1
|
Sanders G, Borbat PP, Georgieva ER. Conformations of influenza A M2 protein in DOPC/DOPS and E. coli native lipids and proteins. Biophys J 2024; 123:2584-2593. [PMID: 38932458 PMCID: PMC11365223 DOI: 10.1016/j.bpj.2024.06.025] [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: 01/08/2024] [Revised: 04/21/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
We compared the conformations of the transmembrane domain (TMD) of influenza A M2 (IM2) protein reconstituted in 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPC/DOPS) bilayers to those in isolated Escherichia coli (E. coli) membranes, having preserved its native proteins and lipids. IM2 is a single-pass transmembrane protein known to assemble into a homo-tetrameric proton channel. To represent this channel, we made a construct containing the IM2's TMD region flanked by the juxtamembrane residues. The single cysteine substitution, L43C, of leucine located in the bilayer polar region was paramagnetically tagged with a methanethiosulfonate nitroxide label for the electron spin resonance (ESR) study. For this particular residue, we probed the conformations of the spin-labeled IM2 reconstituted in DOPC/DOPS and isolated E. coli membranes using continuous-wave ESR and double electron-electron resonance (DEER) spectroscopy. The total protein-to-lipid molar ratio spanned the range from 1:230 to 1:10,400. The continuous-wave ESR spectra corresponded to very slow spin-label motion in both environments. In all cases, the DEER data were reconstructed into distance distributions with well-resolved peaks at 1.68 and 2.37 nm in distance and amplitude ratios of 1.41 ± 0.2 and 2:1, respectively. This suggests four nitroxide spin labels located at the corners of a square, indicative of an axially symmetric tetramer. The distance modeling of DEER data with molecular modeling software applied to the NMR molecular structures (PDB: 2L0J) confirmed the symmetry and closed state of the C-terminal exit pore of the IM2 TMD tetramer in agreement with the model. Thus, we can conclude that, under conditions of pH 7.4 used in this study, IM2 TMD has similar conformations in model lipid bilayers and membranes made of native E. coli lipids and proteins of comparable thickness and fluidity, notwithstanding the complexity of the E. coli membranes caused by their lipid diversity and the abundance of integral and peripheral membrane proteins.
Collapse
Affiliation(s)
- Griffin Sanders
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, ACERT, Cornell University, Ithaca, New York
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas.
| |
Collapse
|
2
|
Qi Z, Ferguson K, Sechrest Y, Munsat T, Park CS, Glaser MA, Maclennan JE, Clark NA, Kuriabova T, Powers TR. Active microrheology of smectic membranes. Phys Rev E 2017; 95:022702. [PMID: 28297876 DOI: 10.1103/physreve.95.022702] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Indexed: 11/07/2022]
Abstract
Thin fluid membranes embedded in a bulk fluid of different viscosity are of fundamental interest as experimental realizations of quasi-two-dimensional fluids and as models of biological membranes. We have probed the hydrodynamics of thin fluid membranes by active microrheology using small tracer particles to observe the highly anisotropic flow fields generated around a rigid oscillating post inserted into a freely suspended smectic liquid crystal film that is surrounded by air. In general, at distances more than a few Saffman lengths from the meniscus around the post, the measured velocities are larger than the flow computed by modeling a moving disklike inclusion of finite extent by superposing Levine-MacKintosh response functions for pointlike inclusions in a viscous membrane. The observed discrepancy is attributed to additional coupling of the film with the air below the film that is displaced directly by the shaft of the moving post.
