgp.201812263] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/17/2019] [Indexed: 12/28/2022] Open
Abstract
The two major classes of antidepressants, tricyclic antidepressants (TCAs) and selective serotonin reuptake inhibitors (SSRIs), inhibit neurotransmitter reuptake at synapses. They also have off-target effects on proteins other than neurotransmitter transporters, which may contribute to both desired changes in brain function and the development of side effects. Many proteins modulated by antidepressants are bilayer spanning and coupled to the bilayer through hydrophobic interactions such that the conformational changes underlying their function will perturb the surrounding lipid bilayer, with an energetic cost (ΔG def) that varies with changes in bilayer properties. Here, we test whether changes in ΔG def caused by amphiphilic antidepressants partitioning into the bilayer are sufficient to alter membrane protein function. Using gramicidin A (gA) channels to probe whether TCAs and SSRIs alter the bilayer contribution to the free energy difference for the gramicidin monomer⇔dimer equilibrium (representing a well-defined conformational transition), we find that antidepressants alter gA channel activity with varying potency and no stereospecificity but with different effects on bilayer elasticity and intrinsic curvature. Measuring the antidepressant partition coefficients using isothermal titration calorimetry (ITC) or cLogP shows that the bilayer-modifying potency is predicted quite well by the ITC-determined partition coefficients, and channel activity is doubled at an antidepressant/lipid mole ratio of 0.02-0.07. These results suggest a mechanism by which antidepressants could alter the function of diverse membrane proteins by partitioning into cell membranes and thereby altering the bilayer contribution to the energetics of membrane protein conformational changes.
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Affiliation(s)
- Ruchi Kapoor
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY
| | - Thasin A Peyear
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY
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16
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Chen H, Panagiotopoulos AZ. Molecular Modeling of Surfactant Micellization Using Solvent-Accessible Surface Area. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:2443-2450. [PMID: 30624073 DOI: 10.1021/acs.langmuir.8b03440] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We report a new implicit solvent simulation model for studying the self-assembly of surfactants, where the hydrophobic interactions were captured by calculating the relative changes of the solvent-accessible surface area (SASA) of the hydrophobic domains. Using histogram-reweighting grand canonical Monte Carlo simulations, we demonstrate that this approach allows us to match both the experimental critical micelle concentrations (cmc) and micellar aggregation numbers simultaneously with a single phenomenological surface tension γSASA for the poly(oxyethylene) monoalkyl ether (C mE n) surfactants in aqueous solutions. Excellent transferability is observed: the same model can accurately predict the experimental cmc and aggregation numbers for the C mE n surfactants with the alkyl lengths m between 6 and 12 and the poly(oxyethylene) lengths n between 1 and 9. The SASA-based implicit solvent model put forward in this work is general and may be applied to study more complex amphiphilic systems such as surfactants with branched alkyl chains or surfactant-hydrocarbon mixtures.
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Affiliation(s)
- Hsieh Chen
- Aramco Services Company: Aramco Research Center-Boston , 400 Technology Square , Cambridge , Massachusetts 02139 , United States
| | - Athanassios Z Panagiotopoulos
- Department of Chemical and Biological Engineering , Princeton University , Princeton , New Jersey 08544 , United States
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17
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Doktorova M, Heberle FA, Marquardt D, Rusinova R, Sanford RL, Peyear TA, Katsaras J, Feigenson GW, Weinstein H, Andersen OS. Gramicidin Increases Lipid Flip-Flop in Symmetric and Asymmetric Lipid Vesicles. Biophys J 2019; 116:860-873. [PMID: 30755300 PMCID: PMC6400823 DOI: 10.1016/j.bpj.2019.01.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/03/2019] [Accepted: 01/09/2019] [Indexed: 01/06/2023] Open
Abstract
Unlike most transmembrane proteins, phospholipids can migrate from one leaflet of the membrane to the other. Because this spontaneous lipid translocation (flip-flop) tends to be very slow, cells facilitate the process with enzymes that catalyze the transmembrane movement and thereby regulate the transbilayer lipid distribution. Nonenzymatic membrane-spanning proteins with unrelated primary functions have also been found to accelerate lipid flip-flop in a nonspecific manner and by various hypothesized mechanisms. Using deuterated phospholipids, we examined the acceleration of flip-flop by gramicidin channels, which have well-defined structures and known functions, features that make them ideal candidates for probing the protein-membrane interactions underlying lipid flip-flop. To study compositionally and isotopically asymmetric proteoliposomes containing gramicidin, we expanded a recently developed protocol for the preparation and characterization of lipid-only asymmetric vesicles. Channel incorporation, conformation, and function were examined with small angle x-ray scattering, circular dichroism, and a stopped-flow spectrofluorometric assay, respectively. As a measure of lipid scrambling, we used differential scanning calorimetry to monitor the effect of gramicidin on the melting transition temperatures of the two bilayer leaflets. The two calorimetric peaks of the individual leaflets merged into a single peak over time, suggestive of scrambling, and the effect of the channel on the transbilayer lipid distribution in both symmetric 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and asymmetric 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles was quantified from proton NMR measurements. Our results show that gramicidin increases lipid flip-flop in a complex, concentration-dependent manner. To determine the molecular mechanism of the process, we used molecular dynamics simulations and further computational analysis of the trajectories to estimate the extent of membrane deformation. Together, the experimental and computational approaches were found to constitute an effective means for studying the effects of transmembrane proteins on lipid distribution in both symmetric and asymmetric model membranes.
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Affiliation(s)
- Milka Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York.
| | - Frederick A Heberle
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas; The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee
| | | | - Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - R Lea Sanford
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Thasin A Peyear
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - John Katsaras
- Large Scale Structures Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Gerald W Feigenson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Greenberg Center, New York, New York
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
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18
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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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19
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Structural insights into positive and negative allosteric regulation of a G protein-coupled receptor through protein-lipid interactions. Sci Rep 2018. [PMID: 29535353 PMCID: PMC5849739 DOI: 10.1038/s41598-018-22735-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Lipids are becoming known as essential allosteric modulators of G protein-coupled receptor (GPCRs). However, how they exert their effects on GPCR conformation at the atomic level is still unclear. In light of recent experimental data, we have performed several long-timescale molecular dynamics (MD) simulations, totalling 24 μs, to rigorously map allosteric modulation and conformational changes in the β2 adrenergic receptor (β2AR) that occur as a result of interactions with three different phospholipids. In particular, we identify different sequential mechanisms behind receptor activation and deactivation, respectively, mediated by specific lipid interactions with key receptor regions. We show that net negatively charged lipids stabilize an active-like state of β2AR that is able to dock Gsα protein. Clustering of anionic lipids around the receptor with local distortion of membrane thickness is also apparent. On the other hand, net-neutral zwitterionic lipids inactivate the receptor, generating either fully inactive or intermediate states, with kinetics depending on lipid headgroup charge distribution and hydrophobicity. These chemical differences alter membrane thickness and density, which differentially destabilize the β2AR active state through lateral compression effects.
