1
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Erastova V, Evans IR, Glossop WN, Guryel S, Hodgkinson P, Kerr HE, Oganesyan VS, Softley LK, Wickins HM, Wilson MR. Unravelling Guest Dynamics in Crystalline Molecular Organics Using 2H Solid-State NMR and Molecular Dynamics Simulation. J Am Chem Soc 2024; 146:18360-18369. [PMID: 38935813 DOI: 10.1021/jacs.4c03246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
2H solid-state NMR and atomistic molecular dynamics (MD) simulations are used to understand the disorder of guest solvent molecules in two cocrystal solvates of the pharmaceutical furosemide. Traditional approaches to interpreting the NMR data fail to provide a coherent model of molecular behavior and indeed give misleading kinetic data. In contrast, the direct prediction of the NMR properties from MD simulation trajectories allows the NMR data to be correctly interpreted in terms of combined jump-type and libration-type motions. Time-independent component analysis of the MD trajectories provides additional insights, particularly for motions that are invisible to NMR. This allows a coherent picture of the dynamics of molecules restricted in molecular-sized cavities to be determined.
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Affiliation(s)
- Valentina Erastova
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K
- Department of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Ivana R Evans
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K
| | - William N Glossop
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K
| | - Songül Guryel
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K
| | - Paul Hodgkinson
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K
| | - Hannah E Kerr
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K
| | | | - Lorna K Softley
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K
| | - Helen M Wickins
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K
| | - Mark R Wilson
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, U.K
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2
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Huster D, Maiti S, Herrmann A. Phospholipid Membranes as Chemically and Functionally Tunable Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312898. [PMID: 38456771 DOI: 10.1002/adma.202312898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/12/2024] [Indexed: 03/09/2024]
Abstract
The sheet-like lipid bilayer is the fundamental structural component of all cell membranes. Its building blocks are phospholipids and cholesterol. Their amphiphilic structure spontaneously leads to the formation of a bilayer in aqueous environment. Lipids are not just structural elements. Individual lipid species, the lipid membrane structure, and lipid dynamics influence and regulate membrane protein function. An exciting field is emerging where the membrane-associated material properties of different bilayer systems are used in designing innovative solutions for widespread applications across various fields, such as the food industry, cosmetics, nano- and biomedicine, drug storage and delivery, biotechnology, nano- and biosensors, and computing. Here, the authors summarize what is known about how lipids determine the properties and functions of biological membranes and how this has been or can be translated into innovative applications. Based on recent progress in the understanding of membrane structure, dynamics, and physical properties, a perspective is provided on how membrane-controlled regulation of protein functions can extend current applications and even offer new applications.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107, Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400 005, India
| | - Andreas Herrmann
- Freie Universität Berlin, Department Chemistry and Biochemistry, SupraFAB, Altensteinstr. 23a, D-14195, Berlin, Germany
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3
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Doktorova M, Khelashvili G, Brown MF. Efficient calculation of orientation-dependent lipid dynamics from membrane simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.23.542012. [PMID: 37292992 PMCID: PMC10245828 DOI: 10.1101/2023.05.23.542012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular dynamics simulations of lipid membranes have become increasingly impactful in biophysics because they offer atomistic resolution of structural fluctuations in relation to their functional outputs. Yet quantitative characterization of multiscale processes is a formidable challenge due to the distribution of motions that evade analysis of discrete simulation data. Here we investigate the efficient calculation of CH bond relaxation rates from membrane simulations. Widely used computational approaches offer numerical simplicity but fall short of capturing crucial aspects of the orientation dependence of the dynamics. To circumvent this problem, we introduced a robust framework based on liquid crystal theory which considers explicitly the CH bond motions with respect to the director axis (bilayer normal). Analysis of the orientation dependence of the dynamics shows excellent agreement with experiment, illustrating how the ordering potential affects the calculated relaxation rates. Furthermore, a fit-based resampling of the autocorrelation function of the bond fluctuations validates the new approach for low-temporal resolution data. The recovered relaxation rates indicate that at short timescales, both with and without cholesterol, the local motions of CH bonds describe the bilayer microviscosity and resemble liquid hydrocarbons. Our results establish the critical role of the orientational anisotropy in analysis of membrane simulations, explain fundamental aspects of lipid dynamics, and provide guidelines for extracting information that can be compared to experimental data.