Collapse
Affiliation(s)
- Zhiyuan Qi
- Department of Physics, University of Colorado, Boulder, Colorado 80309, USA.,Soft Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Kyle Ferguson
- Department of Physics, University of Colorado, Boulder, Colorado 80309, USA.,Soft Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Yancey Sechrest
- Department of Physics, University of Colorado, Boulder, Colorado 80309, USA
| | - Tobin Munsat
- Department of Physics, University of Colorado, Boulder, Colorado 80309, USA
| | - Cheol Soo Park
- Department of Physics, University of Colorado, Boulder, Colorado 80309, USA.,Soft Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Matthew A Glaser
- Department of Physics, University of Colorado, Boulder, Colorado 80309, USA.,Soft Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Joseph E Maclennan
- Department of Physics, University of Colorado, Boulder, Colorado 80309, USA.,Soft Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Noel A Clark
- Department of Physics, University of Colorado, Boulder, Colorado 80309, USA.,Soft Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Tatiana Kuriabova
- Department of Physics, California Polytechnic State University, San Luis Obispo, California 93407, USA
| | - Thomas R Powers
- School of Engineering and Department of Physics, Brown University, Providence, Rhode Island 02912, USA
| |
Collapse
|
3
|
Zhang Z, Chen Y, Tang X, Li J, Wang L, Yang J. Solid-state NMR shows that dynamically different domains of membrane proteins have different hydration dependence. J Phys Chem B 2014; 118:9553-64. [PMID: 25026099 DOI: 10.1021/jp503032h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydration has a profound influence on the structure, dynamics, and functions of membrane and membrane-embedded proteins. So far the hydration response of molecular dynamics of membrane proteins in lipid bilayers is poorly understood. Here, we reveal different hydration dependence of the dynamics in dynamically different domains of membrane proteins by multidimensional magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy using 121-residue integral diacylglycerol kinase (DAGK) in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)/1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DMPG) lipid bilayers as a model system. The highly mobile and immobile domains of DAGK and their water accessibilities are identified site-specifically by scalar- and dipolar-coupling based MAS ssNMR experiments, respectively. Our experiments reveal different hydration dependence of the dynamics in highly mobile and immobile domains of membrane proteins. We demonstrate that the fast, large-amplitude motions in highly mobile domains are not triggered until 20% hydration, enhanced at 20-50% hydration and unchanged at above 50% hydration. In contrast, motions on submicrosecond time scale of immobile residues are observed to be independent of the hydration levels in gel phase of lipids, and at the temperature near gel-liquid crystalline phase transition, amplitude of whole-molecule rotations around the bilayer normal is dominated by the fluidity of lipid bilayers, which is strongly hydration dependent. The hydration dependence of the dynamics of DAGK revealed by this study provides new insights into the correlations of hydration to dynamics and function of membrane proteins in lipid bilayers.
Collapse
Affiliation(s)
- Zhengfeng Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
| | | | | | | | | | | |
Collapse
|
4
|
G-protein-coupled receptor structure, ligand binding and activation as studied by solid-state NMR spectroscopy. Biochem J 2013; 450:443-57. [DOI: 10.1042/bj20121644] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
GPCRs (G-protein-coupled receptors) are versatile signalling molecules at the cell surface and make up the largest and most diverse family of membrane receptors in the human genome. They convert a large variety of extracellular stimuli into intracellular responses through the activation of heterotrimeric G-proteins, which make them key regulatory elements in a broad range of normal and pathological processes, and are therefore one of the most important targets for pharmaceutical drug discovery. Knowledge of a GPCR structure enables us to gain a mechanistic insight into its function and dynamics, and further aid rational drug design. Despite intensive research carried out over the last three decades, resolving the structural basis of GPCR function is still a major activity. The crystal structures obtained in the last 5 years provide the first opportunity to understand how protein structure dictates the unique functional properties of these complex signalling molecules. However, owing to the intrinsic hydrophobicity, flexibility and instability of membrane proteins, it is still a challenge to crystallize GPCRs, and, when this is possible, it is no longer in its native membrane environment and no longer without modification. Furthermore, the conformational change of the transmembrane α-helices associated with the structure activation increases the difficulty of capturing the activation state of a GPCR to a higher resolution by X-ray crystallography. On the other hand, solid-state NMR may offer a unique opportunity to study membrane protein structure, ligand binding and activation at atomic resolution in the native membrane environment, as well as described functionally significant dynamics. In the present review, we discuss some recent achievements of solid-state NMR for understanding GPCRs, the largest mammalian proteome at ~1% of the total expressed proteins. Structural information, details of determination, details of ligand conformations and the consequences of ligand binding to initiate activation can all be explored with solid-state NMR.