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20
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Pandey K, Ploier B, Goren MA, Levitz J, Khelashvili G, Menon AK. An engineered opsin monomer scrambles phospholipids. Sci Rep 2017; 7:16741. [PMID: 29196630 PMCID: PMC5711885 DOI: 10.1038/s41598-017-16842-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022] Open
Abstract
The G protein-coupled receptor opsin is a phospholipid scramblase that facilitates rapid transbilayer phospholipid exchange in liposomes. The mechanism by which opsin scrambles lipids is unknown. It has been proposed that lipid translocation may occur at protein-protein interfaces of opsin dimers. To test this possibility, we rationally engineered QUAD opsin by tryptophan substitution of four lipid-facing residues in transmembrane helix 4 (TM4) that is known to be important for dimerization. Atomistic molecular dynamics simulations of wild type and QUAD opsins combined with continuum modeling revealed that the tryptophan substitutions lower the energetically unfavorable residual hydrophobic mismatch between TM4 and the membrane, reducing the drive of QUAD opsin to dimerize. We purified thermostable wild type and QUAD opsins, with or without a SNAP tag for fluorescence labeling. Single molecule fluorescence measurements of purified SNAP-tagged constructs revealed that both proteins are monomers. Fluorescence-based activity assays indicated that QUAD opsin is a fully functional scramblase. However, unlike wild type opsin which dimerizes en route to insertion into phospholipid vesicles, QUAD opsin reconstitutes as a monomer. We conclude that an engineered opsin monomer can scramble phospholipids, and that the lipid-exposed face of TM4 is unlikely to contribute to transbilayer phospholipid exchange.
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Affiliation(s)
- Kalpana Pandey
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Birgit Ploier
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Michael A Goren
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA.,Institute for Computational Biomedicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA.
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21
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Argudo D, Bethel NP, Marcoline FV, Wolgemuth CW, Grabe M. New Continuum Approaches for Determining Protein-Induced Membrane Deformations. Biophys J 2017; 112:2159-2172. [PMID: 28538153 DOI: 10.1016/j.bpj.2017.03.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/16/2017] [Accepted: 03/27/2017] [Indexed: 01/21/2023] Open
Abstract
The influence of the membrane on transmembrane proteins is central to a number of biological phenomena, notably the gating of stretch activated ion channels. Conversely, membrane proteins can influence the bilayer, leading to the stabilization of particular membrane shapes, topological changes that occur during vesicle fission and fusion, and shape-dependent protein aggregation. Continuum elastic models of the membrane have been widely used to study protein-membrane interactions. These mathematical approaches produce physically interpretable membrane shapes, energy estimates for the cost of deformation, and a snapshot of the equilibrium configuration. Moreover, elastic models are much less computationally demanding than fully atomistic and coarse-grained simulation methodologies; however, 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 and geometrically accurate representations of the protein. Here, we present a fast and reliable hybrid continuum-atomistic model that couples the protein to the membrane. We show that the model is in excellent agreement with fully atomistic simulations of the ion channel gramicidin embedded in a POPC membrane. Our continuum calculations not only reproduce the membrane distortions produced by the channel but also accurately determine the channel's orientation. Finally, we use our method to investigate the role of membrane bending around the charged voltage sensors of the transient receptor potential cation channel TRPV1. We find that membrane deformation significantly stabilizes the energy of insertion of TRPV1 by exposing charged residues on the S4 segment to solution.
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Affiliation(s)
- David Argudo
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Neville P Bethel
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Frank V Marcoline
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Charles W Wolgemuth
- Departments of Molecular and Cellular Biology and Physics, University of Arizona, Tucson, Arizona
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.
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22
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Herold KF, Andersen OS, Hemmings HC. Divergent effects of anesthetics on lipid bilayer properties and sodium channel function. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:617-626. [PMID: 28695248 DOI: 10.1007/s00249-017-1239-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/27/2017] [Accepted: 07/01/2017] [Indexed: 02/07/2023]
Abstract
General anesthetics revolutionized medicine by allowing surgeons to perform more complex and much longer procedures. This widely used class of drugs is essential to patient care, yet their exact molecular mechanism(s) are incompletely understood. One early hypothesis over a century ago proposed that nonspecific interactions of anesthetics with the lipid bilayer lead to changes in neuronal function via effects on membrane properties. This model was supported by the Meyer-Overton correlation between anesthetic potency and lipid solubility and despite more recent evidence for specific protein targets, in particular ion-channels, lipid bilayer-mediated effects of anesthetics is still under debate. We therefore tested a wide range of chemically diverse general anesthetics on lipid bilayer properties using a sensitive and functional gramicidin-based assay. None of the tested anesthetics altered lipid bilayer properties at clinically relevant concentrations. Some anesthetics did affect the bilayer, though only at high supratherapeutic concentrations, which are unlikely relevant for clinical anesthesia. These results suggest that anesthetics directly interact with membrane proteins without altering lipid bilayer properties at clinically relevant concentrations. Voltage-gated Na+ channels are potential anesthetic targets and various isoforms are inhibited by a wide range of volatile anesthetics. They inhibit channel function by reducing peak Na+ current and shifting steady-state inactivation toward more hyperpolarized potentials. Recent advances in crystallography of prokaryotic Na+ channels, which are sensitive to volatile anesthetics, together with molecular dynamics simulations and electrophysiological studies will help identify potential anesthetic interaction sites within the channel protein itself.
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Affiliation(s)
- Karl F Herold
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Hugh C Hemmings
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, 10065, USA. .,Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA.