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Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology & Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
- Department of Physics, University of Arizona, Tucson, AZ, USA
- Program in Applied Mathematics, University of Arizona, Tucson, AZ, USA
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4
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Zumpfe K, Berbon M, Habenstein B, Loquet A, Smith AA. Analytical Framework to Understand the Origins of Methyl Side-Chain Dynamics in Protein Assemblies. J Am Chem Soc 2024; 146:8164-8178. [PMID: 38476076 PMCID: PMC10979401 DOI: 10.1021/jacs.3c12620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
Side-chain motions play an important role in understanding protein structure, dynamics, protein-protein, and protein-ligand interactions. However, our understanding of protein side-chain dynamics is currently limited by the lack of analytical tools. Here, we present a novel analytical framework employing experimental nuclear magnetic resonance (NMR) relaxation measurements at atomic resolution combined with molecular dynamics (MD) simulation to characterize with a high level of detail the methyl side-chain dynamics in insoluble protein assemblies, using amyloid fibrils formed by the prion HET-s. We use MD simulation to interpret experimental results, where rotameric hops, including methyl group rotation and χ1/χ2 rotations, cannot be completely described with a single correlation time but rather sample a broad distribution of correlation times, resulting from continuously changing local structure in the fibril. Backbone motion similarly samples a broad range of correlation times, from ∼100 ps to μs, although resulting from mostly different dynamic processes; nonetheless, we find that the backbone is not fully decoupled from the side-chain motion, where changes in side-chain dynamics influence backbone motion and vice versa. While the complexity of side-chain motion in protein assemblies makes it very challenging to obtain perfect agreement between experiment and simulation, our analytical framework improves the interpretation of experimental dynamics measurements for complex protein assemblies.
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Affiliation(s)
- Kai Zumpfe
- Institute
for Medical Physics and Biophysics, Leipzig
University, Härtelstraße
16-18, 04107 Leipzig, Germany
| | - Mélanie Berbon
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Birgit Habenstein
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Antoine Loquet
- University
of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 33600 Pessac, France
| | - Albert A. Smith
- Institute
for Medical Physics and Biophysics, Leipzig
University, Härtelstraße
16-18, 04107 Leipzig, Germany
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5
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Islam MM, Nawagamuwage SU, Parshin IV, Richard MC, Burin AL, Rubtsov IV. Probing the Hydrophobic Region of a Lipid Bilayer at Specific Depths Using Vibrational Spectroscopy. J Am Chem Soc 2023; 145:26363-26373. [PMID: 37982703 DOI: 10.1021/jacs.3c10178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
A novel spectroscopic approach for studying the flexibility and mobility in the hydrophobic interior of lipid bilayers at specific depths is proposed. A set of test compounds featuring an azido moiety and a cyano or carboxylic acid moiety, connected by an alkyl chain of different lengths, was synthesized. FTIR data and molecular dynamics calculations indicated that the test compounds in a bilayer are oriented so that the cyano or carboxylic acid moiety is located in the lipid head-group region, while the azido group stays inside the bilayer at the depth determined by its alkyl chain length. We found that the asymmetric stretching mode of the azido group (νN3) can serve as a reporter of the membrane interior dynamics. FTIR and two-dimensional infrared (2DIR) studies were performed at different temperatures, ranging from 22 to 45 °C, covering the Lβ-Lα phase transition temperature of dipalmitoylphosphatidylcholine (∼41 °C). The width of the νN3 peak was found to be very sensitive to the phase transition and to the temperature in general. We introduced an order parameter, SN3, which characterizes restrictions to motion inside the bilayer. 2DIR spectra of νN3 showed different extents of inhomogeneity at different depths in the bilayer, with the smallest inhomogeneity in the middle of the leaflet. The spectral diffusion dynamics of the N3 peak was found to be dependent on the depth of the N3 group location in the bilayer. The obtained results enhance our understanding of the bilayer dynamics and can be extended to investigate membranes with more complex compositions.