Collapse
|
5
|
Piggot TJ, Holdbrook DA, Khalid S. Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:284-93. [DOI: 10.1016/j.bbamem.2012.08.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 08/02/2012] [Accepted: 08/23/2012] [Indexed: 11/25/2022]
|
6
|
Iordanov I, Renault M, Réat V, Bosshart PD, Engel A, Saurel O, Milon A. Dynamics of Klebsiella pneumoniae OmpA transmembrane domain: The four extracellular loops display restricted motion behavior in micelles and in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2344-53. [DOI: 10.1016/j.bbamem.2012.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 05/02/2012] [Accepted: 05/03/2012] [Indexed: 10/28/2022]
|
7
|
Nevzorov AA. Orientational and motional narrowing of solid-state NMR lineshapes of uniaxially aligned membrane proteins. J Phys Chem B 2011; 115:15406-14. [PMID: 22073926 DOI: 10.1021/jp2092847] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A unified theory for the NMR line shapes of aligned membrane proteins arising from uniaxial disorder (mosaic spread) and global rotational diffusion about the director axis is presented. A superoperator formalism allows one to take into account the effects of continuous radiofrequency irradiation and frequency offsets in the presence of dynamics. A general method based on the Stochastic Liouville Equation makes it possible to bridge the static and dynamic limits in a single model. Simulations of solid-state NMR spectra are performed for a uniform α helix by considering orientational disorder and diffusion of the helix as a whole relative to the alignment axis. The motional narrowing of the resonance lines is highly inhomogeneous and can be used as an additional angular restraint in structure calculations. Experimental solid-state NMR spectra of Pf1 coat protein support the conclusions of the theory for two limiting cases. The static disorder dominates the (15)N NMR spectra of Pf1 aligned on a phage, while fast uniaxial diffusion provides a line narrowing mechanism for the Pf1 protein reconstituted in magnetically aligned bicelles.
Collapse
Affiliation(s)
- Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695-8240, USA
| |
Collapse
|
8
|
Jeschke G, Anger BC, Bode BE, Matysik J. Theory of Solid-State Photo-CIDNP in the Earth's Magnetic Field. J Phys Chem A 2011; 115:9919-28. [DOI: 10.1021/jp204921q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Ben C. Anger
- Leiden Institute of Chemistry, Leiden, The Netherlands
| | - Bela E. Bode
- Leiden Institute of Chemistry, Leiden, The Netherlands
| | - Jörg Matysik
- Leiden Institute of Chemistry, Leiden, The Netherlands
| |
Collapse
|
9
|
Hall D, Hoshino M. Effects of macromolecular crowding on intracellular diffusion from a single particle perspective. Biophys Rev 2010; 2:39-53. [PMID: 21088688 PMCID: PMC2957576 DOI: 10.1007/s12551-010-0029-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 01/08/2010] [Indexed: 01/07/2023] Open
Abstract
Compared to biochemical reactions taking place in relatively well-defined aqueous solutions in vitro, the corresponding reactions happening in vivo occur in extremely complex environments containing only 60-70% water by volume, with the remainder consisting of an undefined array of bio-molecules. In a biological setting, such extremely complex and volume-occupied solution environments are termed 'crowded'. Through a range of intermolecular forces and pseudo-forces, this complex background environment may cause biochemical reactions to behave differently to their in vitro counterparts. In this review, we seek to highlight how the complex background environment of the cell can affect the diffusion of substances within it. Engaging the subject from the perspective of a single particle's motion, we place the focus of our review on two areas: (1) experimental procedures for conducting single particle tracking experiments within cells along with methods for extracting information from these experiments; (2) theoretical factors affecting the translational diffusion of single molecules within crowded two-dimensional membrane and three-dimensional solution environments. We conclude by discussing a number of recent publications relating to intracellular diffusion in light of the reviewed material.
