1
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Shishmarev D, Fontenelle CQ, Linclau B, Kuprov I, Kuchel PW. Quantitative Analysis of 2D EXSY NMR Spectra of Strongly Coupled Spin Systems in Transmembrane Exchange. Chembiochem 2024; 25:e202300597. [PMID: 37984465 PMCID: PMC10952724 DOI: 10.1002/cbic.202300597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
Solute translocation by membrane transport proteins is a vital biological process that can be tracked, on the sub-second timescale, using nuclear magnetic resonance (NMR). Fluorinated substrate analogues facilitate such studies because of high sensitivity of 19 F NMR and absence of background signals. Accurate extraction of translocation rate constants requires precise quantification of NMR signal intensities. This becomes complicated in the presence of J-couplings, cross-correlations, and nuclear Overhauser effects (NOE) that alter signal integrals through mechanisms unrelated to translocation. Geminal difluorinated motifs introduce strong and hard-to-quantify contributions from non-exchange effects, the nuanced nature of which makes them hard to integrate into data analysis methodologies. With analytical expressions not being available, numerical least squares fitting of theoretical models to 2D spectra emerges as the preferred quantification approach. For large spin systems with simultaneous coherent evolution, cross-relaxation, cross-correlation, conformational exchange, and membrane translocation between compartments with different viscosities, the only available simulation framework is Spinach. In this study, we demonstrate GLUT-1 dependent membrane transport of two model sugars featuring CF2 and CF2 CF2 fluorination motifs, with precise determination of translocation rate constants enabled by numerical fitting of 2D EXSY spectra. For spin systems and kinetic networks of this complexity, this was not previously tractable.
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Affiliation(s)
- Dmitry Shishmarev
- The Australian National UniversityJohn Curtin School of Medical Research2601CanberraACTAustralia
- The Australian National UniversityResearch School of Biology2601CanberraACTAustralia
| | | | - Bruno Linclau
- University of SouthamptonDepartment of ChemistrySO17 1BJSouthamptonUK
- Department of Organic and Macromolecular ChemistryGhent UniversityCampus Sterre, Krijgslaan 281-S49000GhentBelgium
| | - Ilya Kuprov
- University of SouthamptonDepartment of ChemistrySO17 1BJSouthamptonUK
| | - Philip W. Kuchel
- The University of SydneySchool of Life and Environmental Sciences2006SydneyNSWAustralia
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2
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Shafieenezhad A, Mitra S, Wassall SR, Tristram-Nagle S, Nagle JF, Petrache HI. Location of dopamine in lipid bilayers and its relevance to neuromodulator function. Biophys J 2023; 122:1118-1129. [PMID: 36804668 PMCID: PMC10111280 DOI: 10.1016/j.bpj.2023.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/18/2022] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Dopamine (DA) is a neurotransmitter that also acts as a neuromodulator, with both functions being essential to brain function. Here, we present the first experimental measurement of DA location in lipid bilayers using x-ray diffuse scattering, solid-state deuterium NMR, and electron paramagnetic resonance. We find that the association of DA with lipid headgroups as seen in electron density profiles leads to an increase of intermembrane repulsion most likely due to electrostatic charging. DA location in the lipid headgroup region also leads to an increase of the cross-sectional area per lipid without affecting the bending rigidity significantly. The order parameters measured by solid-state deuterium NMR decrease in the presence of DA for the acyl chains of PC and PS lipids, consistent with an increase in the area per lipid due to DA. Most importantly, these results support the hypothesis that three-dimensional diffusion of DA to target membranes could be followed by relatively more efficient two-dimensional diffusion to receptors within those membranes.
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Affiliation(s)
- Azam Shafieenezhad
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | - Saheli Mitra
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Stephen R Wassall
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | | | - John F Nagle
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Horia I Petrache
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana.