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Affiliation(s)
- Md Muhaiminul Islam
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | | | - Igor V Parshin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Margaret C Richard
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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6
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Punia R, Goel G. Free Energy Surface and Molecular Mechanism of Slow Structural Transitions in Lipid Bilayers. J Chem Theory Comput 2023; 19:8245-8257. [PMID: 37947833 DOI: 10.1021/acs.jctc.3c00856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Lipid membrane remodeling, crucial for many cellular processes, is governed by the coupling of membrane structure and shape fluctuations. Given the importance of the ∼ nm length scale, details of the transition intermediates for conformational change are not fully captured by a continuum-mechanical description. Slow dynamics and the lack of knowledge of reaction coordinates (RCs) for biasing methods pose a challenge for all-atom (AA) simulations. Here, we map system dynamics on Langevin dynamics in a normal mode space determined from an elastic network model representation for the lipid-water Hamiltonian. AA molecular dynamics (MD) simulations are used to determine model parameters, and Langevin dynamics predictions for bilayer structural, mechanical, and dynamic properties are validated against MD simulations and experiments. Transferability to describe the dynamics of a larger lipid bilayer and a heterogeneous membrane-protein system is assessed. A set of generic RCs for pore formation in two tensionless bilayers is obtained by coupling Langevin dynamics to the underlying energy landscape for membrane deformations. Structure evolution is carried out by AA MD, wherein the generic RCs are used in a path metadynamics or an umbrella sampling simulation to determine the thermodynamics of pore formation and its molecular determinants, such as the role of distinct bilayer motions, lipid solvation, and lipid packing.
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Affiliation(s)
- Rajat Punia
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
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7
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Smith AA, Pacull EM, Stecher S, Hildebrand PW, Vogel A, Huster D. Analysis of the Dynamics of the Human Growth Hormone Secretagogue Receptor Reveals Insights into the Energy Landscape of the Molecule. Angew Chem Int Ed Engl 2023; 62:e202302003. [PMID: 37205715 DOI: 10.1002/anie.202302003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/04/2023] [Accepted: 05/19/2023] [Indexed: 05/21/2023]
Abstract
G protein-coupled receptors initiate signal transduction in response to ligand binding. Growth hormone secretagogue receptor (GHSR), the focus of this study, binds the 28 residue peptide ghrelin. While structures of GHSR in different states of activation are available, dynamics within each state have not been investigated in depth. We analyze long molecular dynamics simulation trajectories using "detectors" to compare dynamics of the apo and ghrelin-bound states yielding timescale-specific amplitudes of motion. We identify differences in dynamics between apo and ghrelin-bound GHSR in the extracellular loop 2 and transmembrane helices 5-7. NMR of the GHSR histidine residues reveals chemical shift differences in these regions. We evaluate timescale specific correlation of motions between residues of ghrelin and GHSR, where binding yields a high degree of correlation for the first 8 ghrelin residues, but less correlation for the helical end. Finally, we investigate the traverse of GHSR over a rugged energy landscape via principal component analysis.
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Affiliation(s)
- Albert A Smith
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Emelyne M Pacull
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Sabrina Stecher
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Alexander Vogel
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
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8
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Khodov IA, Belov KV, Huster D, Scheidt HA. Conformational State of Fenamates at the Membrane Interface: A MAS NOESY Study. MEMBRANES 2023; 13:607. [PMID: 37367811 DOI: 10.3390/membranes13060607] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023]
Abstract
The present work analyzes the 1H NOESY MAS NMR spectra of three fenamates (mefenamic, tolfenamic, and flufenamic acids) localized in the lipid-water interface of phosphatidyloleoylphosphatidylcholine (POPC) membranes. The observed cross-peaks in the two-dimensional NMR spectra characterized intramolecular proximities between the hydrogen atoms of the fenamates as well as intermolecular interactions between the fenamates and POPC molecules. The peak amplitude normalization for an improved cross-relaxation (PANIC) approach, the isolated spin-pair approximation (ISPA) model, and the two-position exchange model were used to calculate the interproton distances indicative of specific conformations of the fenamates. The results showed that the proportions of the A+C and B+D conformer groups of mefenamic and tolfenamic acids in the presence of POPC were comparable within the experimental error and amounted to 47.8%/52.2% and 47.7%/52.3%, respectively. In contrast, these proportions for the flufenamic acid conformers differed and amounted to 56.6%/43.4%. This allowed us to conclude that when they bind to the POPC model lipid membrane, fenamate molecules change their conformational equilibria.