Collapse
Affiliation(s)
- Damien Hall
- Institute of Basic Medical Science, University of Tsukuba, Lab 225-B, Building D, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki-ken 305-8577 Japan
| | - Masaru Hoshino
- Department of Pharmaceutical Science, Kyoto University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku Kyoto, 606-8501 Japan
| |
Collapse
|
10
|
Henle ML, Levine AJ. Hydrodynamics in curved membranes: the effect of geometry on particulate mobility. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:011905. [PMID: 20365397 DOI: 10.1103/physreve.81.011905] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Indexed: 05/29/2023]
Abstract
We determine the particulate transport properties of fluid membranes with nontrivial geometries that are surrounded by viscous Newtonian solvents. Previously, this problem in membrane hydrodynamics was discussed for the case of flat membranes by Saffman and Delbrück [P. G. Saffman and M. Delbrück, Proc. Natl. Acad. Sci. U.S.A. 72, 3111 (1975)]. We review and develop the formalism necessary to consider the hydrodynamics of membranes with arbitrary curvature and show that the effect of local geometry is twofold. First, local Gaussian curvature introduces in-plane viscous stresses even for situations in which the velocity field is coordinate-independent. Secondly, even in the absence of Gaussian curvature, the geometry of the membrane modifies the momentum transport between the bulk fluids and the membrane. We illustrate these effects by examining in detail the mobilities of particles bound to spherical and cylindrical membranes. These two examples provide experimentally testable predictions for particulate mobilities and membrane velocity fields on giant unilamellar vesicles and membrane tethers. Finally, we use the examples of spherical and cylindrical membranes to demonstrate how the global geometry and topology of the membrane influences the membrane velocities and the particle mobilities.
Collapse
Affiliation(s)
- Mark L Henle
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | | |
Collapse
|
11
|
Ramadurai S, Holt A, Krasnikov V, van den Bogaart G, Killian JA, Poolman B. Lateral diffusion of membrane proteins. J Am Chem Soc 2009; 131:12650-6. [PMID: 19673517 DOI: 10.1021/ja902853g] [Citation(s) in RCA: 263] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We measured the lateral mobility of integral membrane proteins reconstituted in giant unilamellar vesicles (GUVs), using fluorescence correlation spectroscopy. Receptor, channel, and transporter proteins with 1-36 transmembrane segments (lateral radii ranging from 0.5 to 4 nm) and a alpha-helical peptide (radius of 0.5 nm) were fluorescently labeled and incorporated into GUVs. At low protein-to-lipid ratios (i.e., 10-100 proteins per microm(2) of membrane surface), the diffusion coefficient D displayed a weak dependence on the hydrodynamic radius (R) of the proteins [D scaled with ln(1/R)], consistent with the Saffman-Delbruck model. At higher protein-to lipid ratios (up to 3000 microm(-2)), the lateral diffusion coefficient of the molecules decreased linearly with increasing the protein concentration in the membrane. The implications of our findings for protein mobility in biological membranes (protein crowding of approximately 25,000 microm(-2)) and use of diffusion measurements for protein geometry (size, oligomerization) determinations are discussed.
Collapse
Affiliation(s)
- Sivaramakrishnan Ramadurai
- Department of Biochemistry, Groningen Biomolecular science and Biotechnology Institute & Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
12
|
Lee MH, Lapointe CP, Reich DH, Stebe KJ, Leheny RL. Interfacial hydrodynamic drag on nanowires embedded in thin oil films and protein layers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:7976-7982. [PMID: 19594180 DOI: 10.1021/la900408y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We investigate the motion of ferromagnetic nanowires confined to nanometer-scale oil films at an air/aqueous interface in response to the application of external magnetic fields and field gradients. By varying the oil viscosity, film thickness, and wire length, we cover two regimes of response suggested by theory: one where the surface viscosity is expected to dominate the wire's motion and one where the subphase viscosity is expected to dominate [Levine, A. J.; Liverpool, T. B.; MacKintosh, F. C. Phys. Rev. E 2004, 69, 021503]. For wire motion parallel to the long axis of the wire, the observed drag agrees reasonably with theoretical predictions. However, the drag on wires moving perpendicular to their long axis or rotating about a short axis is unexpectedly insensitive to the film properties over the full range of measurements. This behavior is in contrast to the rotational and translational drag on nanowires in molecularly thin protein layers, which follow theoretical expectations. The observations in the oil films, which are explained in terms of the manner in which the wire immerses dynamically in the film and subphase, demonstrate how the effective drag viscosity of an aspherical particle confined to a fluid interface can depend on its direction of motion.