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3
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Kinnun JJ, Scott HL, Bolmatov D, Collier CP, Charlton TR, Katsaras J. Biophysical studies of lipid nanodomains using different physical characterization techniques. Biophys J 2023; 122:931-949. [PMID: 36698312 PMCID: PMC10111277 DOI: 10.1016/j.bpj.2023.01.024] [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: 10/14/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
For the past 50 years, evidence for the existence of functional lipid domains has been steadily accumulating. Although the notion of functional lipid domains, also known as "lipid rafts," is now widely accepted, this was not always the case. This ambiguity surrounding lipid domains could be partly attributed to the fact that they are highly dynamic, nanoscopic structures. Since most commonly used techniques are sensitive to microscale structural features, it is therefore, not surprising that it took some time to reach a consensus regarding their existence. In this review article, we will discuss studies that have used techniques that are inherently sensitive to nanoscopic structural features (i.e., neutron scatting, nuclear magnetic resonance, and Förster resonance energy transfer). We will also mention techniques that may be of use in the future (i.e., cryoelectron microscopy, droplet interface bilayers, inelastic x-ray scattering, and neutron reflectometry), which can further our understanding of the different and unique physicochemical properties of nanoscopic lipid domains.
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Affiliation(s)
- Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Haden L Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Dima Bolmatov
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Timothy R Charlton
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - John Katsaras
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
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4
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Yao S, Keizer DW, Babon JJ, Separovic F. NMR measurement of biomolecular translational and rotational motion for evaluating changes of protein oligomeric state in solution. EUROPEAN BIOPHYSICS JOURNAL 2022; 51:193-204. [PMID: 35380220 PMCID: PMC9034988 DOI: 10.1007/s00249-022-01598-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 11/15/2022]
Abstract
Defining protein oligomeric state and/or its changes in solution is of significant interest for many biophysical studies carried out in vitro, especially when the nature of the oligomeric state is crucial in the subsequent interpretation of experimental results and their biological relevance. Nuclear magnetic resonance (NMR) is a well-established methodology for the characterization of protein structure, dynamics, and interactions at the atomic level. As a spectroscopic method, NMR also provides a compelling means for probing both molecular translational and rotational motion, two predominant measures of effective molecular size in solution, under identical conditions as employed for structural, dynamic and interaction studies. Protein translational diffusion is readily measurable by pulse gradient spin echo (PGSE) NMR, whereas its rotational correlation time, or rotational diffusion tensor when its 3D structure is known, can also be quantified from NMR relaxation parameters, such as 15N relaxation parameters of backbone amides which are frequently employed for probing residue-specific protein backbone dynamics. In this article, we present an introductory overview to the NMR measurement of bimolecular translational and rotational motion for assessing changes of protein oligomeric state in aqueous solution, via translational diffusion coefficients measured by PGSE NMR and rotational correlation times derived from composite 15N relaxation parameters of backbone amides, without need for the protein structure being available.
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5
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Cherniavskyi YK, Fathizadeh A, Elber R, Tieleman DP. Computer simulations of a heterogeneous membrane with enhanced sampling techniques. J Chem Phys 2021; 153:144110. [PMID: 33086798 PMCID: PMC7556882 DOI: 10.1063/5.0014176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Computational determination of the equilibrium state of heterogeneous phospholipid membranes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in membranes are long compared to typical time scales of computer simulations. Here, we evaluate the combination of the enhanced sampling techniques molecular dynamics with alchemical steps and Monte Carlo with molecular dynamics with a coarse-grained model of membranes (Martini) to reduce the number of steps and force evaluations that are needed to reach equilibrium. We illustrate a significant gain compared to straightforward molecular dynamics of the Martini model by factors between 3 and 10. The combination is a useful tool to enhance the study of phase separation and the formation of domains in biological membranes.
