201
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Cappelli M, d'Inzeo G, Apollonio F, Liberti M. A possible mechanism explaining variation in membrane permeability under exposure to weak magnetic fields. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2007; 2004:837-40. [PMID: 17271807 DOI: 10.1109/iembs.2004.1403288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The problem of the interaction between electromagnetic fields and a biological system can be properly faced at cell membrane level. Specifically, in this work, the target of the interaction has been located in the charged lipid group emerging from the membrane surface. A possible mechanism based on the Larmor precession theory is here proposed. The results evidence the possibility of specific exposure conditions that enhance the membrane permeability.
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Affiliation(s)
- M Cappelli
- Dept. of Electron. Eng., La Sapienza Univ., Italy
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202
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Anderson NA, Richter LJ, Stephenson JC, Briggman KA. Characterization and control of lipid layer fluidity in hybrid bilayer membranes. J Am Chem Soc 2007; 129:2094-100. [PMID: 17263532 DOI: 10.1021/ja066588c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The main gel-to-liquid-crystal (LC) phase transition temperature, T(m), of the distal lipid layer in hybrid bilayer membranes (HBMs) under water was investigated using vibrational sum frequency spectroscopy (VSFS). VSFS has unique sensitivity to order/disorder transitions in the lipid acyl chains and can determine T(m) for the lipid monolayers in HBMs. We recently reported the observation that T(m) is raised and the transition width is broadened for the overlying phospholipid monolayer in HBM systems formed on densely packed crystalline self-assembled monolayers (SAMs) as compared to that of vesicles in solution. In this report, we establish that T(m) for the lipid layer of HBMs can be controlled by proper choice of the SAM underlayer. The SAM underlayer of the HBM was systematically altered by using an alkane thiol, a saturated thiolipid, a mixed SAM of a saturated lipid-pyridine disulfide, and finally a mixed SAM of an unsaturated lipid-pyridine disulfide. T(m) was measured for two different chain length saturated phosphatidylcholine lipid overlayers on these SAMs. The values obtained show that Tm of the lipid layer of HBMs is sensitive to the composition and/or packing density of molecules in the underlying SAM.
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Affiliation(s)
- Neil A Anderson
- Department of Physics, National Institute of Standards and Technology, 100 Bureau Drive MS8443, Gaithersburg, Maryland 20899-8443, USA
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203
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Abstract
Reversible unfolding of helical transmembrane proteins could provide valuable information about the free energy of interaction between transmembrane helices. Thermal unfolding experiments suggest that this process for integral membrane proteins is irreversible. Chemical unfolding has been accomplished with organic acids, but the unfolding or refolding pathways involve irreversible steps. Sodium dodecyl sulfate (SDS) has been used as a perturbant to study reversible unfolding and refolding kinetics. However, the interpretation of these experiments is not straightforward. It is shown that the results could be explained by SDS binding without substantial unfolding. Furthermore, the SDS-perturbed state is unlikely to include all of the entropy terms involved in an unfolding process. Alternative directions for future research are suggested: fluorinated alcohols in homogeneous solvent systems, inverse micelles, and fragment association studies.
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Affiliation(s)
- Robert Renthal
- Department of Biology, University of Texas, San Antonio, Texas 78249, USA.
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204
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Andersen OS, Bruno MJ, Sun H, Koeppe RE. Single-molecule methods for monitoring changes in bilayer elastic properties. Methods Mol Biol 2007; 400:543-570. [PMID: 17951759 DOI: 10.1007/978-1-59745-519-0_37] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Membrane-spanning proteins perturb the organization and dynamics of the adjacent bilayer lipids. For example, when the hydrophobic length (l) of a bilayer-spanning protein differs from the average thickness (d0) of the host bilayer, the bilayer thickness will vary locally in the vicinity of the protein in order to "match" the length of the protein's hydrophobic exterior to the thickness of the bilayer hydrophobic core. Such bilayer deformations incur an energetic cost, the bilayer deformation energy (DeltaG0def), which will vary as a function of the protein shape, the protein-bilayer hydrophobic mismatch (d0 - l), the lipid bilayer elastic properties, and the lipid intrinsic curvature (c0). Thus, if the membrane protein conformational changes underlying protein function involve the protein/bilayer interface, the ensuing changes in DeltaG0def (DeltaDeltaG0def) will contribute to the overall free-energy change of the conformational changes (DeltaG0tot)-meaning that the host lipid bilayer will modulate protein function. For a given protein, (DeltaDeltaG0def) varies as a function of the bilayer geometric properties (thickness and intrinsic curvature) and the elastic (bending and compression) moduli, which vary as a function of changes in lipid composition or with the adsorption of amphiphiles at the bilayer/solution interface. To understand how changes in bilayer properties modulate the function of bilayer-spanning proteins, single-molecule methods have been developed to probe changes in bilayer elastic properties using gramicidins as molecular force transducers. Different approaches to measuring the deformation energy are described: (1) measurements of changes in channel lifetimes and appearance rates as the lipid bilayer thickness or channel length are varied, (2) measurements of the equilibrium distribution among channels of different lengths, formed by homo- and heterodimers between gramicidin subunits of different lengths, and (3) measurements of the ratio of the appearance rates of heterodimer channels relative to parent homodimer channels formed by gramicidin subunits of different lengths.
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Affiliation(s)
- Olaf S Andersen
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA
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205
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Abstract
Neurons transmit information through electrical signals generated by voltage-gated ion channels. These channels consist of a large superfamily of proteins that form channels selective for potassium, sodium, or calcium ions. In this review we focus on the molecular mechanisms by which these channels convert changes in membrane voltage into the opening and closing of "gates" that turn ion conductance on and off. An explosion of new studies in the last year, including the first X-ray crystal structure of a mammalian voltage-gated potassium channel, has led to radically different interpretations of the structure and molecular motion of the voltage sensor. The interpretations are as distinct as the techniques employed for the studies: crystallography, fluorescence, accessibility analysis, and electrophysiology. We discuss the likely causes of the discrepant results in an attempt to identify the missing information that will help resolve the controversy and reveal the mechanism by which a voltage sensor controls the channel's gates.
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Affiliation(s)
- Francesco Tombola
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.
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206
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207
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Booth PJ, Curnow P. Membrane proteins shape up: understanding in vitro folding. Curr Opin Struct Biol 2006; 16:480-8. [PMID: 16815700 DOI: 10.1016/j.sbi.2006.06.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 05/19/2006] [Accepted: 06/20/2006] [Indexed: 11/23/2022]
Abstract
Progress in structural biology has begun to reveal the precise architecture of integral membrane proteins. However, the manner in which these complex structures are achieved remains unclear. Recent developments are starting to shed light on the unfolding and folding of a small but growing number of membrane proteins. Mechanistic details derived from kinetic and thermodynamic experiments now enable comparison of the folding of different membrane proteins and their water-soluble cousins. This work also has important implications for other structural and functional studies of membrane proteins in vitro.
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Affiliation(s)
- Paula J Booth
- Department of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK.
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208
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Findlay HE, Booth PJ. The biological significance of lipid-protein interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2006; 18:S1281-S1291. [PMID: 21690841 DOI: 10.1088/0953-8984/18/28/s11] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Biological membranes are complex environments, where membrane proteins are surrounded by a bilayer composed of many different types of lipid. The physical properties of the bilayer influence protein structure, folding and function, while specific interactions with lipid molecules can also contribute towards the biological activity of some membrane proteins. Improving understanding of these interactions has resulted in the development of synthetic lipid systems that allow the bilayer properties to be rationally manipulated in vitro to control protein behaviour.