Collapse
Affiliation(s)
- Myung Han Lee
- Department of Physics and Astronomy, John Hopkins University, Baltimore, MD 21218, USA
| | | | | | | | | |
Collapse
|
13
|
Shu S, Wang Y, Chen W, Wang Z. Influence of dehydration on the desert moss in molecular mobility and membrane fluidity monitored by spin label. BIOCHEM SYST ECOL 2008. [DOI: 10.1016/j.bse.2008.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
14
|
Dynamics and Cleavability at the alpha-cleavage site of APP(684-726) in different lipid environments. Biophys J 2008; 95:1460-73. [PMID: 18390599 DOI: 10.1529/biophysj.108.129726] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The occurrence of late-onset Alzheimer's disease has been related to the lipid homeostasis. We tested whether the membrane lipid environment affects the dynamics and cleavability of a model peptide corresponding to the amino acid sequence 684-726 of the amyloid precursor protein APP reconstituted in liposomes. Solid-state NMR with (2)H-Ala(713), which is located within the putative transmembrane domain, suggested that the peptide observes less rotational motion in egg phosphatidylcholine (PhC) membranes than in dimyristoyl-phosphatidylcholine (DMPC) bilayers above the main phase transition temperature T(c). The residue (15)N-Ala(692), which is in the vicinity of the alpha-cleavage site, i.e., Lys(687), showed less motion after reconstitution in distearoyl-phosphatidylcholine liposomes <T(c) than in PhC, DMPC, or sphingomyelin vesicles. In all tested liposomal systems the alpha-cleavage site was accessible for hydrolysis by trypsin. However, the catalytic rate constant was higher in the PhC and DMPC than in the sphingomyelin and distearoyl-phosphatidylcholine systems. In conclusion, the dynamics of APP(684-726) on the transmembrane level as well as the motion of the alpha-cleavage site and its hydrolysis by a model enzyme are dependent on the bilayer characteristics. This could be relevant for the processing of APP in vivo.
Collapse
|
15
|
Gambin Y, Lopez-Esparza R, Reffay M, Sierecki E, Gov NS, Genest M, Hodges RS, Urbach W. Lateral mobility of proteins in liquid membranes revisited. Proc Natl Acad Sci U S A 2006; 103:2098-102. [PMID: 16461891 PMCID: PMC1413751 DOI: 10.1073/pnas.0511026103] [Citation(s) in RCA: 270] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The biological function of transmembrane proteins is closely related to their insertion, which has most often been studied through their lateral mobility. For >30 years, it has been thought that hardly any information on the size of the diffusing object can be extracted from such experiments. Indeed, the hydrodynamic model developed by Saffman and Delbrück predicts a weak, logarithmic dependence of the diffusion coefficient D with the radius R of the protein. Despite widespread use, its validity has never been thoroughly investigated. To check this model, we measured the diffusion coefficients of various peptides and transmembrane proteins, incorporated into giant unilamellar vesicles of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC) or in model bilayers of tunable thickness. We show in this work that, for several integral proteins spanning a large range of sizes, the diffusion coefficient is strongly linked to the protein dimensions. A heuristic model results in a Stokes-like expression for D, (D proportional, variant 1/R), which fits literature data as well as ours. Diffusion measurement is then a fast and fruitful method; it allows determining the oligomerization degree of proteins or studying lipid-protein and protein-protein interactions within bilayers.