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Affiliation(s)
- Yevhen K Cherniavskyi
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Arman Fathizadeh
- The Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ron Elber
- The Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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6
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Lau S, Stanhope N, Griffin J, Hughes E, Middleton DA. Drug orientations within statin-loaded lipoprotein nanoparticles by 19F solid-state NMR. Chem Commun (Camb) 2019; 55:13287-13290. [PMID: 31626247 DOI: 10.1039/c9cc05344a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
NMR measurements of 19F chemical shift anisotropy and 1H-19F dipolar couplings provide unprecedented information on the molecular orientations of two fluorine-containing statin drugs within the heterogeneous environment of reconstituted high-density lipoprotein (rHDL) nanoparticles, a drug delivery system under clinical investigation.
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Affiliation(s)
- Sophie Lau
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, UK.
| | - Naomi Stanhope
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, UK.
| | - John Griffin
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, UK.
| | - Eleri Hughes
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, UK.
| | - David A Middleton
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, UK.
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7
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Fathizadeh A, Elber R. A mixed alchemical and equilibrium dynamics to simulate heterogeneous dense fluids: Illustrations for Lennard-Jones mixtures and phospholipid membranes. J Chem Phys 2018; 149:072325. [PMID: 30134684 PMCID: PMC6018062 DOI: 10.1063/1.5027078] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
An algorithm to efficiently simulate multi-component fluids is proposed and illustrated. The focus is on biological membranes that are heterogeneous and challenging to investigate quantitatively. To achieve rapid equilibration of spatially inhomogeneous fluids, we mix conventional molecular dynamics simulations with alchemical trajectories. The alchemical trajectory switches the positions of randomly selected pairs of molecules and plays the role of an efficient Monte Carlo move. It assists in accomplishing rapid spatial de-correlations. Examples of phase separation and mixing are given in two-dimensional binary Lennard-Jones fluid and a DOPC-POPC membrane. The performance of the algorithm is analyzed, and tools to maximize its efficiency are provided. It is concluded that the algorithm is vastly superior to conventional molecular dynamics for the equilibrium study of biological membranes.
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Affiliation(s)
- Arman Fathizadeh
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ron Elber
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
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8
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Hughes E, Griffin JM, Coogan MP, Middleton DA. Average orientation of a fluoroaromatic molecule in lipid bilayers from DFT-informed NMR measurements of 1H- 19F dipolar couplings. Phys Chem Chem Phys 2018; 20:18207-18215. [PMID: 29915824 PMCID: PMC6042476 DOI: 10.1039/c8cp01064a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/28/2018] [Indexed: 12/11/2022]
Abstract
Fluorine is often incorporated into the aromatic moieties of synthetic bioactive molecules such as pharmaceuticals and disease diagnostics in order to alter their physicochemical properties. Fluorine substitution may increase a molecule's lipophilicity, thereby enabling its diffusion across cell membranes to enhance bioavailability or to exert a direct physiological effect from within the lipid bilayer. Understanding the structure, dynamics and orientation of fluoroaromatic molecules in lipid bilayers can provide useful insight into the effect of fluorine on their mode of action, and their interactions with membrane-embedded targets or efflux proteins. Here we demonstrate that NMR measurements of 19F chemical shift anisotropy combined with 1H-19F dipolar coupling measurements together report on the average orientation of a lipophilic fluoroaromatic molecule, 4-(6-fluorobenzo[d]thiazol-2-yl)aniline (FBTA), rapidly rotating within a lipid bilayer. The 19F chemical shift tensor orientation in the molecular frame was calculated by density functional theory and corroborated by 1H-19F PISEMA NMR. It was then possible to analyse the line shapes of proton-coupled and proton-decoupled 19F spectra of FBTA in chain perdeuterated dimyristoylphosphatidylcholine (DMPC-d54) bilayers to restrict the average axis of molecular reorientation of FBTA in the bilayer to a limited range orientations. This approach, which exploits the high sensitivity and gyromagnetic ratios of 19F and 1H, will be useful for comparing the membrane properties of related bioactive fluoroaromatic compounds.
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Affiliation(s)
- Eleri Hughes
- Department of Chemistry
, Lancaster University
,
Lancaster
, LA1 4YB
, UK
.
; Tel: +44 1524 594328
| | - John M. Griffin
- Department of Chemistry
, Lancaster University
,
Lancaster
, LA1 4YB
, UK
.