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23
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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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24
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Affiliation(s)
- Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
- Department of Physics, University of Arizona, Tucson, Arizona 85721
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25
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Bethel NP, Grabe M. Atomistic insight into lipid translocation by a TMEM16 scramblase. Proc Natl Acad Sci U S A 2016; 113:14049-14054. [PMID: 27872308 PMCID: PMC5150362 DOI: 10.1073/pnas.1607574113] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The transmembrane protein 16 (TMEM16) family of membrane proteins includes both lipid scramblases and ion channels involved in olfaction, nociception, and blood coagulation. The crystal structure of the fungal Nectria haematococca TMEM16 (nhTMEM16) scramblase suggested a putative mechanism of lipid transport, whereby polar and charged lipid headgroups move through the low-dielectric environment of the membrane by traversing a hydrophilic groove on the membrane-spanning surface of the protein. Here, we use computational methods to explore the membrane-protein interactions involved in lipid scrambling. Fast, continuum membrane-bending calculations reveal a global pattern of charged and hydrophobic surface residues that bends the membrane in a large-amplitude sinusoidal wave, resulting in bilayer thinning across the hydrophilic groove. Atomic simulations uncover two lipid headgroup-interaction sites flanking the groove. The cytoplasmic site nucleates headgroup-dipole stacking interactions that form a chain of lipid molecules that penetrate into the groove. In two instances, a cytoplasmic lipid interdigitates into this chain, crosses the bilayer, and enters the extracellular leaflet, and the reverse process happens twice as well. Continuum membrane-bending analysis carried out on homology models of mammalian homologs shows that these family members also bend the membrane-even those that lack scramblase activity. Sequence alignments show that the lipid-interaction sites are conserved in many family members but less so in those with reduced scrambling ability. Our analysis provides insight into how large-scale membrane bending and protein chemistry facilitate lipid permeation in the TMEM16 family, and we hypothesize that membrane interactions also affect ion permeation.
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Affiliation(s)
- Neville P Bethel
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- Graduate Group in Biophysics, University of California, San Francisco, CA 94158
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;
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26
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Periole X. Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations. Chem Rev 2016; 117:156-185. [PMID: 28073248 DOI: 10.1021/acs.chemrev.6b00344] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
G protein-coupled receptors (GPCRs) are central to many fundamental cellular signaling pathways. They transduce signals from the outside to the inside of cells in physiological processes ranging from vision to immune response. It is extremely challenging to look at them individually using conventional experimental techniques. Recently, a pseudo atomistic molecular model has emerged as a valuable tool to access information on GPCRs, more specifically on their interactions with their environment in their native cell membrane and the consequences on their supramolecular organization. This approach uses the Martini coarse grain (CG) model to describe the receptors, lipids, and solvent in molecular dynamics (MD) simulations and in enough detail to allow conserving the chemical specificity of the different molecules. The elimination of unnecessary degrees of freedom has opened up large-scale simulations of the lipid-mediated supramolecular organization of GPCRs. Here, after introducing the Martini CGMD method, we review these studies carried out on various members of the GPCR family, including rhodopsin (visual receptor), opioid receptors, adrenergic receptors, adenosine receptors, dopamine receptor, and sphingosine 1-phosphate receptor. These studies have brought to light an interesting set of novel biophysical principles. The insights range from revealing localized and heterogeneous deformations of the membrane bilayer at the surface of the protein, specific interactions of lipid molecules with individual GPCRs, to the effect of the membrane matrix on global GPCR self-assembly. The review ends with an overview of the lessons learned from the use of the CGMD method, the biophysical-chemical findings on lipid-protein interplay.
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Affiliation(s)
- Xavier Periole
- Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747AG Groningen, The Netherlands
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27
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Gahbauer S, Böckmann RA. Membrane-Mediated Oligomerization of G Protein Coupled Receptors and Its Implications for GPCR Function. Front Physiol 2016; 7:494. [PMID: 27826255 PMCID: PMC5078798 DOI: 10.3389/fphys.2016.00494] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/11/2016] [Indexed: 12/18/2022] Open
Abstract
The dimerization or even oligomerization of G protein coupled receptors (GPCRs) causes ongoing, controversial debates about its functional role and the coupled biophysical, biochemical or biomedical implications. A continously growing number of studies hints to a relation between oligomerization and function of GPCRs and strengthens the assumption that receptor assembly plays a key role in the regulation of protein function. Additionally, progress in the structural analysis of GPCR-G protein and GPCR-ligand interactions allows to distinguish between actively functional and non-signaling complexes. Recent findings further suggest that the surrounding membrane, i.e., its lipid composition may modulate the preferred dimerization interface and as a result the abundance of distinct dimeric conformations. In this review, the association of GPCRs and the role of the membrane in oligomerization will be discussed. An overview of the different reported oligomeric interfaces is provided and their capability for signaling discussed. The currently available data is summarized with regard to the formation of GPCR oligomers, their structures and dependency on the membrane microenvironment as well as the coupling of oligomerization to receptor function.
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Affiliation(s)
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-NürnbergErlangen, Germany
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28
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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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29
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Baylon JL, Vermaas JV, Muller MP, Arcario MJ, Pogorelov TV, Tajkhorshid E. Atomic-level description of protein-lipid interactions using an accelerated membrane model. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:1573-83. [PMID: 26940626 PMCID: PMC4877275 DOI: 10.1016/j.bbamem.2016.02.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 02/19/2016] [Accepted: 02/20/2016] [Indexed: 01/03/2023]
Abstract
Peripheral membrane proteins are structurally diverse proteins that are involved in fundamental cellular processes. Their activity of these proteins is frequently modulated through their interaction with cellular membranes, and as a result techniques to study the interfacial interaction between peripheral proteins and the membrane are in high demand. Due to the fluid nature of the membrane and the reversibility of protein-membrane interactions, the experimental study of these systems remains a challenging task. Molecular dynamics simulations offer a suitable approach to study protein-lipid interactions; however, the slow dynamics of the lipids often prevents sufficient sampling of specific membrane-protein interactions in atomistic simulations. To increase lipid dynamics while preserving the atomistic detail of protein-lipid interactions, in the highly mobile membrane-mimetic (HMMM) model the membrane core is replaced by an organic solvent, while short-tailed lipids provide a nearly complete representation of natural lipids at the organic solvent/water interface. Here, we present a brief introduction and a summary of recent applications of the HMMM to study different membrane proteins, complementing the experimental characterization of the presented systems, and we offer a perspective of future applications of the HMMM to study other classes of membrane proteins. 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)
- Javier L Baylon
- Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology.
| | - Josh V Vermaas
- Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology.
| | - Melanie P Muller
- Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology; College of Medicine.
| | - Mark J Arcario
- Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology; College of Medicine.
| | - Taras V Pogorelov
- Beckman Institute for Advanced Science and Technology; School of Chemical Sciences; Department of Chemistry; National Center for Supercomputing Applications.