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209
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Oz M. Receptor-independent actions of cannabinoids on cell membranes: Focus on endocannabinoids. Pharmacol Ther 2006; 111:114-44. [PMID: 16584786 DOI: 10.1016/j.pharmthera.2005.09.009] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Accepted: 09/30/2005] [Indexed: 01/08/2023]
Abstract
Cannabinoids are a structurally diverse group of mostly lipophilic molecules that bind to cannabinoid receptors. In fact, endogenous cannabinoids (endocannabinoids) are a class of signaling lipids consisting of amides and esters of long-chain polyunsaturated fatty acids. They are synthesized from lipid precursors in plasma membranes via Ca(2+) or G-protein-dependent processes and exhibit cannabinoid-like actions by binding to cannabinoid receptors. However, endocannabinoids can produce effects that are not mediated by these receptors. In pharmacologically relevant concentrations, endocannabinoids modulate the functional properties of voltage-gated ion channels including Ca(2+) channels, Na(+) channels, various types of K(+) channels, and ligand-gated ion channels such as serotonin type 3, nicotinic acetylcholine, and glycine receptors. In addition, modulatory effects of endocannabinoids on other ion-transporting membrane proteins such as transient potential receptor-class channels, gap junctions and transporters for neurotransmitters have also been demonstrated. Furthermore, functional properties of G-protein-coupled receptors for different types of neurotransmitters and neuropeptides are altered by direct actions of endocannabinoids. Although the mechanisms of these effects are currently not clear, it is likely that these direct actions of endocannabinoids are due to their lipophilic structures. These findings indicate that additional molecular targets for endocannabinoids exist and that these targets may represent novel sites for cannabinoids to alter either the excitability of the neurons or the response of the neuronal systems. This review focuses on the results of recent studies indicating that beyond their receptor-mediated effects, endocannabinoids alter the functions of ion channels and other integral membrane proteins directly.
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Affiliation(s)
- Murat Oz
- National Institute on Drug Abuse, NIH/DHHS, Intramural Research Program, Cellular Neurobiology Branch, 5500 Nathan Shock Drive, Baltimore MD, 21224, USA.
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210
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Renart ML, Barrera FN, Molina ML, Encinar JA, Poveda JA, Fernández AM, Gómez J, González-Ros JM. Effects of conducting and blocking ions on the structure and stability of the potassium channel KcsA. J Biol Chem 2006; 281:29905-15. [PMID: 16815844 DOI: 10.1074/jbc.m602636200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
This article reports on the interaction of conducting (K(+)) and blocking (Na(+)) monovalent metal ions with detergent-solubilized and lipid-reconstituted forms of the K(+) channel KcsA. Monitoring of the protein intrinsic fluorescence reveals that the two ions bind competitively to KcsA with distinct affinities (dissociation constants for the KcsA.K(+) and KcsA.Na(+) complexes of approximately 8 and 190 mm, respectively) and induce different conformations of the ion-bound protein. The differences in binding affinity as well as the higher K(+) concentration bathing the intracellular mouth of the channel, through which the cations gain access to the protein binding sites, should favor that only KcsA.K(+) complexes are formed under physiological-like conditions. Nevertheless, despite such prediction, it was also found that concentrations of Na(+) well below its dissociation constant and even in the presence of higher K(+) concentrations, cause a remarkable decrease in the protein thermal stability and facilitate thermal dissociation into subunits of the tetrameric KcsA, as concluded from the temperature dependence of the protein infrared spectra and from gel electrophoresis, respectively. These latter observations cannot be explained based on the occupancy of the binding sites from above and suggest that there must be additional ion binding sites, whose occupancy could not be detected by fluorescence and in which the affinity for Na(+) must be higher or at least similar to that of K(+). Moreover, cation binding as reported by means of fluorescence does not suffice to explain the large differences in free energy of stabilization involved in the formation of the KcsA.Na(+) and KcsA.K(+) complexes, which for the most part should arise from synergistic effects of the ion-mediated intersubunit interactions.
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Affiliation(s)
- María L Renart
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
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211
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Ramu Y, Xu Y, Lu Z. Enzymatic activation of voltage-gated potassium channels. Nature 2006; 442:696-9. [PMID: 16799569 DOI: 10.1038/nature04880] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Accepted: 05/08/2006] [Indexed: 11/09/2022]
Abstract
Voltage-gated ion channels in excitable nerve, muscle, and endocrine cells generate electric signals in the form of action potentials. However, they are also present in non-excitable eukaryotic cells and prokaryotes, which raises the question of whether voltage-gated channels might be activated by means other than changing the voltage difference between the solutions separated by the plasma membrane. The search for so-called voltage-gated channel activators is motivated in part by the growing importance of such agents in clinical pharmacology. Here we report the apparent activation of voltage-gated K+ (Kv) channels by a sphingomyelinase.
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Affiliation(s)
- Yajamana Ramu
- Department of Physiology, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, Pennsylvania 19104, USA
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212
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Powl A, Carney J, Marius P, East J, Lee A. Lipid interactions with bacterial channels: fluorescence studies. Biochem Soc Trans 2006; 33:905-9. [PMID: 16246007 PMCID: PMC2034676 DOI: 10.1042/bst20050905] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Interactions between a membrane protein and the lipid molecules that surround it in the membrane are important in determining the structure and function of the protein. These interactions can be pictured at the molecular level using fluorescence spectroscopy, making use of the ability to introduce tryptophan residues into regions of interest in bacterial membrane proteins. Fluorescence quenching methods have been developed to study lipid binding separately on the two sides of the membrane. Lipid binding to the surface of the mechanosensitive channel MscL is heterogeneous, with a hot-spot for binding anionic lipid on the cytoplasmic side, associated with a cluster of three positively charged residues. The environmental sensitivity of tryptophan fluorescence emission has been used to identify the residues at the ends of the hydrophobic core of the second transmembrane alpha-helix in MscL. The efficiency of hydrophobic matching between MscL and the surrounding lipid bilayer is high. Fluorescence quenching methods can also be used to study binding of lipids to non-annular sites such as those between monomers in the homotetrameric potassium channel KcsA.
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Affiliation(s)
| | | | | | | | - A.G. Lee
- To whom correspondence should be addressed (email )
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213
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Sobko AA, Kotova EA, Antonenko YN, Zakharov SD, Cramer WA. Lipid Dependence of the Channel Properties of a Colicin E1-Lipid Toroidal Pore. J Biol Chem 2006; 281:14408-16. [PMID: 16556601 DOI: 10.1074/jbc.m513634200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Colicin E1 belongs to a group of bacteriocins whose cytotoxicity toward Escherichia coli is exerted through formation of ion channels that depolarize the cytoplasmic membrane. The lipid dependence of colicin single-channel conductance demonstrated intimate involvement of lipid in the structure of this channel. The colicin formed "small" conductance 60-picosiemens (pS) channels, with properties similar to those previously characterized, in 1,2-dieicosenoyl-sn-glycero-3-phosphocholine (C20) or thinner membranes, whereas it formed a novel "large" conductance 600-pS state in thicker 1,2-dierucoyl-sn-glycero-3-phosphocholine (C22) bilayers. Both channel states were anion-selective and voltage-gated and displayed a requirement for acidic pH. Lipids having negative spontaneous curvature inhibited the formation of both channels but increased the ratio of open 600 pS to 60 pS conductance states. Different diameters of small and large channels, 12 and 16 A, were determined from the dependence of single-channel conductance on the size of nonelectrolyte solute probes. Colicin-induced lipid "flip-flop" and the decrease in anion selectivity of the channel in the presence of negatively charged lipids implied a significant contribution of lipid to the structure of the channel, most readily described as toroidal organization of lipid and protein to form the channel pore.
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Affiliation(s)
- Alexander A Sobko
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
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214
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Páli T, Bashtovyy D, Marsh D. Stoichiometry of lipid interactions with transmembrane proteins--Deduced from the 3D structures. Protein Sci 2006; 15:1153-61. [PMID: 16641489 PMCID: PMC2242517 DOI: 10.1110/ps.052021406] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 02/02/2006] [Accepted: 02/16/2006] [Indexed: 10/24/2022]
Abstract
The stoichiometry of the first shell of lipids interacting with a transmembrane protein is defined operationally by the population of spin-labeled lipid chains whose motion is restricted directly by the protein. Interaction stoichiometries have been determined experimentally for a wide range of alpha-helical integral membrane proteins by using spin-label ESR spectroscopy. Here, we determine the spatially defined number of first-shell lipids at the hydrophobic perimeter of integral membrane proteins whose 3D structure has been determined by X-ray crystallography and lipid-protein interactions characterized by spin-labeling. Molecular modeling is used to build a single shell of lipids surrounding transmembrane structures derived from the PDB. Constrained energy optimization of the protein-lipid assemblies is performed by molecular mechanics. For relatively small proteins (up to 7-12 transmembrane helices), the geometrical first shell corresponds to that defined experimentally by perturbation of the lipid-chain dynamics. For larger, multi-subunit alpha-helical proteins, the lipids perturbed directly by the protein may either exceed or be less in number than those that can be accommodated at the intramembranous perimeter. In these latter cases, the motionally restricted spin-labeled lipids can be augmented by intercalation, or can correspond to a specific subpopulation at the protein interface, respectively. For monomeric beta-barrel proteins, the geometrical lipid stoichiometry corresponds to that determined from lipid mobility for a 22-stranded barrel, but fewer lipids are motionally restricted than can be accommodated around an eight-stranded barrel. Deviations from the geometrical first shell, in the beta-barrel case, are for the smaller protein with a highly curved barrel.