; Tel: +44 1524 594328
| | - Michael P. Coogan
- Department of Chemistry
, Lancaster University
,
Lancaster
, LA1 4YB
, UK
.
; Tel: +44 1524 594328
| | - David A. Middleton
- Department of Chemistry
, Lancaster University
,
Lancaster
, LA1 4YB
, UK
.
; Tel: +44 1524 594328
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9
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Novel approaches to probe the binding of recoverin to membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:679-691. [DOI: 10.1007/s00249-018-1304-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 02/08/2023]
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10
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Molugu TR, Lee S, Brown MF. Concepts and Methods of Solid-State NMR Spectroscopy Applied to Biomembranes. Chem Rev 2017; 117:12087-12132. [PMID: 28906107 DOI: 10.1021/acs.chemrev.6b00619] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Concepts of solid-state NMR spectroscopy and applications to fluid membranes are reviewed in this paper. Membrane lipids with 2H-labeled acyl chains or polar head groups are studied using 2H NMR to yield knowledge of their atomistic structures in relation to equilibrium properties. This review demonstrates the principles and applications of solid-state NMR by unifying dipolar and quadrupolar interactions and highlights the unique features offered by solid-state 2H NMR with experimental illustrations. For randomly oriented multilamellar lipids or aligned membranes, solid-state 2H NMR enables direct measurement of residual quadrupolar couplings (RQCs) due to individual C-2H-labeled segments. The distribution of RQC values gives nearly complete profiles of the segmental order parameters SCD(i) as a function of acyl segment position (i). Alternatively, one can measure residual dipolar couplings (RDCs) for natural abundance lipid samples to obtain segmental SCH order parameters. A theoretical mean-torque model provides acyl-packing profiles representing the cumulative chain extension along the normal to the aqueous interface. Equilibrium structural properties of fluid bilayers and various thermodynamic quantities can then be calculated, which describe the interactions with cholesterol, detergents, peptides, and integral membrane proteins and formation of lipid rafts. One can also obtain direct information for membrane-bound peptides or proteins by measuring RDCs using magic-angle spinning (MAS) in combination with dipolar recoupling methods. Solid-state NMR methods have been extensively applied to characterize model membranes and membrane-bound peptides and proteins, giving unique information on their conformations, orientations, and interactions in the natural liquid-crystalline state.
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Affiliation(s)
- Trivikram R Molugu
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Soohyun Lee
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Michael F Brown
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
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11
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Auger M. Membrane solid-state NMR in Canada: A historical perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1483-1489. [PMID: 28652206 DOI: 10.1016/j.bbapap.2017.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/17/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022]
Abstract
This manuscript presents an overview of more than 40years of membrane solid-state nuclear magnetic resonance (NMR) research in Canada. This technique is a method of choice for the study of the structure and dynamics of lipid bilayers; bilayer interactions with a variety of molecules such as membrane peptides, membrane proteins and drugs; and to investigate membrane peptide and protein structure, dynamics, and topology. Canada has a long tradition in this field of research, starting with pioneering work on natural and model membranes in the 1970s in a context of emergence of biophysics in the country. The 1980s and 1990s saw an emphasis on studying lipid structures and dynamics, and peptide-lipid and protein-lipid interactions. The study of bicelles began in the 1990s, and in the 2000s there was a rise in the study of membrane protein structures. Novel perspectives include using dynamic nuclear polarization (DNP) for membrane studies and using NMR in live cells. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Michèle Auger
- Département de chimie, PROTEO, CERMA, CQMF, Université Laval, Québec, Québec G1V 0A6, Canada.