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology; College of Medicine; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
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30
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Kahraman O, Koch PD, Klug WS, Haselwandter CA. Bilayer-thickness-mediated interactions between integral membrane proteins. Phys Rev E 2016; 93:042410. [PMID: 27176332 DOI: 10.1103/physreve.93.042410] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Indexed: 12/14/2022]
Abstract
Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations can yield energetically favorable bilayer-mediated interactions between integral membrane proteins, and large-scale organization of integral membrane proteins into protein clusters in cell membranes. Within the continuum elasticity theory of membranes, the energy cost of protein-induced bilayer thickness deformations can be captured by considering compression and expansion of the bilayer hydrophobic core, membrane tension, and bilayer bending, resulting in biharmonic equilibrium equations describing the shape of lipid bilayers for a given set of bilayer-protein boundary conditions. Here we develop a combined analytic and numerical methodology for the solution of the equilibrium elastic equations associated with protein-induced lipid bilayer deformations. Our methodology allows accurate prediction of thickness-mediated protein interactions for arbitrary protein symmetries at arbitrary protein separations and relative orientations. We provide exact analytic solutions for cylindrical integral membrane proteins with constant and varying hydrophobic thickness, and develop perturbative analytic solutions for noncylindrical protein shapes. We complement these analytic solutions, and assess their accuracy, by developing both finite element and finite difference numerical solution schemes. We provide error estimates of our numerical solution schemes and systematically assess their convergence properties. Taken together, the work presented here puts into place an analytic and numerical framework which allows calculation of bilayer-mediated elastic interactions between integral membrane proteins for the complicated protein shapes suggested by structural biology and at the small protein separations most relevant for the crowded membrane environments provided by living cells.
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Affiliation(s)
- Osman Kahraman
- Department of Physics & Astronomy and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Peter D Koch
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - William S Klug
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA
| | - Christoph A Haselwandter
- Department of Physics & Astronomy and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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31
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LeVine MV, Cuendet MA, Khelashvili G, Weinstein H. Allosteric Mechanisms of Molecular Machines at the Membrane: Transport by Sodium-Coupled Symporters. Chem Rev 2016; 116:6552-87. [PMID: 26892914 DOI: 10.1021/acs.chemrev.5b00627] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Solute transport across cell membranes is ubiquitous in biology as an essential physiological process. Secondary active transporters couple the unfavorable process of solute transport against its concentration gradient to the energetically favorable transport of one or several ions. The study of such transporters over several decades indicates that their function involves complex allosteric mechanisms that are progressively being revealed in atomistic detail. We focus on two well-characterized sodium-coupled symporters: the bacterial amino acid transporter LeuT, which is the prototype for the "gated pore" mechanism in the mammalian synaptic monoamine transporters, and the archaeal GltPh, which is the prototype for the "elevator" mechanism in the mammalian excitatory amino acid transporters. We present the evidence for the role of allostery in the context of a quantitative formalism that can reconcile biochemical and biophysical data and thereby connects directly to recent insights into the molecular structure and dynamics of these proteins. We demonstrate that, while the structures and mechanisms of these transporters are very different, the available data suggest a common role of specific models of allostery in their functions. We argue that such allosteric mechanisms appear essential not only for sodium-coupled symport in general but also for the function of other types of molecular machines in the membrane.
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Affiliation(s)
- Michael V LeVine
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
| | - Michel A Cuendet
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
| | - George Khelashvili
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
| | - Harel Weinstein
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
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32
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LeVine MV, Khelashvili G, Shi L, Quick M, Javitch JA, Weinstein H. Role of Annular Lipids in the Functional Properties of Leucine Transporter LeuT Proteomicelles. Biochemistry 2016; 55:850-9. [PMID: 26811944 PMCID: PMC4757857 DOI: 10.1021/acs.biochem.5b01268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Recent
work has shown that the choice of the type and concentration
of detergent used for the solubilization of membrane proteins can
strongly influence the results of functional experiments. In particular,
the amino acid transporter LeuT can bind two substrate molecules in
low concentrations of n-dodecyl β-d-maltopyranoside (DDM), whereas high concentrations reduce the molar
binding stoichiometry to 1:1. Subsequent molecular dynamics (MD) simulations
of LeuT in DDM proteomicelles revealed that DDM can penetrate to the
extracellular vestibule and make stable contacts in the functionally
important secondary substrate binding site (S2), suggesting a potential
competitive mechanism for the reduction in binding stoichiometry.
Because annular lipids can be retained during solubilization, we performed
MD simulations of LeuT proteomicelles at various stages of the solubilization
process. We find that at low DDM concentrations, lipids are retained
around the protein and penetration of detergent into the S2 site does
not occur, whereas at high concentrations, lipids are displaced and
the probability of DDM binding in the S2 site is increased. This behavior
is dependent on the type of detergent, however, as we find in the
simulations that the detergent lauryl maltose-neopentyl glycol, which
is approximately twice the size of DDM and structurally more closely
resembles lipids, does not penetrate the protein even at very high
concentrations. We present functional studies that confirm the computational
findings, emphasizing the need for careful consideration of experimental
conditions, and for cautious interpretation of data in gathering mechanistic
information about membrane proteins.
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Affiliation(s)
- Michael V LeVine
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States
| | - Lei Shi
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health , Baltimore, Maryland 21224, United States
| | | | - Jonathan A Javitch
- Division of Molecular Therapeutics, New York State Psychiatric Institute , New York, New York 10032, United States
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States.,HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
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33
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Kahraman O, Koch PD, Klug WS, Haselwandter CA. Architecture and Function of Mechanosensitive Membrane Protein Lattices. Sci Rep 2016; 6:19214. [PMID: 26771082 PMCID: PMC4725903 DOI: 10.1038/srep19214] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/07/2015] [Indexed: 12/04/2022] Open
Abstract
Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms yielding supramolecular organization and collective function of membrane proteins remain largely unknown. Here we show that bilayer-mediated elastic interactions between membrane proteins can yield regular and distinctive lattice architectures of protein clusters, and may provide a link between lattice architecture and lattice function. Using the mechanosensitive channel of large conductance (MscL) as a model system, we obtain relations between the shape of MscL and the supramolecular architecture of MscL lattices. We predict that the tetrameric and pentameric MscL symmetries observed in previous structural studies yield distinct lattice architectures of MscL clusters and that, in turn, these distinct MscL lattice architectures yield distinct lattice activation barriers. Our results suggest general physical mechanisms linking protein symmetry, the lattice architecture of membrane protein clusters, and the collective function of membrane protein lattices.