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Affiliation(s)
- Tibor Páli
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, 37070 Göttingen, Germany
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215
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Zimmer J, Doyle DA. Phospholipid requirement and pH optimum for the in vitro enzymatic activity of the E. coli P-type ATPase ZntA. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:645-52. [PMID: 16730648 DOI: 10.1016/j.bbamem.2006.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2005] [Revised: 04/12/2006] [Accepted: 04/13/2006] [Indexed: 11/16/2022]
Abstract
Detergent solubilization and purification of the E. coli heavy metal P-type ATPase ZntA yields an enzyme with reduced hydrolytic activity in vitro. Here, it is shown that the in vitro hydrolytic activity of detergent solubilized ZntA is increased in the presence of negatively charged phospholipids and at slightly acidic pH. The protein-lipid interaction of ZntA was characterized by enzyme-coupled ATPase assays and fluorescence spectroscopy. Among the most abundant naturally occurring phospholipids, only phosphatidyl-glycerol lipids (PG) enhance the in vitro enzymatic ATPase activity of ZntA. Re-lipidation of detergent purified ZntA with 1,2-dioleoylphosphatidyl-glycerol (DOPG) increases the ATPase activity four-fold compared to the purified state. All other E. coli phospholipids fail to activate the ATPase. Among the phosphatidyl-glycerol family, highest activity was observed for 1,2-dioleoyl-PG followed by 1,2-dimyristoyl-PG, 1,2-dipalmitoyl-PG and 1,2-distearoyl-PG. Increasing intrinsic Trp fluorescence quantum yield upon relipidation of ZntA was used to determine a pH maximum for lipid binding at pH 6.7. The pH dependence of the lipid binding was confirmed by pH-dependent ATPase assays showing maximum activity at pH 6.7. The biophysical characterization of detergent solubilized membrane proteins crucially relies on the conformational stability and functional integrity of the protein under investigation. The present study describes how the E. coli ZntA P-type ATPase can be stabilized and functionally activated in a detergent solubilized system.
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Affiliation(s)
- Jochen Zimmer
- University of Oxford, Department of Biochemistry, Laboratory of Molecular Biophysics, South Parks Road, OX1 3QU Oxford, UK
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216
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Minetti CASA, Remeta DP. Energetics of membrane protein folding and stability. Arch Biochem Biophys 2006; 453:32-53. [PMID: 16712771 DOI: 10.1016/j.abb.2006.03.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 03/23/2006] [Indexed: 11/24/2022]
Abstract
The critical role of membrane proteins in a myriad of biological and physiological functions has spawned numerous investigations over the past several decades with the long-term goal of identifying the molecular origins and energetic forces that stabilize these proteins within the membrane. Parallel structural and thermodynamics studies on several systems have provided significant insight regarding the driving forces governing folding, assembly, insertion, and translocation of membrane proteins. The present review surveys families of membrane-associated proteins including alpha-helical and beta-barrel structures, viral surface receptors, and pore-forming toxins, citing representative proteins within each of these classes for further scrutiny in terms of structure-function relationships and global conformational stability. This overview presents seminal findings from pioneering studies on the energetics of membrane protein folding and stability to modern techniques that are exploiting the use of molecular genetics and single molecule studies. An overall consensus regarding the molecular origins of membrane protein stability is that a number of intrinsic properties resemble features of soluble proteins, yet there are distinct energetic differences arising from specific intra- and intermolecular interactions within the membrane. The combined efforts from structural, energetics, and dynamics approaches offer unique insights and improve our fundamental understanding of the driving forces dictating membrane protein folding and stability.
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Affiliation(s)
- Conceição A S A Minetti
- Rutgers-The State University of New Jersey, Department of Chemistry and Chemical Biology, Piscataway, NJ 08854, USA.
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217
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Sperotto MM, May S, Baumgaertner A. Modelling of proteins in membranes. Chem Phys Lipids 2006; 141:2-29. [PMID: 16620797 DOI: 10.1016/j.chemphyslip.2006.02.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Accepted: 02/20/2006] [Indexed: 11/17/2022]
Abstract
This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly affected by the lipid environment. Theoretical predictions are pointed out, and compared to experimental findings, if available. Among others, the following phenomena are discussed: interactions of interfacially adsorbed peptides, pore-forming amphipathic peptides, adsorption of charged proteins onto oppositely charged lipid membranes, lipid-induced tilting of proteins embedded in lipid bilayers, protein-induced bilayer deformations, protein insertion and assembly, and lipid-controlled functioning of membrane proteins.
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218
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Marsh D, Páli T. Lipid conformation in crystalline bilayers and in crystals of transmembrane proteins. Chem Phys Lipids 2006; 141:48-65. [PMID: 16603141 DOI: 10.1016/j.chemphyslip.2006.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Accepted: 02/20/2006] [Indexed: 11/27/2022]
Abstract
Dihedral torsion angles evaluated for the phospholipid molecules resolved in the X-ray structures of transmembrane proteins in crystals are compared with those of phospholipids in bilayer crystals, and with the phospholipid conformations in fluid membranes. Conformations of the lipid glycerol backbone in protein crystals are not restricted to the gauche C1-C2 rotamers found invariably in phospholipid bilayer crystals. Lipid headgroup conformations in protein crystals also do not conform solely to the bent-down conformation, with gauche-gauche configuration of the phospho-diester, that is characteristic of phospholipid bilayer membranes. This suggests that the lipids that are resolved in crystals of membrane proteins are not representative of the entire lipid-protein interface. Much of the chain configurational disorder of the membrane-bound lipids in crystals arises from energetically disallowed skew conformations. This indicates a configurational heterogeneity in the lipids at a single binding site: eclipsed conformations occur also in some glycerol backbone torsion angles and C-C torsion angles in the lipid headgroups. Stereochemical violations in the protein-bound lipids are evidenced by one-third of the ester carboxyl groups in non-planar configurations, and certain of the carboxyls in the cis configuration. Some of the lipid structures in protein crystals have the incorrect enantiomeric configuration of the glycerol backbone, and many of the branched methyl groups in structures of the phytanyl chains associated with bacteriorhodopsin crystals are in the incorrect S-configuration.
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Affiliation(s)
- Derek Marsh
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Spektroskopie, Göttingen, Germany.
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219
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Wilding TJ, Zhou Y, Huettner JE. Q/R site editing controls kainate receptor inhibition by membrane fatty acids. J Neurosci 2006; 25:9470-8. [PMID: 16221857 PMCID: PMC6725705 DOI: 10.1523/jneurosci.2826-05.2005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
RNA editing within the pore loop controls the pharmacology and permeation properties of ion channels formed by neuronal AMPA and kainate receptor subunits. Genomic sequences for the glutamate receptor 2 (GluR2) subunit of AMPA receptors and the GluR5 and GluR6 subunits of kainate receptors all encode a neutral glutamine (Q) residue within the channel pore that can be converted by RNA editing to a positively charged arginine (R). Receptors comprised of unedited subunits are permeable to calcium and display inwardly rectifying current-voltage relationships, because of blocking of outward current by intracellular polyamines. In contrast, receptors that include edited subunits conduct less calcium, resist polyamine block, and have relatively linear current-voltage relationships. We showed previously that cis-unsaturated fatty acids, including arachidonic acid and docosahexanoic acid, exert a potent block of native kainate receptors as well as homomeric recombinant receptors formed by transfection of heterologous cells with cDNA for the GluR6(R) subunit. Here, we show that fatty acid blockade of recombinant homomeric and heteromeric kainate receptors is strongly dependent on editing at the Q/R site. Recombinant channels that include unedited subunits exhibit significantly weaker block than channels made up of fully edited subunits. Inhibition of fully edited channels is equivalent at voltages from -70 to +40 mV and is noncompetitive, consistent with allosteric regulation of channel function.