Collapse
Affiliation(s)
- Y Gambin
- Laboratoire de Physique Statistique de l'Ecole Normale Supérieure, Unité Mixte de Recherche 8550, Centre National de la Recherche Scientifique-Université Paris 6, 24 Rue Lhomond, 75005 Paris, France.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Geertsma ER, Duurkens RH, Poolman B. Functional interactions between the subunits of the lactose transporter from Streptococcus thermophilus. J Mol Biol 2005; 350:102-11. [PMID: 15919090 DOI: 10.1016/j.jmb.2005.04.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 04/21/2005] [Accepted: 04/22/2005] [Indexed: 11/16/2022]
Abstract
Although the quaternary state has been assessed in detail for only a few members of the major facilitator superfamily (MFS), it is clear that multiple oligomeric states are represented within the MFS. One of its members, the lactose transporter LacS from Streptococcus thermophilus assumes a dimeric structure in the membrane and in vitro analysis showed functional interactions between both subunits when proton motive force ((Delta)p)-driven transport was assayed. To study the interactions in further detail, a covalent dimer was constructed consisting of in tandem fused LacS subunits. These covalent dimers, composed of active and completely inactive subunits, were expressed in Escherichia coli, and initial rates of (Delta)p-driven lactose uptake and lactose counterflow were determined. We now show that also in vivo, both subunits interact functionally; that is, partial complementation of the inactive subunit was observed for both transport modes. Thus, both subunits interact functionally in (Delta)p-driven uptake and in counterflow transport. In addition, analysis of in tandem fused LacS subunits containing one regulatory LacS-IIA domain showed that regulation is primarily an intramolecular event.
Collapse
Affiliation(s)
- Eric R Geertsma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | | | | |
Collapse
|
17
|
Levine AJ, Liverpool TB, MacKintosh FC. Dynamics of rigid and flexible extended bodies in viscous films and membranes. PHYSICAL REVIEW LETTERS 2004; 93:038102. [PMID: 15323875 DOI: 10.1103/physrevlett.93.038102] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2003] [Indexed: 05/24/2023]
Abstract
We study the dynamics of extended rodlike bodies in (or associated with) membranes and films. We demonstrate a striking difference between the mobilities in films and bulk fluids, even when the dissipation is dominated by the fluid stress: For large inclusions, we find that rotation and motion perpendicular to the rod axis exhibit purely local drag, in which the drag coefficient is algebraic in the rod dimensions. We also study the dynamics of the internal modes of a semiflexible inclusion and find two dynamical regimes in the relaxation spectrum.
Collapse
Affiliation(s)
- Alex J Levine
- The Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
| | | | | |
Collapse
|
18
|
Levine AJ, Liverpool TB, MacKintosh FC. Mobility of extended bodies in viscous films and membranes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2004; 69:021503. [PMID: 14995445 DOI: 10.1103/physreve.69.021503] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2003] [Indexed: 05/24/2023]
Abstract
We develop general methods to calculate the mobilities of extended bodies in (or associated with) membranes and films. We demonstrate a striking difference between in-plane motion of rodlike inclusions and the corresponding case of bulk (three-dimensional) fluids: for rotations and motion perpendicular to the rod axis, we find purely local drag, in which the drag coefficient is purely algebraic in the rod dimensions. These results as well as the calculational methods are applicable to such problems as the diffusion of objects in or associated with Langmuir films and lipid membranes. These methods can also be simply extended to treat viscoelastic systems.
Collapse
Affiliation(s)
- Alex J Levine
- The Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA.
| | | | | |
Collapse
|
19
|
Geertsma ER, Duurkens RH, Poolman B. Identification of the dimer interface of the lactose transport protein from Streptococcus thermophilus. J Mol Biol 2003; 332:1165-74. [PMID: 14499618 DOI: 10.1016/j.jmb.2003.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The lactose transporter from Streptococcus thermophilus catalyses the symport of galactosides and protons. The carrier domain of the protein harbours the contact sites for dimerization, and the individual subunits in the dimer interact functionally during the transport reaction. As a first step towards the elucidation of the mechanism behind the cooperation between the subunits, regions involved in the dimer interface were determined by oxidative and chemical cross-linking of 12 cysteine substitution mutants. Four positions in the protein were found to be susceptible to intermolecular cross-linking. To ensure that the observed cross-links were not the result of randomly colliding particles, the cross-linking was studied in samples in which either the concentration of LacS in the membrane was varied or the oligomeric state was manipulated. These experiments showed that the cross-links were formed specifically within the dimer. The four regions of the protein located at the dimer interface are close to the extracellular ends of transmembrane segments V and VIII and the intracellular ends of transmembrane segments VI and VII.