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Affiliation(s)
- Osman Kahraman
- Departments of Physics &Astronomy and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter D Koch
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - William S Klug
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA 90095, USA
| | - Christoph A Haselwandter
- Departments of Physics &Astronomy and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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34
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Rhodopsin/lipid hydrophobic matching-rhodopsin oligomerization and function. Biophys J 2016; 108:1125-32. [PMID: 25762324 DOI: 10.1016/j.bpj.2015.01.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/23/2014] [Accepted: 01/08/2015] [Indexed: 02/07/2023] Open
Abstract
Lipid composition of the membrane and rhodopsin packing density strongly modulate the early steps of the visual response of photoreceptor membranes. In this study, lipid-order and bovine rhodopsin function in proteoliposomes composed of the sn-1 chain perdeuterated lipids 14:0d27-14:1-PC, 16:0d31-16:1-PC, 18:0d35-18:1-PC, or 20:0d39-20:1-PC at rhodopsin/lipid molar ratios from 1:70 to 1:1000 (mol/mol) were investigated. Clear evidence for matching of hydrophobic regions on rhodopsin transmembrane helices and hydrophobic thickness of lipid bilayers was observed from (2)H nuclear magnetic resonance order parameter measurements at low rhodopsin concentrations. Thin bilayers stretched to match the length of transmembrane helices observed as increase of sn-1 chain order, while thicker bilayers were compressed near the protein. A quantitative analysis of lipid-order parameter changes suggested that the protein adjusts its conformation to bilayer hydrophobic thickness as well, which confirmed our earlier circular-dichroism measurements. Changes in lipid order parameters upon rhodopsin incorporation vanished for bilayers with a hydrophobic thickness of 27 ± 1 Å, suggesting that this is the bilayer thickness at which rhodopsin packs in bilayers at the lowest membrane perturbation. The lipid-order parameter studies also indicated that a hydrophobic mismatch between rhodopsin and lipids triggers rhodopsin oligomerization with increasing rhodopsin concentrations. Both hydrophobic mismatch and rhodopsin oligomerization result in substantial shifts of the equilibrium between the photointermediates metarhodopsin I and metarhodopsin II; increasing bilayer thickness favors formation of metarhodopsin II while oligomerization favors metarhodopsin I. The results highlight the importance of hydrophobic matching for rhodopsin structure, oligomerization, and function.
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35
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Zhang L, Yethiraj A, Cui Q. Free Energy Calculations for the Peripheral Binding of Proteins/Peptides to an Anionic Membrane. 1. Implicit Membrane Models. J Chem Theory Comput 2015; 10:2845-59. [PMID: 26586509 DOI: 10.1021/ct500218p] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The binding of peptides and proteins to the surface of complex lipid membranes is important in many biological processes such as cell signaling and membrane remodeling. Computational studies can aid experiments by identifying physical interactions and structural motifs that determine the binding affinity and specificity. However, previous studies focused on either qualitative behaviors of protein/membrane interactions or the binding affinity of small peptides. Motivated by this observation, we set out to develop computational protocols for bimolecular binding to charged membranes that are applicable to both peptides and large proteins. In this work, we explore a method based on an implicit membrane/solvent model (generalized Born with a simple switching in combination with the Gouy-Chapman-Stern model for a charged interface), which we expect to lead to useful results when the binding does not implicate significant membrane deformation and local demixing of lipids. We show that the binding free energy can be efficiently computed following a thermodynamic cycle similar to protein-ligand binding calculations, especially when a Bennett acceptance ratio based protocol is used to consider both the membrane bound and solution conformational ensembles. Test calculations on a series of peptides show that our computational approach leads to binding affinities in encouraging agreement with experimental data, including for the challenging example of the bringing of flexible MARCKS-ED peptides to membranes. The calculations highlight that for a membrane with a significant fraction of anionic lipids, it is essential to include the effect of ion adsorption using the Stern model, which significantly modifies the effective surface charge. This implicit membrane model based computational protocol helps lay the groundwork for more systematic analysis of protein/peptide binding to membranes of complex shape and composition.
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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
| | - 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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36
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Ferreira RJ, Ferreira MJU, dos Santos DJVA. Do adsorbed drugs onto P-glycoprotein influence its efflux capability? Phys Chem Chem Phys 2015; 17:22023-34. [PMID: 26235302 DOI: 10.1039/c5cp03216d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The membrane biophysical aspects by which multidrug resistance (MDR) relate to the ABC transporter function still remain largely unknown. Notwithstanding the central role that efflux pumps like P-glycoprotein have in MDR onset, experimental studies classified additionally the lipid micro-environment where P-gp is inserted as a determinant for the increased efflux capability demonstrated in MDR cell lines. Recently, a nonlinear model for drug-membrane interactions showed that, upon drug adsorption, long-range mechanical alterations are predicted to affect the P-gp ATPase function at external drug concentrations of ∼10-100 μM. However, our results also show that drug adsorption may also occur at P-gp nucleotide-binding domains where conformational changes drive the efflux cycle. Thus, we assessed the effect of drug adsorption to both protein-water and lipid-water interfaces by means of molecular dynamics simulations. The results show that free energies of adsorption are lower for modulators in both lipid/water and protein/water interfaces. Important differences in drug-protein interactions, protein dynamics and membrane biophysical characteristics were observed between the different classes. Therefore, we hypothesize that drug adsorption to the protein and lipid-water interface accounts for a complex network of events that affect the ability of transporters to efflux drugs.
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Affiliation(s)
- Ricardo J Ferreira
- Research Institute for Medicines (iMed.Ulisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, Lisboa, Portugal.
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37
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Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. J Membr Biol 2015; 248:611-40. [PMID: 26063070 PMCID: PMC4515176 DOI: 10.1007/s00232-015-9802-0] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/26/2015] [Indexed: 01/05/2023]
Abstract
Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.
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Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Toby W. Allen
- School of Applied Sciences & Health Innovations Research Institute, RMIT University, GPO Box 2476, Melbourne, Vic, 3001, Australia; and Department of Chemistry, University of California, Davis. Davis, CA 95616, USA
| | - Ioan Andricioaei
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Daniel Baum
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Grace Brannigan
- Center for Computational and Integrative Biology and Department of Physics, Rutgers University-Camden, Camden, NJ, USA
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Lucie Delemotte
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Coral del Val
- Department of Artificial Intelligence, University of Granada, E-18071 Granada, Spain
| | - Ran Friedman
- Linnæus University, Department of Chemistry and Biomedical Sciences & Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
| | - Paraskevi Gkeka
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Hans-Christian Hege
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, IBPC and CNRS, Paris, France
| | - Marina A. Kasimova
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Antonios Kolocouris
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Michael L. Klein
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Syma Khalid
- Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - M. Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, and Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
| | - Norbert Lindow
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Mahua Roy
- Department of Chemistry, University of California, Irvine
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Mounir Tarek
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- CNRS, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
| | - Florentina Tofoleanu
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Sinisa Urban
- Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, 725 N. Wolfe Street, 507 Preclinical Teaching Building, Baltimore, MD 21205, USA
| | - David J. Wales
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jeremy C. Smith
- Oak Ridge National Laboratory, PO BOX 2008 MS6309, Oak Ridge, TN 37831-6309, USA
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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Provasi D, Boz MB, Johnston JM, Filizola M. Preferred supramolecular organization and dimer interfaces of opioid receptors from simulated self-association. PLoS Comput Biol 2015; 11:e1004148. [PMID: 25822938 PMCID: PMC4379167 DOI: 10.1371/journal.pcbi.1004148] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/22/2015] [Indexed: 11/18/2022] Open
Abstract
Substantial evidence in support of the formation of opioid receptor (OR) di-/oligomers suggests previously unknown mechanisms used by these proteins to exert their biological functions. In an attempt to guide experimental assessment of the identity of the minimal signaling unit for ORs, we conducted extensive coarse-grained (CG) molecular dynamics (MD) simulations of different combinations of the three major OR subtypes, i.e., μ-OR, δ-OR, and κ-OR, in an explicit lipid bilayer. Specifically, we ran multiple, independent MD simulations of each homomeric μ-OR/μ-OR, δ-OR/δ-OR, and κ-OR/κ-OR complex, as well as two of the most studied heteromeric complexes, i.e., δ-OR/μ-OR and δ-OR/κ-OR, to derive the preferred supramolecular organization and dimer interfaces of ORs in a cell membrane model. These simulations yielded over 250 microseconds of accumulated data, which correspond to approximately 1 millisecond of effective simulated dynamics according to established scaling factors of the CG model we employed. Analysis of these data indicates similar preferred supramolecular organization and dimer interfaces of ORs across the different receptor subtypes, but also important differences in the kinetics of receptor association at specific dimer interfaces. We also investigated the kinetic properties of interfacial lipids, and explored their possible role in modulating the rate of receptor association and in promoting the formation of filiform aggregates, thus supporting a distinctive role of the membrane in OR oligomerization and, possibly, signaling.