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Affiliation(s)
- Timothy J Wilding
- Department of Cell Biology and Physiology, Washington University Medical School, St. Louis, Missouri 63110, USA
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220
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Chill JH, Louis JM, Miller C, Bax A. NMR study of the tetrameric KcsA potassium channel in detergent micelles. Protein Sci 2006; 15:684-98. [PMID: 16522799 PMCID: PMC2242490 DOI: 10.1110/ps.051954706] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Nuclear magnetic resonance (NMR) studies of large membrane-associated proteins are limited by the difficulties in preparation of stable protein-detergent mixed micelles and by line broadening, which is typical of these macroassemblies. We have used the 68-kDa homotetrameric KcsA, a thermostable N-terminal deletion mutant of a bacterial potassium channel from Streptomyces lividans, as a model system for applying NMR methods to membrane proteins. Optimization of measurement conditions enabled us to perform the backbone assignment of KcsA in SDS micelles and establish its secondary structure, which was found to closely agree with the KcsA crystal structure. The C-terminal cytoplasmic domain, absent in the original structure, contains a 14-residue helix that could participate in tetramerization by forming an intersubunit four-helix bundle. A quantitative estimate of cross- relaxation between detergent and KcsA backbone amide protons, together with relaxation and light scattering data, suggests SDS-KcsA mixed micelles form an oblate spheroid with approximately 180 SDS molecules per channel. K(+) ions bind to the micelle-solubilized channel with a K(D) of 3 +/- 0.5 mM, resulting in chemical shift changes in the selectivity filter. Related pH-induced changes in chemical shift along the "outer" transmembrane helix and the cytoplasmic membrane interface hint at a possible structural explanation for the observed pH-gating of the potassium channel.
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Affiliation(s)
- Jordan H Chill
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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222
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Compton ELR, Farmer NA, Lorch M, Mason JM, Moreton KM, Booth PJ. Kinetics of an individual transmembrane helix during bacteriorhodopsin folding. J Mol Biol 2006; 357:325-38. [PMID: 16426635 DOI: 10.1016/j.jmb.2005.12.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Revised: 12/07/2005] [Accepted: 12/08/2005] [Indexed: 10/25/2022]
Abstract
The kinetics of an individual helix of bacteriorhodopsin have been monitored during folding of the protein into lipid bilayer vesicles. A fluorescence probe was introduced at individual sites throughout helix D of bacteriorhodopsin and the changes in the fluorescence of the label were time-resolved. Partially denatured, labelled bacteriorhodopsin in SDS was folded directly into phosphatidylcholine lipid vesicles. Stopped-flow mixing of the reactants allowed the folding kinetics to be monitored with millisecond time resolution by time-resolving changes in the label fluorescence, intrinsic protein fluorescence as well as in the absorption of the retinal chromophore. Monitoring specific positions on helix D showed that two kinetic phases were altered compared to those determined by monitoring the average protein behaviour. These two phases, of 6.7 s(-1) and 0.33 s(-1), were previously assigned to formation of a key apoprotein intermediate during bacteriorhodopsin folding. The faster 6.7s(-1) phase was missing when time-resolving fluorescence changes of labels attached to the middle of helix D. The amplitude of the 0.33 s(-1) phase increased along the helix, as single labels were attached in turn from the cytoplasmic to the extracellular side. An interpretation of these results is that the 6.7 s(-1) phase involves partitioning of helix D within the lipid headgroups of the bilayer vesicle, while the 0.33 s(-1) phase could reflect transmembrane insertion of this helix. In addition, a single site on helix G was monitored during folding. The results indicate that, unlike helix D, the insertion of helix G cannot be differentiated from the average protein behaviour. The data show that, while folding of bacteriorhodopsin from SDS into lipids is a co-operative process, it is nevertheless possible to obtain information on specific regions of a membrane protein during folding in vitro.
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Affiliation(s)
- Emma L R Compton
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
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223
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Vinothkumar KR, Raunser S, Jung H, Kühlbrandt W. Oligomeric structure of the carnitine transporter CaiT from Escherichia coli. J Biol Chem 2005; 281:4795-801. [PMID: 16365043 DOI: 10.1074/jbc.m508993200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The carnitine transporter CaiT from Escherichia coli belongs to the betaine, choline, and carnitine transporter family of secondary transporters. It acts as an L-carnitine/gamma-butyrobetaine exchanger and is predicted to span the membrane 12 times. Unlike the other members of this transporter family, it does not require an ion gradient and does not respond to osmotic stress (Jung, H., Buchholz, M., Clausen, J., Nietschke, M., Revermann, A., Schmid, R., and Jung, K. (2002) J. Biol. Chem. 277, 39251-39258). The structure and oligomeric state of the protein was examined in detergent and in lipid bilayers. Blue native gel electrophoresis indicated that CaiT was a trimer in detergent solution. This result was further supported by gel filtration and cross-linking studies. Electron microscopy and single particle analysis of the protein showed a triangular structure of three masses or two parallel elongated densities. Reconstitution of CaiT into lipid bilayers yielded two-dimensional crystals that indicated that CaiT was a trimer in the membrane, similar to its homologue BetP. The implications of the trimeric structure on the function of CaiT are discussed.
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224
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Abstract
One of the great challenges for molecular biologists is to learn how a protein sequence defines its three-dimensional structure. For many years, the problem was even more difficult for membrane proteins because so little was known about what they looked like. The situation has improved markedly in recent years, and we now know over 90 unique structures. Our enhanced view of the structure universe, combined with an increasingly quantitative understanding of fold determination, engenders optimism that a solution to the folding problem for membrane proteins can be achieved.
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Affiliation(s)
- James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Center for Genomics and Proteomics, Molecular Biology Institute, Boyer Hall, UCLA, 611 Charles E. Young Drive E, Los Angeles, California 90095-1570, USA.
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225
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Deol SS, Domene C, Bond PJ, Sansom MSP. Anionic phospholipid interactions with the potassium channel KcsA: simulation studies. Biophys J 2005; 90:822-30. [PMID: 16272446 PMCID: PMC1367107 DOI: 10.1529/biophysj.105.071407] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics (MD) simulations have been used to unmask details of specific interactions of anionic phospholipids with intersubunit binding sites on the surface of the bacterial potassium channel KcsA. Crystallographic data on a diacyl glycerol fragment at this site were used to model phosphatidylethanolamine (PE), or phosphatidylglycerol (PG), or phosphatidic acid (PA) at the intersubunit binding sites. Each of these models of a KcsA-lipid complex was embedded in phosphatidyl choline bilayer and explored in a 20 ns MD simulation. H-bond analysis revealed that in terms of lipid-protein interactions PA > PG >> PE and revealed how anionic lipids (PG and PA) bind to a site provided by two key arginine residues (R(64) and R(89)) at the interface between adjacent subunits. A 27 ns simulation was performed in which KcsA (without any lipids initially modeled at the R(64)/R(89) sites) was embedded in a PE/PG bilayer. There was a progressive specific increase over the course of the simulation in the number of H-bonds of PG with KcsA. Furthermore, two specific PG binding events at R(64)/R(89) sites were observed. The phosphate oxygen atoms of bound PG formed H-bonds to the guanidinium group of R(89), whereas the terminal glycerol H-bonded to R(64). Overall, this study suggests that simulations can help identify and characterize sites for specific lipid interactions on a membrane protein surface.
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Affiliation(s)
- Sundeep S Deol
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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226
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Molecular simulations and lipid–protein interactions: potassium channels and other membrane proteins. Biochem Soc Trans 2005. [DOI: 10.1042/bst0330916] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Molecular dynamics simulations may be used to probe the interactions of membrane proteins with lipids and with detergents at atomic resolution. Examples of such simulations for ion channels and for bacterial outer membrane proteins are described. Comparison of simulations of KcsA (an α-helical bundle) and OmpA (a β-barrel) reveals the importance of two classes of side chains in stabilizing interactions with the head groups of lipid molecules: (i) tryptophan and tyrosine; and (ii) arginine and lysine. Arginine residues interacting with lipid phosphate groups play an important role in stabilizing the voltage-sensor domain of the KvAP channel within a bilayer. Simulations of the bacterial potassium channel KcsA reveal specific interactions of phosphatidylglycerol with an acidic lipid-binding site at the interface between adjacent protein monomers. A combination of molecular modelling and simulation reveals a potential phosphatidylinositol 4,5-bisphosphate-binding site on the surface of Kir6.2.