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Affiliation(s)
- Ilya A Khodov
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - Konstantin V Belov
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, 04107 Leipzig, Germany
| | - Holger A Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University, 04107 Leipzig, Germany
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9
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Doktorova M, Khelashvili G, Ashkar R, Brown MF. Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics. Biophys J 2023; 122:984-1002. [PMID: 36474442 PMCID: PMC10111610 DOI: 10.1016/j.bpj.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/21/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022] Open
Abstract
Lipid bilayers form the main matrix of functional cell membranes, and their dynamics underlie a host of physical and biological processes. Here we show that elastic membrane properties and collective molecular dynamics (MD) are related by the mean-square amplitudes (order parameters) and relaxation rates (correlation times) of lipid acyl chain motions. We performed all-atom MD simulations of liquid-crystalline bilayers that allow direct comparison with carbon-hydrogen (CH) bond relaxations measured with NMR spectroscopy. Previous computational and theoretical approaches have assumed isotropic relaxation, which yields inaccurate description of lipid chain dynamics and incorrect data interpretation. Instead, the new framework includes a fixed bilayer normal (director axis) and restricted anisotropic motion of the CH bonds in accord with their segmental order parameters, enabling robust validation of lipid force fields. Simulated spectral densities of thermally excited CH bond fluctuations exhibited well-defined spin-lattice (Zeeman) relaxations analogous to those in NMR measurements. Their frequency signature could be fit to a simple power-law function, indicative of nematic-like collective dynamics. Moreover, calculated relaxation rates scaled as the squared order parameters yielding an apparent κC modulus for bilayer bending. Our results show a strong correlation with κC values obtained from solid-state NMR studies of bilayers without and with cholesterol as validated by neutron spin-echo measurements of membrane elasticity. The simulations uncover a critical role of interleaflet coupling in membrane mechanics and thus provide important insights into molecular sites of emerging elastic properties within lipid bilayers.
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Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York; Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, Virginia; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona; Department of Physics, University of Arizona, Tucson, Arizona; Program in Applied Mathematics, University of Arizona, Tucson, Arizona.
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10
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Gupta A, Kallianpur M, Roy DS, Engberg O, Chakrabarty H, Huster D, Maiti S. Different membrane order measurement techniques are not mutually consistent. Biophys J 2023; 122:964-972. [PMID: 36004780 PMCID: PMC10111216 DOI: 10.1016/j.bpj.2022.08.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022] Open
Abstract
"Membrane order" is a term commonly used to describe the elastic and mechanical properties of the lipid bilayer, though its exact meaning is somewhat context- and method dependent. These mechanical properties of the membrane control many cellular functions and are measured using various biophysical techniques. Here, we ask if the results obtained from various techniques are mutually consistent. Such consistency cannot be assumed a priori because these techniques probe different spatial locations and different spatial and temporal scales. We evaluate the change of membrane order induced by serotonin using nine different techniques in lipid bilayers of three different compositions. Serotonin is an important neurotransmitter present at 100s of mM concentrations in neurotransmitter vesicles, and therefore its interaction with the lipid bilayer is biologically relevant. Our measurement tools include fluorescence of lipophilic dyes (Nile Red, Laurdan, TMA-DPH, DPH), whose properties are a function of membrane order; atomic force spectroscopy, which provides a measure of the force required to indent the lipid bilayer; 2H solid-state NMR spectroscopy, which measures the molecular order of the lipid acyl chain segments; fluorescence correlation spectroscopy, which provides a measure of the diffusivity of the probe in the membrane; and Raman spectroscopy, where spectral intensity ratios are affected by acyl chain order. We find that different measures often do not correlate with each other and sometimes even yield conflicting results. We conclude that no probe provides a general measure of membrane order and that any inference based on the change of membrane order measured by a particular probe may be unreliable.
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Affiliation(s)
- Ankur Gupta
- Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | | | | | - Oskar Engberg
- Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | | | - Daniel Huster
- Tata Institute of Fundamental Research, Colaba, Mumbai, India; Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany.
| | - Sudipta Maiti
- Tata Institute of Fundamental Research, Colaba, Mumbai, India.