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Affiliation(s)
- Davide Provasi
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Mustafa Burak Boz
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jennifer M. Johnston
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Marta Filizola
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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39
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Haselwandter CA, Wingreen NS. The role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices. PLoS Comput Biol 2014; 10:e1003932. [PMID: 25503274 PMCID: PMC4263354 DOI: 10.1371/journal.pcbi.1003932] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 09/22/2014] [Indexed: 01/04/2023] Open
Abstract
In vivo fluorescence microscopy and electron cryo-tomography have revealed that chemoreceptors self-assemble into extended honeycomb lattices of chemoreceptor trimers with a well-defined relative orientation of trimers. The signaling response of the observed chemoreceptor lattices is remarkable for its extreme sensitivity, which relies crucially on cooperative interactions among chemoreceptor trimers. In common with other membrane proteins, chemoreceptor trimers are expected to deform the surrounding lipid bilayer, inducing membrane-mediated anisotropic interactions between neighboring trimers. Here we introduce a biophysical model of bilayer-chemoreceptor interactions, which allows us to quantify the role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices. We find that, even in the absence of direct protein-protein interactions, membrane-mediated interactions can yield assembly of chemoreceptor lattices at very dilute trimer concentrations. The model correctly predicts the observed honeycomb architecture of chemoreceptor lattices as well as the observed relative orientation of chemoreceptor trimers, suggests a series of “gateway” states for chemoreceptor lattice assembly, and provides a simple mechanism for the localization of large chemoreceptor lattices to the cell poles. Our model of bilayer-chemoreceptor interactions also helps to explain the observed dependence of chemotactic signaling on lipid bilayer properties. Finally, we consider the possibility that membrane-mediated interactions might contribute to cooperativity among neighboring chemoreceptor trimers. The chemotaxis system allows bacteria to respond to minute changes in chemical concentration, and serves as a paradigm for biological signal processing and the self-assembly of large protein lattices in living cells. The sensitivity of the chemotaxis system relies crucially on cooperative interactions among chemoreceptor trimers, which are organized into intricate honeycomb lattices. Chemoreceptors are membrane proteins and, hence, are expected to deform the surrounding lipid bilayer, leading to membrane-mediated interactions between chemoreceptor trimers. Using a biophysical model of bilayer-chemoreceptor interactions we show that the membrane-mediated interactions induced by chemoreceptor trimers provide a mechanism for the observed self-assembly of chemoreceptor lattices. We find that the directionality of membrane-mediated interactions between trimers complements protein-protein interactions in the stabilization of the observed honeycomb architecture of chemoreceptor lattices. Our results suggest that the symmetry of membrane protein complexes such as chemoreceptor trimers is reflected in the anisotropy of membrane-mediated interactions, yielding a general mechanism for the self-assembly of ordered protein lattices in cell membranes.
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Affiliation(s)
- Christoph A. Haselwandter
- Departments of Physics & Astronomy and Biological Sciences, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (CAH); (NSW)
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (CAH); (NSW)
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40
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Johner N, Harries D, Khelashvili G. Curvature and Lipid Packing Modulate the Elastic Properties of Lipid Assemblies: Comparing HII and Lamellar Phases. J Phys Chem Lett 2014; 5:4201-4206. [PMID: 26278954 DOI: 10.1021/jz5022284] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Accumulating evidence indicates that membrane reshaping and fusion processes, as well as regulation of membrane protein function, depend on lipid composition. Although it is widely accepted that cell membranes are under considerable stress and frustration and can be locally highly curved, experimental approaches to determine the material properties of lipids usually rely on their study in a relaxed environment or in flat bilayers. Here, we propose a computational method to determine the elastic properties of lipid assemblies of arbitrarily shaped interfaces and apply it to lipidic mixtures in the inverted hexagonal and lamellar phases. We find that the bending rigidity critically depends on the geometry of the system and correlates with the changes in lipid chain order imposed by the specific environment. Our results are relevant for resolving local lipid properties of deformed, stressed, or frustrated membranes that notably emerge around integral membrane proteins or during different membrane remodeling processes.
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Affiliation(s)
- Niklaus Johner
- †Biozentrum - Center for Molecular Sciences, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Daniel Harries
- ‡Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - George Khelashvili
- §Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10065, United States
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41
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Herold KF, Sanford RL, Lee W, Schultz MF, Ingólfsson HI, Andersen OS, Hemmings HC. Volatile anesthetics inhibit sodium channels without altering bulk lipid bilayer properties. J Gen Physiol 2014; 144:545-60. [PMID: 25385786 PMCID: PMC4242807 DOI: 10.1085/jgp.201411172] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 10/08/2014] [Indexed: 01/05/2023] Open
Abstract
Although general anesthetics are clinically important and widely used, their molecular mechanisms of action remain poorly understood. Volatile anesthetics such as isoflurane (ISO) are thought to alter neuronal function by depressing excitatory and facilitating inhibitory neurotransmission through direct interactions with specific protein targets, including voltage-gated sodium channels (Na(v)). Many anesthetics alter lipid bilayer properties, suggesting that ion channel function might also be altered indirectly through effects on the lipid bilayer. We compared the effects of ISO and of a series of fluorobenzene (FB) model volatile anesthetics on Na(v) function and lipid bilayer properties. We examined the effects of these agents on Na(v) in neuronal cells using whole-cell electrophysiology, and on lipid bilayer properties using a gramicidin-based fluorescence assay, which is a functional assay for detecting changes in lipid bilayer properties sensed by a bilayer-spanning ion channel. At clinically relevant concentrations (defined by the minimum alveolar concentration), both the FBs and ISO produced prepulse-dependent inhibition of Na(v) and shifted the voltage dependence of inactivation toward more hyperpolarized potentials without affecting lipid bilayer properties, as sensed by gramicidin channels. Only at supra-anesthetic (toxic) concentrations did ISO alter lipid bilayer properties. These results suggest that clinically relevant concentrations of volatile anesthetics alter Na(v) function through direct interactions with the channel protein with little, if any, contribution from changes in bulk lipid bilayer properties. Our findings further suggest that changes in lipid bilayer properties are not involved in clinical anesthesia.