Collapse
Affiliation(s)
- Eric R Geertsma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | | | | |
Collapse
|
20
|
Abstract
Membranes are important sites for the regulation of metabolic functions because they contain transport molecules, which often catalyze the first step in a pathway, and signal-transduction components, which allow the cell to communicate with the environment. Given the catalytic importance of transport proteins and their role in membrane stability, it is possible that oligomerization is used to regulate their function. This review evaluates knowledge of the functions that are associated with the oligomeric organization of secondary transport proteins, which are a major class of solute-translocation systems in all living species.
Collapse
Affiliation(s)
- Liesbeth M Veenhoff
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4 9747 AG Groningen, The Netherlands
| | | | | |
Collapse
|
21
|
Heuberger EHML, Veenhoff LM, Duurkens RH, Friesen RHE, Poolman B. Oligomeric state of membrane transport proteins analyzed with blue native electrophoresis and analytical ultracentrifugation. J Mol Biol 2002; 317:591-600. [PMID: 11955011 DOI: 10.1006/jmbi.2002.5416] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Blue native electrophoresis is used widely for the analysis of non-dissociated protein complexes with respect to composition, oligomeric state and molecular mass. However, the effects of detergent or dye binding on the mass and stability of the integral membrane proteins have not been studied. By comparison with analytical ultracentrifugation, we have evaluated whether the oligomeric state of membrane transport proteins is reflected reliably with blue native electrophoresis. For the analysis we have used two well-characterized transporters, that is, the major facilitator superfamily protein LacS and the phosphotransferase system EII(Mtl). For another member of the major facilitator superfamily, the xyloside transporter XylP from Lactobacillus pentosus, the complete analysis of the quaternary structure determined by analytical ultracentrifugation and freeze-fracture electron microscopy is presented. Our experiments show that during blue native electrophoresis the detergent bound to the proteins is replaced by the amphipathic Coomassie brilliant blue (CBB) dye. The mass of the bound CBB dye was quantified. Provided this additional mass of bound CBB dye is accounted for and care is taken in the choice and concentration of the detergent used, the mass of LacS, XylP and EII(Mtl) and four other membrane (transport) proteins could be deduced within 10 % error. Our data underscore the fact that the oligomeric state of many membrane transport proteins is dimeric.
Collapse
Affiliation(s)
- Esther H M L Heuberger
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands
| | | | | | | | | |
Collapse
|
22
|
Veenhoff LM, Heuberger EH, Poolman B. The lactose transport protein is a cooperative dimer with two sugar translocation pathways. EMBO J 2001; 20:3056-62. [PMID: 11406582 PMCID: PMC150208 DOI: 10.1093/emboj/20.12.3056] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Major Facilitator Superfamily lactose transport protein (LacS) undergoes reversible self-association in the detergent-solubilized state, and is present in the membrane as a dimer. We determined the functional unit for proton motive force (Deltap)-driven lactose uptake and lactose/methyl-beta-D-galactopyranoside equilibrium exchange in a proteoliposomal system in which a single cysteine mutant, LacS-C67, defective in Deltap-driven uptake, was co-reconstituted with fully functional cysteine-less protein, LacS-cl. From the quadratic relationship between the uptake activity and the ratio of LacS-C67/LacS-cl, we conclude that the dimeric state of LacS is required for Deltap-driven uptake. N-ethylmaleimide (NEM) treatment of proteoliposomes abolished the LacS-C67 exchange activity but left the LacS-cl unaffected. After NEM treatment, the exchange activity decreased linearly with increasing ratios of LacS-C67/LacS-cl, suggesting that the monomeric state of LacS is sufficient for this mode of transport. We propose that the two subunits of LacS are functionally coupled in the step associated with conformational reorientation of the empty binding site, a step unique for Deltap-driven uptake.