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11
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Fandrei F, Havrišák T, Opálka L, Engberg O, Smith A, Pullmannová P, Kučerka N, Ondrejčeková V, Demé B, Nováková L, Steinhart M, Vávrová K, Huster D. The Intriguing Molecular Dynamics of Cer[EOS] in Rigid Skin Barrier Lipid Layers Requires Improvement of the Model. J Lipid Res 2023; 64:100356. [PMID: 36948272 PMCID: PMC10154977 DOI: 10.1016/j.jlr.2023.100356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/24/2023] Open
Abstract
Omega-O-acyl ceramides such as 32-linoleoyloxydotriacontanoyl sphingosine (Cer[EOS]) are essential components of the lipid skin barrier, which protects our body from excessive water loss and the penetration of unwanted substances. These ceramides drive the lipid assembly to epidermal-specific long periodicity phase (LPP), structurally much different than conventional lipid bilayers. Here, we synthesized Cer[EOS] with selectively deuterated segments of the ultralong N-acyl chain or deuterated or 13C-labeled linoleic acid and studied their molecular behavior in a skin lipid model. Solid-state 2H NMR data revealed surprising molecular dynamics for the ultralong N-acyl chain of Cer[EOS] with increased isotropic motion towards the isotropic ester-bound linoleate. The sphingosine moiety of Cer[EOS] is also highly mobile at skin temperature, in stark contrast to the other LPP components, N-lignoceroyl sphingosine acyl, lignoceric acid and cholesterol, which are predominantly rigid. The dynamics of the linoleic chain is quantitatively described by distributions of correlation times and using dynamic detector analysis. These NMR results along with neutron diffraction data suggest an LPP structure with alternating fluid (sphingosine chain-rich), rigid (acyl chain-rich), isotropic (linoleate-rich), rigid (acyl-chain rich), and fluid layers (sphingosine chain-rich). Such an arrangement of the skin barrier lipids with rigid layers separated with two different dynamic "fillings" i) agrees well with ultrastructural data, ii) satisfies the need for simultaneous rigidity (to ensure low permeability) and fluidity (to ensure elasticity, accommodate enzymes or antimicrobial peptides), and iii) offers a straightforward way to remodel the lamellar body lipids into the final lipid barrier.
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Affiliation(s)
- Ferdinand Fandrei
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04275 Leipzig, Germany
| | - Tomáš Havrišák
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Lukáš Opálka
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Oskar Engberg
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04275 Leipzig, Germany
| | - AlbertA Smith
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04275 Leipzig, Germany
| | - Petra Pullmannová
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Norbert Kučerka
- Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 832 32 Bratislava, Slovakia
| | - Veronika Ondrejčeková
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Bruno Demé
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, CEDEX 9, France
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Miloš Steinhart
- Institute of Macromolecular Chemistry, Czech Academy of Science in Prague, Heyrovského nám. 2, 162 06 Prague, Czech Republic
| | - Kateřina Vávrová
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04275 Leipzig, Germany
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12
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Svenningsson L, Mueller LJ. TensorView for MATLAB: Visualizing tensors with Euler angle decoding. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2023; 123:101849. [PMID: 36610267 PMCID: PMC10238149 DOI: 10.1016/j.ssnmr.2022.101849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 05/29/2023]
Abstract
TensorView for MATLAB is a GUI-based visualization tool for depicting second-rank Cartesian tensors as surfaces on three-dimensional molecular models. Both ellipsoid and ovaloid tensor display formats are supported, and the software allows for easy conversion of Euler angles from common rotation schemes (active, passive, ZXZ, and ZYZ conventions) with visual feedback. In addition, the software displays all four orientation-equivalent Euler angle solutions for the placement of a single tensor in the molecular frame and can report relative orientations of two tensors with all 16 orientation-equivalent Euler angle sets that relate them. The salient relations are derived and illustrated through several examples. TensorView for MATLAB expands and complements the earlier implementation of TensorView within the Mathematica programming environment and can be run without a MATLAB license. TensorView for MATLAB is available through github at https://github.com/LeoSvenningsson/TensorViewforMatlab, and can also be accessed directly via the NMRbox resource.
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Affiliation(s)
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, CA, USA.
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13
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How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation. Curr Opin Struct Biol 2022; 77:102459. [PMID: 36148743 DOI: 10.1016/j.sbi.2022.102459] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022]
Abstract
Nuclear magnetic resonance (NMR) spin relaxation experiments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from 15N relaxation and side-chain dynamics from 13C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics.
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14
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Bolik-Coulon N, Languin-Cattoën O, Carnevale D, Zachrdla M, Laage D, Sterpone F, Stirnemann G, Ferrage F. Explicit Models of Motion to Understand Protein Side-Chain Dynamics. PHYSICAL REVIEW LETTERS 2022; 129:203001. [PMID: 36462011 DOI: 10.1103/physrevlett.129.203001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/04/2022] [Indexed: 06/17/2023]
Abstract
Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motion. Model-free types of correlation functions cannot describe a large carbon-13 relaxation dataset in protein side chains. Here, we use molecular dynamics simulations to design explicit models of motion and solve Fokker-Planck diffusion equations. These models of motion provide better agreement with relaxation data, mechanistic insight, and a direct link to configuration entropy.