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Affiliation(s)
- Karl F Herold
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - R Lea Sanford
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - William Lee
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Margaret F Schultz
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Helgi I Ingólfsson
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Olaf S Andersen
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Hugh C Hemmings
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065 Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
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42
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Guixà-González R, Ramírez-Anguita JM, Kaczor AA, Selent J. Simulating G protein-coupled receptors in native-like membranes: from monomers to oligomers. Methods Cell Biol 2014; 117:63-90. [PMID: 24143972 DOI: 10.1016/b978-0-12-408143-7.00004-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
G protein-coupled receptors (GPCRs) are one of the most relevant superfamilies of transmembrane proteins as they participate in an important variety of biological events. Recently, the scientific community is witnessing an advent of a GPCR crystallization age along with impressive improvements achieved in the field of computer simulations during the last two decades. Computer simulation techniques such as molecular dynamics (MD) simulations are now frequent tools to study the dynamic behavior of GPCRs and, more importantly, to model the complex membrane environment where these proteins spend their lifetime. Thanks to these tools, GPCRs can be simulated not only longer but also in a more "physiological" fashion. In this scenario, scientists are taking advantage of such advances to approach certain phenomena such as GPCR oligomerization occurring only at timescales not reachable until now. Thus, despite current MD simulations having important limitations today, they have become an essential tool to study key biophysical properties of GPCRs and GPCR oligomers.
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Affiliation(s)
- Ramon Guixà-González
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra/IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader, Barcelona, Spain
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43
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Mondal S, Khelashvili G, Weinstein H. Not just an oil slick: how the energetics of protein-membrane interactions impacts the function and organization of transmembrane proteins. Biophys J 2014; 106:2305-16. [PMID: 24896109 PMCID: PMC4052241 DOI: 10.1016/j.bpj.2014.04.032] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/31/2014] [Accepted: 04/23/2014] [Indexed: 01/12/2023] Open
Abstract
The membrane environment, its composition, dynamics, and remodeling, have been shown to participate in the function and organization of a wide variety of transmembrane (TM) proteins, making it necessary to study the molecular mechanisms of such proteins in the context of their membrane settings. We review some recent conceptual advances enabling such studies, and corresponding computational models and tools designed to facilitate the concerted experimental and computational investigation of protein-membrane interactions. To connect productively with the high resolution achieved by cognate experimental approaches, the computational methods must offer quantitative data at an atomistically detailed level. We show how such a quantitative method illuminated the mechanistic importance of a structural characteristic of multihelical TM proteins, that is, the likely presence of adjacent polar and hydrophobic residues at the protein-membrane interface. Such adjacency can preclude the complete alleviation of the well-known hydrophobic mismatch between TM proteins and the surrounding membrane, giving rise to an energy cost of residual hydrophobic mismatch. The energy cost and biophysical formulation of hydrophobic mismatch and residual hydrophobic mismatch are reviewed in the context of their mechanistic role in the function of prototypical members of multihelical TM protein families: 1), LeuT, a bacterial homolog of mammalian neurotransmitter sodium symporters; and 2), rhodopsin and the β1- and β2-adrenergic receptors from the G-protein coupled receptor family. The type of computational analysis provided by these examples is poised to translate the rapidly growing structural data for the many TM protein families that are of great importance to cell function into ever more incisive insights into mechanisms driven by protein-ligand and protein-protein interactions in the membrane environment.
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Affiliation(s)
- Sayan Mondal
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York.
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44
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Latorraca NR, Callenberg KM, Boyle JP, Grabe M. Continuum approaches to understanding ion and peptide interactions with the membrane. J Membr Biol 2014; 247:395-408. [PMID: 24652510 PMCID: PMC4096575 DOI: 10.1007/s00232-014-9646-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 02/22/2014] [Indexed: 12/22/2022]
Abstract
Experimental and computational studies have shown that cellular membranes deform to stabilize the inclusion of transmembrane (TM) proteins harboring charge. Recent analysis suggests that membrane bending helps to expose charged and polar residues to the aqueous environment and polar head groups. We previously used elasticity theory to identify membrane distortions that minimize the insertion of charged TM peptides into the membrane. Here, we extend our work by showing that it also provides a novel, computationally efficient method for exploring the energetics of ion and small peptide penetration into membranes. First, we show that the continuum method accurately reproduces energy profiles and membrane shapes generated from molecular simulations of bare ion permeation at a fraction of the computational cost. Next, we demonstrate that the dependence of the ion insertion energy on the membrane thickness arises primarily from the elastic properties of the membrane. Moreover, the continuum model readily provides a free energy decomposition into components not easily determined from molecular dynamics. Finally, we show that the energetics of membrane deformation strongly depend on membrane patch size both for ions and peptides. This dependence is particularly strong for peptides based on simulations of a known amphipathic, membrane binding peptide from the human pathogen Toxoplasma gondii. In total, we address shortcomings and advantages that arise from using a variety of computational methods in distinct biological contexts.
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Affiliation(s)
- Naomi R Latorraca
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
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45
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Li H, Gorfe AA. Membrane Remodeling by Surface-Bound Protein Aggregates: Insights from Coarse-Grained Molecular Dynamics Simulation. J Phys Chem Lett 2014; 5:1457-1462. [PMID: 24803997 PMCID: PMC3999789 DOI: 10.1021/jz500451a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 04/03/2014] [Indexed: 06/03/2023]
Abstract
The mechanism of curvature generation in membranes has been studied for decades due to its important role in many cellular functions. However, it is not clear if, or how, aggregates of lipid-anchored proteins might affect the geometry and elastic property of membranes. As an initial step toward addressing this issue, we performed structural, geometrical, and stress field analyses of coarse-grained molecular dynamics trajectories of a domain-forming bilayer in which an aggregate of lipidated proteins was asymmetrically bound. The results suggest a general mechanism whereby asymmetric incorporation of lipid-modified protein aggregates curve multidomain membranes primarily by expanding the surface area of the monolayer in which the lipid anchor is inserted.