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12
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Bärenwald R, Achilles A, Lange F, Ferreira TM, Saalwächter K. Applications of Solid-State NMR Spectroscopy for the Study of Lipid Membranes with Polyphilic Guest (Macro)Molecules. Polymers (Basel) 2016; 8:E439. [PMID: 30974716 PMCID: PMC6432237 DOI: 10.3390/polym8120439] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/01/2016] [Accepted: 12/08/2016] [Indexed: 11/16/2022] Open
Abstract
The incorporation of polymers or smaller complex molecules into lipid membranes allows for property modifications or the introduction of new functional elements. The corresponding molecular-scale details, such as changes in dynamics or features of potential supramolecular structures, can be studied by a variety of solid-state NMR techniques. Here, we review various approaches to characterizing the structure and dynamics of the guest molecules as well as the lipid phase structure and dynamics by different high-resolution magic-angle spinning proton and 13C NMR experiments as well as static 31P NMR experiments. Special emphasis is placed upon the incorporation of novel synthetic polyphilic molecules such as shape-persistent T- and X-shaped molecules as well as di- and tri-block copolymers. Most of the systems studied feature dynamic heterogeneities, for instance those arising from the coexistence of different phases; possibilities for a quantitative assessment are of particular concern.
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Affiliation(s)
- Ruth Bärenwald
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Anja Achilles
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Frank Lange
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Tiago Mendes Ferreira
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Kay Saalwächter
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany.
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13
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Schmidt ML, Davis JH. Liquid disordered–liquid ordered phase coexistence in bicelles containing unsaturated lipids and cholesterol. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:619-26. [DOI: 10.1016/j.bbamem.2015.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/04/2015] [Accepted: 12/15/2015] [Indexed: 10/22/2022]
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14
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Affiliation(s)
- M. J. Greenall
- Institute of Mathematics,
Physics and Computer Science, Physical Sciences Building, Aberystwyth University, Aberystwyth SY23 3BZ, United Kingdom
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15
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The study of transient protein-nanoparticle interactions by solution NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:102-14. [PMID: 25936778 DOI: 10.1016/j.bbapap.2015.04.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 12/30/2022]
Abstract
The rapid development of novel nanoscale materials for applications in biomedicine urges an improved characterization of the nanobio interfaces. Nanoparticles exhibit unique structures and properties, often different from the corresponding bulk materials, and the nature of their interactions with biological systems remains poorly characterized. Solution NMR spectroscopy is a mature technique for the investigation of biomolecular structure, dynamics, and intermolecular associations, however its use in protein-nanoparticle interaction studies remains scarce and highly challenging, particularly due to unfavorable hydrodynamic properties of most nanoscale assemblies. Nonetheless, recent efforts demonstrated that a number of NMR observables, such as chemical shifts, signal intensities, amide exchange rates and relaxation parameters, together with newly designed saturation transfer experiments, could be successfully employed to characterize the orientation, structure and dynamics of proteins adsorbed onto nanoparticle surfaces. This review provides the first survey and critical assessment of the contributions from solution NMR spectroscopy to the study of transient interactions between proteins and both inorganic (gold, silver, and silica) and organic (polymer, carbon and lipid based) nanoparticles. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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16
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Ding Y, Fujimoto LM, Yao Y, Marassi FM. Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation. JOURNAL OF BIOMOLECULAR NMR 2015; 61:275-86. [PMID: 25578899 PMCID: PMC4398618 DOI: 10.1007/s10858-014-9893-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/20/2014] [Indexed: 05/22/2023]
Abstract
Solid-state NMR studies of sedimented soluble proteins has been developed recently as an attractive approach for overcoming the size limitations of solution NMR spectroscopy while bypassing the need for sample crystallization or precipitation (Bertini et al. Proc Natl Acad Sci USA 108(26):10396-10399, 2011). Inspired by the potential benefits of this method, we have investigated the ability to sediment lipid bilayer nanodiscs reconstituted with a membrane protein. In this study, we show that nanodiscs containing the outer membrane protein Ail from Yersinia pestis can be sedimented for solid-state NMR structural studies, without the need for precipitation or lyophilization. Optimized preparations of Ail in phospholipid nanodiscs support both the structure and the fibronectin binding activity of the protein. The same sample can be used for solution NMR, solid-state NMR and activity assays, facilitating structure-activity correlation experiments across a wide range of timescales.