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227
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Abstract
Many membrane proteins selectively bind defined lipid species. This specificity has an impact on correct insertion, folding, structural integrity and full functionality of the protein. How are these different tasks achieved? Recent advances in structural research of membrane proteins provide new information about specific protein–lipid interactions. Tightly bound lipids in membrane protein structures are described and general principles of the binding interactions are deduced. Lipid binding is stabilized by multiple non-covalent interactions from protein residues to lipid head groups and hydrophobic tails. Distinct lipid-binding motifs have been identified for lipids with defined head groups in membrane protein structures. The stabilizing interactions differ between the electropositive and electronegative membrane sides. The importance of lipid binding for vertical positioning and tight integration of proteins in the membrane, for assembly and stabilization of oligomeric and multisubunit complexes, for supercomplexes, as well as for functional roles are pointed out.
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228
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Abstract
Interactions between a membrane protein and the lipid molecules that surround it in the membrane are important in determining the structure and function of the protein. These interactions can be pictured at the molecular level using fluorescence spectroscopy, making use of the ability to introduce tryptophan residues into regions of interest in bacterial membrane proteins. Fluorescence quenching methods have been developed to study lipid binding separately on the two sides of the membrane. Lipid binding to the surface of the mechanosensitive channel MscL is heterogeneous, with a hot-spot for binding anionic lipid on the cytoplasmic side, associated with a cluster of three positively charged residues. The environmental sensitivity of tryptophan fluorescence emission has been used to identify the residues at the ends of the hydrophobic core of the second transmembrane α-helix in MscL. The efficiency of hydrophobic matching between MscL and the surrounding lipid bilayer is high. Fluorescence quenching methods can also be used to study binding of lipids to non-annular sites such as those between monomers in the homotetrameric potassium channel KcsA.
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229
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Encinar JA, Molina ML, Poveda JA, Barrera FN, Renart ML, Fernández AM, González-Ros JM. The influence of a membrane environment on the structure and stability of a prokaryotic potassium channel, KcsA. FEBS Lett 2005; 579:5199-204. [PMID: 16150445 DOI: 10.1016/j.febslet.2005.08.038] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 08/22/2005] [Accepted: 08/22/2005] [Indexed: 11/22/2022]
Abstract
The lack of a membrane environment in membrane protein crystals is considered one of the major limiting factors to fully imply X-ray structural data to explain functional properties of ion channels [Gulbis, J.M. and Doyle, D. (2004) Curr. Opin. Struct. Biol. 14, 440-446]. Here, we provide infrared spectroscopic evidence that the structure and stability of the potassium channel KcsA and its chymotryptic derivative 1-125 KcsA reconstituted into native-like membranes differ from those exhibited by these proteins in detergent solution, the latter taken as an approximation of the mixed detergent-protein crystal conditions.
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Affiliation(s)
- J A Encinar
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
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230
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Marius P, Alvis SJ, East JM, Lee AG. The interfacial lipid binding site on the potassium channel KcsA is specific for anionic phospholipids. Biophys J 2005; 89:4081-9. [PMID: 16199503 PMCID: PMC1366973 DOI: 10.1529/biophysj.105.070755] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lipid binding to the potassium channel KcsA from Streptomyces lividans has been studied using quenching of the fluorescence of Trp residues by brominated phospholipids. It is shown that binding of phospholipids to nonannular lipid binding sites on KcsA, located one each at the four protein-protein interfaces in the tetrameric structure, is specific for anionic phospholipids, zwitterionic phosphatidylcholine being unable to bind at the sites. The binding constant for phosphatidylglycerol of 3.0 +/- 0.7 mol fraction(-1) means that in a membrane containing approximately 20 mol% phosphatidylglycerol, as in the Escherichia coli inner membrane, the nonannular sites will be approximately 37% occupied by phosphatidylglycerol. The binding constant for phosphatidic acid is similar to that for phosphatidylglycerol but binding constants for phosphatidylserine and cardiolipin are about double those for phosphatidylglycerol. Binding to annular sites around the circumference of the KcsA tetramer are different on the extracellular and intracellular faces of the membrane. On the extracellular face of the membrane the binding constants for anionic lipids are similar to those for phosphatidylcholine, the lack of specificity being consistent with the lack of any marked clusters of charged residues on KcsA close to the membrane on the extracellular side. In contrast, binding to annular sites on the intracellular side of the membrane shows a distinct structural specificity, with binding of phosphatidic acid and phosphatidylglycerol being stronger than binding of phosphatidylcholine, whereas binding constants for phosphatidylserine and cardiolipin are similar to that for phosphatidylcholine. It is suggested that this pattern of binding follows from the pattern of charge distribution on KcsA on the intracellular side of the membrane.
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Affiliation(s)
- Phedra Marius
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
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231
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Krishnan MN, Bingham JP, Lee SH, Trombley P, Moczydlowski E. Functional role and affinity of inorganic cations in stabilizing the tetrameric structure of the KcsA K+ channel. J Gen Physiol 2005; 126:271-83. [PMID: 16129774 PMCID: PMC2266582 DOI: 10.1085/jgp.200509323] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Accepted: 08/02/2005] [Indexed: 11/20/2022] Open
Abstract
Crystal structures of the tetrameric KcsA K+ channel reveal seven distinct binding sites for K+ ions within the central pore formed at the fourfold rotational symmetry axis. Coordination of an individual K+ ion by eight protein oxygen atoms within the selectivity filter suggests that ion-subunit bridging by cation-oxygen interactions contributes to structural stability of the tetramer. To test this hypothesis, we examined the effect of inorganic cations on the temperature dependence of the KcsA tetramer as monitored by SDS-PAGE. Inorganic cations known to permeate or strongly block K+ channels (K+, Rb+, Cs+, Tl+, NH4+, Ba2+, and Sr2+) confer tetramer stability at higher temperatures (T0.5 range = 87 degrees C to >99 degrees C) than impermeant cations and weak blockers (Li+, Na+, Tris+, choline+; T0.5 range = 59 degrees C to 77 degrees C). Titration of K+, Ba2+, and other stabilizing cations protects against rapid loss of KcsA tetramer observed in 100 mM choline Cl at 90 degrees C. Tetramer protection titrations of K+, Rb+, Cs+, Tl+, and NH4+ at 85 degrees C or 90 degrees C exhibit apparent Hill coefficients (N) ranging from 1.7 to 3.3 and affinity constants (K0.5) ranging from 1.1 to 9.6 mM. Ba2+ and Sr2+ titrations exhibit apparent one-site behavior (N congruent with 1) with K0.5 values of 210 nM and 11 microM, respectively. At 95 degrees C in the presence of 5 mM K+, titration of Li+ or Na+ destabilizes the tetramer with K0.5 values of 57 mM and 109 mM, respectively. We conclude that specific binding interactions of inorganic cations with the selectivity filter are an important determinant of tetramer stability of KscA.
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Affiliation(s)
- Manoj N Krishnan
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA
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232
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Grottesi A, Domene C, Haider S, Sansom MSP. Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function. IEEE Trans Nanobioscience 2005; 4:112-20. [PMID: 15816177 DOI: 10.1109/tnb.2004.842473] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Molecular modeling and simulations enable extrapolation for the structure of bacterial potassium channels to the function of their mammalian homologues. Molecular dynamics simulations have revealed the concerted single-file motion of potassium ions and water molecules through the selectivity filter of K channels and the role of filter flexibility in ion permeation and in "fast gating." Principal components analysis of extended K channel simulations suggests that hinge-bending of pore-lining M2 (or S6) helices plays a key role in K channel gating. Based on these and other simulations, a molecular model for gating of inward rectifier K channel gating is presented.
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Affiliation(s)
- Alessandro Grottesi
- Department of Biochemistry, University of Oxford, Oxford OX 3QU, United Kingdom.