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46
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Johner N, Mondal S, Morra G, Caffrey M, Weinstein H, Khelashvili G. Protein and lipid interactions driving molecular mechanisms of in meso crystallization. J Am Chem Soc 2014; 136:3271-84. [PMID: 24494670 PMCID: PMC3985912 DOI: 10.1021/ja4129839] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The recent advances in the in meso crystallization technique for the structural characterization of G-protein coupled receptor (GPCR) proteins have established the usefulness of the lipidic-cubic phases (LCPs) in the field of crystallography of membrane proteins. It is surprising that despite the success of the approach, the molecular mechanisms of the in meso method are still not well understood. Therefore, the approach must rely on extensive screening for a suitable protein construct, for host and additive lipids, and for the appropriate precipitants and temperature. To shed light on the in meso crystallization mechanisms, we used extensive coarse-grained molecular dynamics simulations to study, in molecular detail, LCPs under different conditions (compositions and temperatures relevant to crystallogenesis) and their interactions with different types of GPCR constructs. The results presented show how the modulation of the lattice constant of the LCP (triggered by the addition of precipitant during the in meso assay), or of the host lipid type, can destabilize monomeric proteins in the bilayer of the LCP and thus drive their aggregation into the stacked lamellae, where the residual hydrophobic mismatch between the protein and the membrane can drive the formation of lateral contacts leading to nucleation and crystal growth. Moreover, we demonstrate how particular protein designs (such as transmembrane proteins engineered to contain large polar regions) can promote protein stacking interactions in the third, out-of-plane, dimension. The insights provided by the new aspects of the specific molecular mechanisms responsible for protein-protein interactions inside the cubic phase presented here should be helpful in guiding the rational design of future in meso trials with successful outcomes.
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Affiliation(s)
- Niklaus Johner
- Weill Cornell Medical College of Cornell University , New York, New York, 10065, United States
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47
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Van Lehn RC, Alexander-Katz A. Free energy change for insertion of charged, monolayer-protected nanoparticles into lipid bilayers. SOFT MATTER 2014; 10:648-58. [PMID: 24795979 DOI: 10.1039/c3sm52329b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Charged, monolayer-protected gold nanoparticles (AuNPs) with core diameters smaller than 10 nm have recently emerged as a prominent class of nanomaterial for use in targeted drug delivery and biosensing. In particular, recent experimental studies showed that AuNPs protected by a binary mixture of purely hydrophobic and anionic, end-functionalized alkanethiol ligands were able to spontaneously penetrate through cell membranes via a non-endocytic, non-disruptive mechanism. The critical step in the penetration process is a fusion step during which the AuNPs insert into the hydrophobic core of the bilayer. This fusion step is driven by hydrophobic forces as inserted AuNPs minimize their exposed hydrophobic surface area and thereby lower their free energy compared to particles in the bulk. Here, we explore the effect of the large parameter space of composition, size, ligand length, morphology, and hydrophobicity strength on the change in the free energy upon insertion. Using a newly developed implicit bilayer, implicit solvent simulation model, our work shows that there is a size cutoff for insertion that has a strong dependence on surface composition and ligand chemistry. Our results agree well with previous experimental findings for a particular value of the hydrophobicity strength. This work provides physical insight that may be used to both understand the insertion of AuNPs into bilayers and guide the design of monolayers to either encourage or inhibit insertion.
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48
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Mondal S, Khelashvili G, Johner N, Weinstein H. How the dynamic properties and functional mechanisms of GPCRs are modulated by their coupling to the membrane environment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:55-74. [PMID: 24158801 DOI: 10.1007/978-94-007-7423-0_4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Experimental observations of the dependence of function and organization of G protein-coupled receptors (GPCRs) on their lipid environment have stimulated new quantitative studies of the coupling between the proteins and the membrane. It is important to develop such a quantitative understanding at the molecular level because the effects of the coupling are seen to be physiologically and clinically significant. Here we review findings that offer insight into how membrane-GPCR coupling is connected to the structural characteristics of the GPCR, from sequence to 3D structural detail, and how this coupling is involved in the actions of ligands on the receptor. The application of a recently developed computational approach designed for quantitative evaluation of membrane remodeling and the energetics of membrane-protein interactions brings to light the importance of the radial asymmetry of the membrane-facing surface of GPCRs in their interaction with the surrounding membrane. As the radial asymmetry creates adjacencies of hydrophobic and polar residues at specific sites of the GPCR, the ability of membrane remodeling to achieve complete hydrophobic matching is limited, and the residual mismatch carries a significant energy cost. The adjacencies are shown to be affected by ligand-induced conformational changes. Thus, functionally important organization of GPCRs in the cell membrane can depend both on ligand-determined properties and on the lipid composition of various membrane regions with different remodeling capacities. That this functionally important reorganization can be driven by oligomerization patterns that reduce the energy cost of the residual mismatch, suggests a new perspective on GPCR dimerization and ligand-GPCR interactions. The relation between the modulatory effects on GPCRs from the binding of specific cell-membrane components, e.g., cholesterol, and those produced by the non-local energetics of hydrophobic mismatch are discussed in this context.
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Affiliation(s)
- Sayan Mondal
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, Room E-509, 1300 York Avenue, 10065, New York City, NY, USA
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49
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GPCR & Company: Databases and Servers for GPCRs and Interacting Partners. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:185-204. [DOI: 10.1007/978-94-007-7423-0_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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50
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Abstract
Spatial organization of G-protein coupled receptors (GPCRs) into dimers and higher order oligomers has been demonstrated in vitro and in vivo. The pharmacological readout was shown to depend on the specific interfaces, but why particular regions of the GPCR structure are involved, and how ligand-determined states change them remains unknown. Here we show why protein-membrane hydrophobic matching is attained upon oligomerization at specific interfaces from an analysis of coarse-grained molecular dynamics simulations of the spontaneous diffusion-interaction of the prototypical beta2-adrenergic (β2AR) receptors in a POPC lipid bilayer. The energy penalty from mismatch is significantly reduced in the spontaneously emerging oligomeric arrays, making the spatial organization of the GPCRs dependent on the pattern of mismatch in the monomer. This mismatch pattern is very different for β2AR compared to the highly homologous and structurally similar β1AR, consonant with experimentally observed oligomerization patterns of β2AR and β1AR. The results provide a mechanistic understanding of the structural context of oligomerization.
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