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Affiliation(s)
- Yi Ding
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
| | - L. Miya Fujimoto
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
| | - Yong Yao
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
| | - Francesca M. Marassi
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla CA 92037, USA. [Tel: 858-795-5282; Mail: ]
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17
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Saxton MJ. Wanted: scalable tracers for diffusion measurements. J Phys Chem B 2014; 118:12805-17. [PMID: 25319586 PMCID: PMC4234437 DOI: 10.1021/jp5059885] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/03/2014] [Indexed: 12/02/2022]
Abstract
Scalable tracers are potentially a useful tool to examine diffusion mechanisms and to predict diffusion coefficients, particularly for hindered diffusion in complex, heterogeneous, or crowded systems. Scalable tracers are defined as a series of tracers varying in size but with the same shape, structure, surface chemistry, deformability, and diffusion mechanism. Both chemical homology and constant dynamics are required. In particular, branching must not vary with size, and there must be no transition between ordinary diffusion and reptation. Measurements using scalable tracers yield the mean diffusion coefficient as a function of size alone; measurements using nonscalable tracers yield the variation due to differences in the other properties. Candidate scalable tracers are discussed for two-dimensional (2D) diffusion in membranes and three-dimensional diffusion in aqueous solutions. Correlations to predict the mean diffusion coefficient of globular biomolecules from molecular mass are reviewed briefly. Specific suggestions for the 3D case include the use of synthetic dendrimers or random hyperbranched polymers instead of dextran and the use of core-shell quantum dots. Another useful tool would be a series of scalable tracers varying in deformability alone, prepared by varying the density of crosslinking in a polymer to make say "reinforced Ficoll" or "reinforced hyperbranched polyglycerol."
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Affiliation(s)
- Michael J. Saxton
- Department of Biochemistry
and Molecular Medicine, University of California, One Shields Ave., Davis, California 95616, United States
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Beaugrand M, Arnold A, Hénin J, Warschawski DE, Williamson PTF, Marcotte I. Lipid concentration and molar ratio boundaries for the use of isotropic bicelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:6162-70. [PMID: 24797658 PMCID: PMC4072726 DOI: 10.1021/la5004353] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/02/2014] [Indexed: 05/27/2023]
Abstract
Bicelles are model membranes generally made of long-chain dimyristoylphosphatidylcholine (DMPC) and short-chain dihexanoyl-PC (DHPC). They are extensively used in the study of membrane interactions and structure determination of membrane-associated peptides, since their composition and morphology mimic the widespread PC-rich natural eukaryotic membranes. At low DMPC/DHPC (q) molar ratios, fast-tumbling bicelles are formed in which the DMPC bilayer is stabilized by DHPC molecules in the high-curvature rim region. Experimental constraints imposed by techniques such as circular dichroism, dynamic light scattering, or microscopy may require the use of bicelles at high dilutions. Studies have shown that such conditions induce the formation of small aggregates and alter the lipid-to-detergent ratio of the bicelle assemblies. The objectives of this work were to determine the exact composition of those DMPC/DHPC isotropic bicelles and study the lipid miscibility. This was done using (31)P nuclear magnetic resonance (NMR) and exploring a wide range of lipid concentrations (2-400 mM) and q ratios (0.15-2). Our data demonstrate how dilution modifies the actual DMPC/DHPC molar ratio in the bicelles. Care must be taken for samples with a total lipid concentration ≤250 mM and especially at q ∼ 1.5-2, since moderate dilutions could lead to the formation of large and slow-tumbling lipid structures that could hinder the use of solution NMR methods, circular dichroism or dynamic light scattering studies. Our results, supported by infrared spectroscopy and molecular dynamics simulations, also show that phospholipids in bicelles are largely segregated only when q > 1. Boundaries are presented within which control of the bicelles' q ratio is possible. This work, thus, intends to guide the choice of q ratio and total phospholipid concentration when using isotropic bicelles.