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233
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Comella N, Grossman AD. Conservation of genes and processes controlled by the quorum response in bacteria: characterization of genes controlled by the quorum-sensing transcription factor ComA in Bacillus subtilis. Mol Microbiol 2005; 57:1159-74. [PMID: 16091051 DOI: 10.1111/j.1365-2958.2005.04749.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Quorum or diffusion responses in bacteria are mediated by secreted signalling molecules that accumulate extracellularly as cultures grow to high density. The regulatory response to these signalling molecules can result in dramatic changes in gene expression. In Bacillus subtilis, a quorum response is mediated by a secreted 10-amino-acid modified peptide (ComX pheromone) that activates a receptor histidine kinase (ComP) that activates a response regulator transcription factor (ComA). We have used DNA microarrays to identify genes controlled by the ComX-ComP-ComA quorum-sensing pathway. We found that ComX, ComP and ComA affect the same set of genes, indicating that the kinase ComP is the only receptor for the signalling molecule ComX, and that ComA is the only transcription factor activated directly by ComP, under the conditions tested. Expression of over 20 genes appears to be controlled directly by this signalling pathway, and expression of over 150 additional genes, including those involved in competence development, appears to be controlled indirectly. The genes affected appear to have three general functions: (i) to co-ordinate physiological changes involved in developmental pathways, (ii) to produce extracellular products under conditions in which high concentrations of product are needed to be effective and (iii) to enhance survival, growth and colonization under conditions of crowding or limited diffusion. Many of the genes and processes controlled by the quorum response in B. subtilis are also regulated by quorum sensing in Gram-positive and Gram-negative bacteria. The quorum-sensing signalling molecules and regulatory proteins are quite different between Gram-positives and Gram-negatives and the convergent physiological regulation of similar genes and processes indicate the important and conserved nature of the quorum response.
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Affiliation(s)
- Natalia Comella
- Department of Biology, Building 68-530, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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234
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Abstract
Significant progress has been made in membrane protein engineering over the last 5 years, based largely on the re-design of existing scaffolds. Engineering techniques that have been employed include direct genetic engineering, both covalent and non-covalent modification, unnatural amino acid mutagenesis and total synthesis aided by chemical ligation of unprotected fragments. Combinatorial mutagenesis and directed evolution remain, by contrast, underemployed. Techniques for assembling and purifying heteromeric multisubunit pores have been improved. Progress in the de novo design of channels and pores has been slower. But, we are at the beginning of a new era in membrane protein engineering based on the accelerating acquisition of structural information, a better understanding of molecular motion in membrane proteins, technical improvements in membrane protein refolding and the application of computational approaches developed for soluble proteins. In addition, the next 5 years should see further advances in the applications of engineered channels and pores, notably in therapeutics and sensor technology.
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Affiliation(s)
- Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.
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235
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Mitra A, Bailey TD, Auerbach AL. Structural dynamics of the M4 transmembrane segment during acetylcholine receptor gating. Structure 2005; 12:1909-18. [PMID: 15458639 DOI: 10.1016/j.str.2004.08.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Revised: 08/03/2004] [Accepted: 08/04/2004] [Indexed: 11/22/2022]
Abstract
The transition state structures that link the stable end states of allosteric proteins are largely unresolved. We used single-molecule kinetic analysis to probe the dynamics of the M4 transmembrane segments during the closed<==>open isomerization of the neuromuscular acetylcholine receptor ion channel (AChR). We measured the slopes (phi) of the free energy relationships for 87 mutants, which reveal the open- versus closed-like characters of the mutated residues at the transition state and hence the sequence and organization of gating molecular motions. phi was constant throughout the length of the alpha subunit M4 segment with an average value of 0.54, suggesting that this domain moves as a unit, approximately midway through the reaction. Analysis of a hybrid construct indicates that the two alpha subunits move synchronously. Between subunits, the sequence of M4 motions is alpha-epsilon-beta. The AChR ion channel emerges as a dynamic nanomachine with many moving parts.
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Affiliation(s)
- Ananya Mitra
- Center for Single-Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214, USA
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236
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van Dalen A, de Kruijff B. The role of lipids in membrane insertion and translocation of bacterial proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1694:97-109. [PMID: 15546660 DOI: 10.1016/j.bbamcr.2004.03.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2003] [Revised: 02/03/2004] [Accepted: 03/01/2004] [Indexed: 11/20/2022]
Abstract
Phospholipids are essential building blocks of membranes and maintain the membrane permeability barrier of cells and organelles. They provide not only the bilayer matrix in which the functional membrane proteins reside, but they also can play direct roles in many essential cellular processes. In this review, we give an overview of the lipid involvement in protein translocation across and insertion into the Escherichia coli inner membrane. We describe the key and general roles that lipids play in these processes in conjunction with the protein components involved. We focus on the Sec-mediated insertion of leader peptidase. We describe as well the more direct roles that lipids play in insertion of the small coat proteins Pf3 and M13. Finally, we focus on the role of lipids in membrane assembly of oligomeric membrane proteins, using the potassium channel KcsA as model protein. In all cases, the anionic lipids and lipids with small headgroups play important roles in either determining the efficiency of the insertion and assembly process or contributing to the directionality of the insertion process.
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Affiliation(s)
- Annemieke van Dalen
- Department Biochemistry of Membranes, Centre for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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237
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Galdiero S, Gouaux E. High resolution crystallographic studies of alpha-hemolysin-phospholipid complexes define heptamer-lipid head group interactions: implication for understanding protein-lipid interactions. Protein Sci 2005; 13:1503-11. [PMID: 15152085 PMCID: PMC2279993 DOI: 10.1110/ps.03561104] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The alpha-hemolysin is an archetypal pore-forming protein that is secreted from Staphylococcus aureus as a water-soluble monomer. When the monomer binds to the membrane of a susceptible cell, the membrane-bound molecules assemble into the lytic heptamer. Although a bilayer or a bilayer-like environment are essential to toxin assembly, there is no high resolution information on toxin-phospholipid complexes. We have determined the structures of detergent-solubilized alpha-hemolysin heptamer bound to glycerophosphocholine or dipropanoyl glycerophosphocholine at 1.75-1.80 A resolution and 110 K. The phosphocholine head group binds to each subunit in a crevice between the rim and the stem domains. The quaternary ammonium group interacts primarily with aromatic residues, whereas the phosphodiester moiety interacts with a conserved arginine residue. These structures provide a molecular basis for understanding why alpha-hemolysin preferentially assembles on membranes comprised of phosphocholine lipids.
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Affiliation(s)
- Stefania Galdiero
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.
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238
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Lee AG. How lipids affect the activities of integral membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1666:62-87. [PMID: 15519309 DOI: 10.1016/j.bbamem.2004.05.012] [Citation(s) in RCA: 884] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2004] [Accepted: 05/28/2004] [Indexed: 11/30/2022]
Abstract
The activities of integral membrane proteins are often affected by the structures of the lipid molecules that surround them in the membrane. One important parameter is the hydrophobic thickness of the lipid bilayer, defined by the lengths of the lipid fatty acyl chains. Membrane proteins are not rigid entities, and deform to ensure good hydrophobic matching to the surrounding lipid bilayer. The structure of the lipid headgroup region is likely to be important in defining the structures of those parts of a membrane protein that are located in the lipid headgroup region. A number of examples are given where the conformation of the headgroup-embedded region of a membrane protein changes during the reaction cycle of the protein; activities of such proteins might be expected to be particularly sensitive to lipid headgroup structure. Differences in hydrogen bonding potential and hydration between the headgroups of phosphatidycholines and phosphatidylethanolamines could be important factors in determining the effects of these lipids on protein activities, as well as any effects related to the tendency of the phosphatidylethanolamines to form a curved, hexagonal H(II) phase. Effects of lipid structure on protein aggregation and helix-helix interactions are also discussed, as well as the effects of charged lipids on ion concentrations close to the surface of the bilayer. Interpretations of lipid effects in terms of changes in protein volume, lipid free volume, and curvature frustration are also described. Finally, the role of non-annular, or 'co-factor' lipids, tightly bound to membrane proteins, is described.
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Affiliation(s)
- Anthony G Lee
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Southampton SO16 7PX, UK.