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Affiliation(s)
- Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Olivier Languin-Cattoën
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologique Physico-Chimique, Université Paris Cité, PSL University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Diego Carnevale
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Milan Zachrdla
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologique Physico-Chimique, Université Paris Cité, PSL University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Damien Laage
- PASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologique Physico-Chimique, Université Paris Cité, PSL University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologique Physico-Chimique, Université Paris Cité, PSL University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
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15
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Molugu TR, Thurmond RL, Alam TM, Trouard TP, Brown MF. Phospholipid headgroups govern area per lipid and emergent elastic properties of bilayers. Biophys J 2022; 121:4205-4220. [PMID: 36088534 PMCID: PMC9674990 DOI: 10.1016/j.bpj.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/10/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022] Open
Abstract
Phospholipid bilayers are liquid-crystalline materials whose intermolecular interactions at mesoscopic length scales have key roles in the emergence of membrane physical properties. Here we investigated the combined effects of phospholipid polar headgroups and acyl chains on biophysical functions of membranes with solid-state 2H NMR spectroscopy. We compared the structural and dynamic properties of phosphatidylethanolamine and phosphatidylcholine with perdeuterated acyl chains in the solid-ordered (so) and liquid-disordered (ld) phases. Our analysis of spectral lineshapes of 1,2-diperdeuteriopalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE-d62) and 1,2-diperdeuteriopalmitoyl-sn-glycero-3-phosphocholine (DPPC-d62) in the so (gel) phase indicated an all-trans rotating chain structure for both lipids. Greater segmental order parameters (SCD) were observed in the ld (liquid-crystalline) phase for DPPE-d62 than for DPPC-d62 membranes, while their mixtures had intermediate values irrespective of the deuterated lipid type. Our results suggest the SCD profiles of the acyl chains are governed by methylation of the headgroups and are averaged over the entire system. Variations in the acyl chain molecular dynamics were further investigated by spin-lattice (R1Z) and quadrupolar-order relaxation (R1Q) measurements. The two acyl-perdeuterated lipids showed distinct differences in relaxation behavior as a function of the order parameter. The R1Z rates had a square-law dependence on SCD, implying collective mesoscopic dynamics, with a higher bending rigidity for DPPE-d62 than for DPPC-d62 lipids. Remodeling of lipid average and dynamic properties by methylation of the headgroups thus provides a mechanism to control the actions of peptides and proteins in biomembranes.
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Affiliation(s)
- Trivikram R Molugu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | | | - Todd M Alam
- Department of Organic Materials Science, Sandia National Laboratories, Albuquerque, New Mexico
| | - Theodore P Trouard
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona; Department of Physics, University of Arizona, Tucson, Arizona.
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16
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Doole FT, Kumarage T, Ashkar R, Brown MF. Cholesterol Stiffening of Lipid Membranes. J Membr Biol 2022; 255:385-405. [PMID: 36219221 PMCID: PMC9552730 DOI: 10.1007/s00232-022-00263-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022]
Abstract
Biomembrane order, dynamics, and other essential physicochemical parameters are controlled by cholesterol, a major component of mammalian cell membranes. Although cholesterol is well known to exhibit a condensing effect on fluid lipid membranes, the extent of stiffening that occurs with different degrees of lipid acyl chain unsaturation remains an enigma. In this review, we show that cholesterol locally increases the bending rigidity of both unsaturated and saturated lipid membranes, suggesting there may be a length-scale dependence of the bending modulus. We review our published data that address the origin of the mechanical effects of cholesterol on unsaturated and polyunsaturated lipid membranes and their role in biomembrane functions. Through a combination of solid-state deuterium NMR spectroscopy and neutron spin-echo spectroscopy, we show that changes in molecular packing cause the universal effects of cholesterol on the membrane bending rigidity. Our findings have broad implications for the role of cholesterol in lipid–protein interactions as well as raft-like mixtures, drug delivery applications, and the effects of antimicrobial peptides on lipid membranes.
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Affiliation(s)
- Fathima T Doole
- Deaprtment of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85712, USA
| | - Teshani Kumarage
- Department of Physics, Virginia Tech, Blacksburg, VA, 24061, USA.,Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA, 24061, USA. .,Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Michael F Brown
- Deaprtment of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85712, USA. .,Department of Physics, University of Arizona, Tucson, AZ, 85712, USA.
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