Collapse
Affiliation(s)
| | | | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
Corresponding author e-mail:
| |
Collapse
|
23
|
McDonald TP, Henderson PJ. Cysteine residues in the D-galactose-H+ symport protein of Escherichia coli: effects of mutagenesis on transport, reaction with N-ethylmaleimide and antibiotic binding. Biochem J 2001; 353:709-17. [PMID: 11171069 PMCID: PMC1221618 DOI: 10.1042/0264-6021:3530709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The galactose-H(+) membrane-transport protein, GalP, of Escherichia coli is similar in substrate specificity and susceptibility to cytochalasin B and forskolin, to the human GLUT1 sugar-transport protein; furthermore, they are about 30% identical in amino acid sequence. Transport activities of both GalP and GLUT1 are inhibited by the thiol-group-specific reagent, N-ethylmaleimide. GalP contains only three cysteine residues at positions 19, 374 and 389, each of which we have mutated, singly and in combination, to serine. Each single change of Cys-->Ser has only a minor effect on transport activity, whereas alteration of all three simultaneously profoundly diminishes V(max) for transport. The high level of expression of the GalP protein facilitates measurements of the reactivity of each mutant with N-ethylmaleimide or eosin 5-maleimide, which conclusively demonstrate that Cys(374) is the site of covalent modification by the reagents. By comparing the reactivity of Cys(374) in right-side-out and inside-out vesicles it appears that Cys(374) is located on the cytoplasmic face of the GalP protein. Although impaired in transport activity, the 'Cys-free' mutant, with all three cysteine residues mutated into serine, binds cytochalasin B and forskolin with wild-type affinities. All these results are interpreted in terms of a 12-helix model of the folding of the protein, in which the relative orientations of helix 10, containing the reactive Cys(374) residue, and helix 11, containing the unreactive Cys(389) residue, can now be defined.
Collapse
Affiliation(s)
- T P McDonald
- School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | | |
Collapse
|
24
|
Friesen RH, Knol J, Poolman B. Quaternary structure of the lactose transport protein of Streptococcus thermophilus in the detergent-solubilized and membrane-reconstituted state. J Biol Chem 2000; 275:33527-35. [PMID: 10921919 DOI: 10.1074/jbc.m004066200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The quaternary structure of LacS, the lactose transporter of Streptococcus thermophilus, has been determined for the detergent-solubilized and the membrane-reconstituted state of the protein. The quaternary structure of the n-dodecyl-beta-d-maltoside-solubilized state was studied using a combination of sedimentation velocity and equilibrium centrifugation analysis. From these measurements it followed that the detergent-solubilized LacS undergoes reversible self-association with a monomer to dimer mode of association. The association constants were 5.4 +/- 3.6 and 4.4 +/- 1.0 ml mg(-1) as determined from the velocity and equilibrium sedimentation measurements, respectively. The experiments did not indicate significant changes in the shape of the protein-detergent complex or the amount of detergent bound in going from the monomeric to dimeric state of LacS. Importantly, a single Cys mutant of LacS is labeled by 2-(4'-maleimidylanilino)naphthalene-6-sulfonic acid in a substrate-dependent manner, indicating that the detergent-solubilized protein exhibits ligand binding activity. The quaternary structure of membrane-reconstituted LacS was determined by freeze-fracture electron microscopy analysis. Recent developments in the analysis of freeze-fracture images (Eskandari, S. P., Wright, E. M., Freman, M., Starace, D. M., and Zampighi, G. A. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 11235-11240) allowed us to directly correlate the cross-sectional area of the transmembrane segment to a dimeric state of the functionally membrane-reconstituted LacS protein. The cross-sectional area of the LacS protein was calibrated using the membrane-reconstituted transmembrane domain of the mannitol transporter enzyme II, an intramembrane particle for which the cross-sectional area was obtained from maps of two-dimensional crystals. The consequences of the determined quaternary structure for the transport function and regulation of LacS are discussed.
Collapse
Affiliation(s)
- R H Friesen
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | | |
Collapse
|