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239
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Ash WL, Zlomislic MR, Oloo EO, Tieleman DP. Computer simulations of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1666:158-89. [PMID: 15519314 DOI: 10.1016/j.bbamem.2004.04.012] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 04/29/2004] [Indexed: 11/30/2022]
Abstract
Computer simulations are rapidly becoming a standard tool to study the structure and dynamics of lipids and membrane proteins. Increasing computer capacity allows unbiased simulations of lipid and membrane-active peptides. With the increasing number of high-resolution structures of membrane proteins, which also enables homology modelling of more structures, a wide range of membrane proteins can now be simulated over time spans that capture essential biological processes. Longer time scales are accessible by special computational methods. We review recent progress in simulations of membrane proteins.
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Affiliation(s)
- Walter L Ash
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary AB, Canada T2N 1N4
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240
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Lee AG. How lipids and proteins interact in a membrane: a molecular approach. MOLECULAR BIOSYSTEMS 2005; 1:203-12. [PMID: 16880984 DOI: 10.1039/b504527d] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Membrane proteins in a biological membrane are surrounded by a shell or annulus of 'solvent' lipid molecules. These lipid molecules in general interact rather non-specifically with the protein molecules, although a few 'hot-spots' may be present on the protein where anionic lipids bind with high affinity. Because of the low structural specificity of most of the annular sites, the composition of the lipid annulus will be rather similar to the bulk lipid composition of the membrane. The structures of the solvent lipid molecules are important in determining the conformational state of a membrane protein, and hence its activity, through charge and hydrogen bonding interactions between the lipid headgroups and residues in the protein, and through hydrophobic matching between the protein and the surrounding lipid bilayer. Evidence is also accumulating for the presence of 'co-factor' lipid molecules binding with high specificity to membrane proteins, often between transmembrane alpha-helices, and often being essential for activity.
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Affiliation(s)
- Anthony G Lee
- School of Biological Sciences, University of Southampton, Southampton, UK.
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241
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Deisz RA, Meske V, Treiber-Held S, Albert F, Ohm TG. Pathological cholesterol metabolism fails to modify electrophysiological properties of afflicted neurones in Niemann-Pick disease type C. Neuroscience 2005; 130:867-73. [PMID: 15652985 DOI: 10.1016/j.neuroscience.2004.09.065] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2004] [Indexed: 11/22/2022]
Abstract
Niemann-Pick disease type C (NPC) is a recessive inherited neurovisceral lipid storage disease characterized by progressive motor impairment and a loss of neurones including those integrated into the motor system. One of the key neuropathological findings is the intracellular accumulation of lysosomes enriched with free cholesterol. This accumulation is due to impaired transport proteins named NPC1 (approx. 95% of the cases) or NPC2 (approx. 5%) responsible for the transport of endocytosed cholesterol from lysomes to plasma membranes. The perturbed lipid-transport in NPC cells leads to an altered lipid composition of the plasma membrane. Available evidence suggests that the lipid matrix influences the electrophysical properties of ion channels in membranes. We therefore evaluated whether electrophysiological properties of NPC neurones differ from healthy neurones. Both, acute brain slices and primary neuronal cell cultures from wildtype and NPC mice, a well-established mouse model for the Niemann-Pick type C disease, were used for a comparison of electrophysiological properties like resting membrane potential, input resistance, action potential amplitudes and synaptic properties of the neurones. In addition we optically recorded the changes of intraneuronal calcium levels elicited by depolarization. Our results show that the characteristics of ion channels in NPC neurones do not differ significantly from wildtype neurones. We therefore conclude that gross alterations of the electrophysiological properties of neurones will probably not initiate or substantially contribute to the development of the motor impairment or other neurological signs of NPC.
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Affiliation(s)
- R A Deisz
- Center of Anatomy, Charité, Institute of Integrative Neuroanatomy, Department of Clinical Cell and Neurobiology, Schumann Strasse 20-21, 10098 Berlin, Germany
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242
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daCosta CJB, Kaiser DEE, Baenziger JE. Role of glycosylation and membrane environment in nicotinic acetylcholine receptor stability. Biophys J 2004; 88:1755-64. [PMID: 15626708 PMCID: PMC1305231 DOI: 10.1529/biophysj.104.052944] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The effects of glycosylation and membrane environment on the structural stability of the nicotinic acetylcholine receptor (nAChR) from Torpedo have been investigated to improve our understanding of factors that influence eukaryotic membrane protein crystallization. Gel shift assays and carbohydrate-specific staining show that the deglycosylation enzyme, Endo F1, removes at least 50% of membrane-reconstituted nAChR glycosylation. The extent of deglycosylation with Endo F1 increases upon detergent solubilization. Removal of between 60-100% of high mannose moieties from the nAChR has no effect on nAChR secondary structure, stability, or flexibility. Deglycosylation does not influence either agonist binding or the ability of the nAChR to undergo agonist-induced conformational change. In contrast, nAChR structural stability, flexibility, and function are all negatively influenced by simple changes in reconstituted membrane lipid composition. Our results suggest that deglycosylation may represent a feasible approach for enhancing the crystallizability of the nAChR. Our data also demonstrate that the dependence of nAChR structural stability on lipid environment may represent a significant obstacle to nAChR crystallization. Some membrane proteins may have evolved complex interactions with their lipid environments. Understanding the complexity of these interactions may be essential for devising an appropriate strategy for the crystallization of some membrane proteins.
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Affiliation(s)
- Corrie J B daCosta
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Rd., Ottawa, Ontario, ON K1H 8M5, Canada
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243
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Cascio M. Connexins and their environment: effects of lipids composition on ion channels. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2004; 1711:142-53. [PMID: 15955299 DOI: 10.1016/j.bbamem.2004.12.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Revised: 11/25/2004] [Accepted: 12/02/2004] [Indexed: 11/16/2022]
Abstract
Intercellular communication is mediated through paired connexons that form an aqueous pore between two adjacent cells. These membrane proteins reside in the plasma membrane of their respective cells and their activity is modulated by the composition of the lipid bilayer. The effects of the bilayer on connexon structure and function may be direct or indirect, and may arise from specific binding events or the physicochemical properties of the bilayer. While the effects of the bilayer and its constituent lipids on gap junction activity have been described in the literature, the underlying mechanisms of the interaction of connexin with its lipidic microenvironment are not as well characterized. Given that the information regarding connexons is limited, in this review, the specific roles of lipids and the properties of the bilayer on membrane protein structure and function are described for other ion channels as well as for connexons.
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Affiliation(s)
- Michael Cascio
- Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States.
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244
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Abstract
The insertion and folding of proteins in biological membranes during protein synthesis in vivo is fundamental to membrane biogenesis. At present, however, certain molecular aspects of this process can only be understood by complementary studies in vitro. We bring together in vitro and in vivo results, highlighting how the studies inform each other and increase our knowledge of the folding and assembly of polytopic membrane proteins. A notable recent advance is the high-resolution crystal structure of the protein machinery responsible for membrane protein insertion into the endoplasmic reticulum. This provides an opportunity to combine in vitro and in vivo studies at a more sophisticated level and address mechanistic aspects of polytopic protein insertion and folding. Quality control is another important aspect of membrane biogenesis, and we give an overview of the current understanding of this process, focusing on cystic fibrosis as a well-studied paradigm. Mutations in the associated membrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR), can cause the quality control mechanisms to prevent the mutant protein reaching its normal site of action, the cell surface. In vitro studies of CFTR shed light on the possible origins of other clinically relevant folding mutants and highlight the potential synergy between in vitro and in vivo approaches.
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Affiliation(s)
- Paula J Booth
- Department of Biochemistry, School of Medical Sciences University of Bristol, University Walk BS8 1TD Bristol, UK.