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Affiliation(s)
- Maïwenn Beaugrand
- Department
of Chemistry, Université du Québec
à Montréal and Centre Québécois sur les
Matériaux Fonctionnels, P.O. Box 8888, Downtown Station, Montreal, Canada H3C 3P8
| | - Alexandre
A. Arnold
- Department
of Chemistry, Université du Québec
à Montréal and Centre Québécois sur les
Matériaux Fonctionnels, P.O. Box 8888, Downtown Station, Montreal, Canada H3C 3P8
| | - Jérôme Hénin
- Laboratoire
de Biochimie Théorique, CNRS, Université
Paris Diderot and Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie-Curie, 75005 Paris, France
| | - Dror E. Warschawski
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS, Université Paris Diderot and Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie-Curie, 75005 Paris, France
| | - Philip T. F. Williamson
- School
of Biological Sciences, Highfield Campus,
University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Isabelle Marcotte
- Department
of Chemistry, Université du Québec
à Montréal and Centre Québécois sur les
Matériaux Fonctionnels, P.O. Box 8888, Downtown Station, Montreal, Canada H3C 3P8
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Johansson B, Höök F, Klenerman D, Jönsson P. Label-free measurements of the diffusivity of molecules in lipid membranes. Chemphyschem 2014; 15:486-91. [PMID: 24402971 DOI: 10.1002/cphc.201301136] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Indexed: 11/05/2022]
Abstract
An important and characteristic property of a cell membrane is the lateral mobility of protein molecules in the lipid bilayer. This has conventionally been measured by labeling the molecules with fluorescent markers and monitoring their mobility by different fluorescence-based techniques. However, adding the label to the studied molecule may affect the system, so it is an assumption in almost all experiments that the measured mobility of the biomolecule with its label is the same as that of the unlabeled molecule. However, this assumption is rarely tested due to a lack of suitable methods. In this work, a new technique to perform label-free diffusivity measurements is developed and used to measure the effect of the label for two common protein-lipid systems: 1) streptavidin (SA) coupled to a supported lipid bilayer (SLB) through biotinylated lipids and 2) the extracellular part of the T-cell adhesion protein CD2, coupled to an SLB through histidine tags to nickel-chelating lipids. A measurable (≈12%) decrease in diffusivity is found for both labeled proteins, even though the molecular mass of the label is almost 100 times smaller than those of the proteins (≈50 kDa). The results illustrate the importance of being able to study different biophysical properties of cell membranes and their mimics without relying on fluorescent labels, especially if fluorescent labeling is difficult or is expected to affect the nature of the intermolecular interactions being studied.
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Affiliation(s)
- Björn Johansson
- Department of Applied Physics, Chalmers University of Technology, 41296 Gothenburg (Sweden)
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Huster D. Solid-state NMR spectroscopy to study protein-lipid interactions. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:1146-60. [PMID: 24333800 DOI: 10.1016/j.bbalip.2013.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/04/2013] [Indexed: 12/22/2022]
Abstract
The appropriate lipid environment is crucial for the proper function of membrane proteins. There is a tremendous variety of lipid molecules in the membrane and so far it is often unclear which component of the lipid matrix is essential for the function of a respective protein. Lipid molecules and proteins mutually influence each other; parameters such as acyl chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation are strongly modulated by proteins. More recent data also indicates that the influence of proteins goes beyond a single annulus of next-neighbor boundary lipids. Therefore, a mesoscopic approach to membrane lipid-protein interactions in terms of elastic membrane deformations has been developed. Solid-state NMR has greatly contributed to the understanding of lipid-protein interactions and the modern view of biological membranes. Methods that detect the influence of proteins on the membrane as well as direct lipid-protein interactions have been developed and are reviewed here. Examples for solid-state NMR studies on the interaction of Ras proteins, the antimicrobial peptide protegrin-1, the G protein-coupled receptor rhodopsin, and the K(+) channel KcsA are discussed. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany.
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