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245
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Lundbaek JA, Birn P, Hansen AJ, Søgaard R, Nielsen C, Girshman J, Bruno MJ, Tape SE, Egebjerg J, Greathouse DV, Mattice GL, Koeppe RE, Andersen OS. Regulation of sodium channel function by bilayer elasticity: the importance of hydrophobic coupling. Effects of Micelle-forming amphiphiles and cholesterol. ACTA ACUST UNITED AC 2004; 123:599-621. [PMID: 15111647 PMCID: PMC2234500 DOI: 10.1085/jgp.200308996] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Membrane proteins are regulated by the lipid bilayer composition. Specific lipid–protein interactions rarely are involved, which suggests that the regulation is due to changes in some general bilayer property (or properties). The hydrophobic coupling between a membrane-spanning protein and the surrounding bilayer means that protein conformational changes may be associated with a reversible, local bilayer deformation. Lipid bilayers are elastic bodies, and the energetic cost of the bilayer deformation contributes to the total energetic cost of the protein conformational change. The energetics and kinetics of the protein conformational changes therefore will be regulated by the bilayer elasticity, which is determined by the lipid composition. This hydrophobic coupling mechanism has been studied extensively in gramicidin channels, where the channel–bilayer hydrophobic interactions link a “conformational” change (the monomer↔dimer transition) to an elastic bilayer deformation. Gramicidin channels thus are regulated by the lipid bilayer elastic properties (thickness, monolayer equilibrium curvature, and compression and bending moduli). To investigate whether this hydrophobic coupling mechanism could be a general mechanism regulating membrane protein function, we examined whether voltage-dependent skeletal-muscle sodium channels, expressed in HEK293 cells, are regulated by bilayer elasticity, as monitored using gramicidin A (gA) channels. Nonphysiological amphiphiles (β-octyl-glucoside, Genapol X-100, Triton X-100, and reduced Triton X-100) that make lipid bilayers less “stiff”, as measured using gA channels, shift the voltage dependence of sodium channel inactivation toward more hyperpolarized potentials. At low amphiphile concentration, the magnitude of the shift is linearly correlated to the change in gA channel lifetime. Cholesterol-depletion, which also reduces bilayer stiffness, causes a similar shift in sodium channel inactivation. These results provide strong support for the notion that bilayer–protein hydrophobic coupling allows the bilayer elastic properties to regulate membrane protein function.
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246
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Valiyaveetil FI, Sekedat M, Mackinnon R, Muir TW. Glycine as a D-amino acid surrogate in the K(+)-selectivity filter. Proc Natl Acad Sci U S A 2004; 101:17045-9. [PMID: 15563591 PMCID: PMC535378 DOI: 10.1073/pnas.0407820101] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The K(+) channel-selectivity filter consists of two absolutely conserved glycine residues. Crystal structures show that the first glycine in the selectivity filter, Gly-77 in KcsA, is in a left-handed helical conformation. Although the left-handed helical conformation is not favorable for the naturally occurring L-amino acids, it is favorable for the chirally opposite D-amino acids. Here, we demonstrate that Gly-77 can be replaced by D-Ala with almost complete retention of function. In contrast, substitution with an L-amino acid results in a nonfunctional channel. This finding suggests that glycine is used as a surrogate D-amino acid in the selectivity filter. The absolute conservation of glycine in the K(+)-selectivity filter can be explained as a result of glycine being the only natural amino acid that can play this role.
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Affiliation(s)
- Francis I Valiyaveetil
- Laboratory of Molecular Neurobiology and Biophysics and Howard Hughes Medical Institute, The Rockefeller University, Box 47, 1230 York Avenue, New York, NY 10021, USA
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247
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Saiz L, Klein ML. The transmembrane domain of the acetylcholine receptor: insights from simulations on synthetic peptide models. Biophys J 2004; 88:959-70. [PMID: 15556982 PMCID: PMC1305168 DOI: 10.1529/biophysj.104.049726] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have studied the structure and properties of a bundle of alpha-helical peptides embedded in a 1,2-dimyristoyl-3-phosphatidylcholine phospholipid bilayer by molecular dynamics simulations. The bundle of five transmembrane deltaM2 segments constitutes the model for the pore region of the nicotinic acetylcholine receptor, which is the neurotransmitter-gated ion-channel responsible for the fast propagation of electrical signals between cells at the nerve-muscle synapse. The deltaM2 segments were shown to oligomerize in biomembranes resulting in ion-channel activity with characteristics similar to the native protein, and the structure of the isolated peptides was studied in 1,2-dimyristoyl-3-phosphatidylcholine bilayers and micelles by NMR experiments (Opella, S. J., et al. 1999. Nat. Struct. Biol. 6:374-379). Our analyses indicate that the structure, helix tilt, and the overall shape of the channel are in good agreement with the NMR experiments and the proposed model for the channel, which we show is formed by rings of functional residues. The studied geometry resulted in a closed pore state, where the channel is partially dehydrated at the hydrophobic extracellular half and the extracellular mouth of the channel blocked by the hydrocarbon chains of Arg+ residues. The arginine amino acids form intermolecular salt-bridges with the C-terminus, which contribute as well to the bundle stabilization.
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Affiliation(s)
- Leonor Saiz
- Center for Molecular Modeling, Chemistry Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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248
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Allen SJ, Curran AR, Templer RH, Meijberg W, Booth PJ. Folding kinetics of an alpha helical membrane protein in phospholipid bilayer vesicles. J Mol Biol 2004; 342:1279-91. [PMID: 15351651 DOI: 10.1016/j.jmb.2004.07.040] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Revised: 07/09/2004] [Accepted: 07/09/2004] [Indexed: 11/29/2022]
Abstract
We report a detailed kinetic study of the folding of an alpha-helical membrane protein in a lipid bilayer environment. SDS denatured bacteriorhodopsin was folded directly into phosphatidylcholine lipid vesicles by stopped-flow mixing. The folding kinetics were monitored with millisecond time resolution by time-resolving changes in protein fluorescence as well as in the absorption of the retinal chromophore. The kinetics were similar to those previously reported for folding bacteriorhodopsin in detergent or lipid micelles, except for the presence of an additional apoprotein intermediate. We suggest this intermediate is a result of the greater internal two-dimensional pressure present in these lipid vesicles as compared to micelles. These results lay the groundwork for future studies aimed at understanding the mechanistic origin of the effect of lipid bilayer properties on protein folding. Furthermore, the use of biologically relevant phosphatidylcholine lipids, together with a straightforward rapid mixing process to initiate the folding reaction, means the method is generally applicable, and thus paves the way for an improved understanding of the in vitro folding of transmembrane alpha-helical proteins.
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Affiliation(s)
- Samantha J Allen
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
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249
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van den Brink-van der Laan E, Killian JA, de Kruijff B. Nonbilayer lipids affect peripheral and integral membrane proteins via changes in the lateral pressure profile. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2004; 1666:275-88. [PMID: 15519321 DOI: 10.1016/j.bbamem.2004.06.010] [Citation(s) in RCA: 330] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Revised: 06/16/2004] [Accepted: 06/24/2004] [Indexed: 11/23/2022]
Abstract
Nonbilayer lipids can be defined as cone-shaped lipids with a preference for nonbilayer structures with a negative curvature, such as the hexagonal phase. All membranes contain these lipids in large amounts. Yet, the lipids in biological membranes are organized in a bilayer. This leads to the question: what is the physiological role of nonbilayer lipids? Different models are discussed in this review, with a focus on the lateral pressure profile within the membrane. Based on this lateral pressure model, predictions can be made for the effect of nonbilayer lipids on peripheral and integral membrane proteins. Recent data on the catalytic domain of Leader Peptidase and the potassium channel KcsA are discussed in relation to these predictions and in relation to the different models on the function of nonbilayer lipids. The data suggest a general mechanism for the interaction between nonbilayer lipids and membrane proteins via the membrane lateral pressure.
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Affiliation(s)
- Els van den Brink-van der Laan
- Department Biochemistry of Membranes, Centre for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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250
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Marsh D, Páli T. The protein–lipid interface: perspectives from magnetic resonance and crystal structures. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2004; 1666:118-41. [PMID: 15519312 DOI: 10.1016/j.bbamem.2004.08.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2004] [Revised: 08/13/2004] [Accepted: 08/13/2004] [Indexed: 10/26/2022]
Abstract
Lipid-protein interactions in membranes are dynamic, and consequently are well studied by magnetic resonance spectroscopy. More recently, lipids associated with integral membrane proteins have been resolved in crystals by X-ray diffraction, mostly at cryogenic temperatures. The conformation and chain ordering of lipids in crystals of integral proteins are reviewed here and are compared and contrasted with results from magnetic resonance and with the crystal structures of phospholipid bilayers. Various aspects of spin-label magnetic resonance studies on lipid interactions with single integral proteins are also reviewed: specificity for phosphatidylcholine, competition with local anaesthetics, oligomer formation of single transmembrane helices, and protein-linked lipid chains. Finally, the interactions between integral proteins and peripheral or lipid-linked proteins, as reflected by the lipid-protein interactions in double reconstitutions, are considered.
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Affiliation(s)
- Derek Marsh
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, 37070 Göttingen, Germany.
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