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Abstract
Electron crystallography is used to study membrane proteins in the form of planar, two-dimensional (2D) crystals, or other crystalline arrays such as tubular crystals. This method has been used to determine the atomic resolution structures of bacteriorhodopsin, tubulin, aquaporins, and several other membrane proteins. In addition, a large number of membrane protein structures were studied at a slightly lower resolution, whereby at least secondary structure motifs could be identified.In order to conserve the structural details of delicate crystalline arrays, cryo-electron microscopy (cryo-EM) allows imaging and/or electron diffraction of membrane proteins in their close-to-native state within a lipid bilayer membrane.To achieve ultimate high-resolution structural information of 2D crystals, meticulous sample preparation for electron crystallography is of outmost importance. Beam-induced specimen drift and lack of specimen flatness can severely affect the attainable resolution of images for tilted samples. Sample preparations that sandwich the 2D crystals between symmetrical carbon films reduce the beam-induced specimen drift, and the flatness of the preparations can be optimized by the choice of the grid material and the preparation protocol.Data collection in the cryo-electron microscope using either the imaging or the electron diffraction mode has to be performed applying low-dose procedures. Spot-scanning further reduces the effects of beam-induced drift. Data collection using automated acquisition schemes, along with improved and user-friendlier data processing software, is increasingly being used and is likely to bring the technique to a wider user base.
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Kim LY, Johnson MC, Schmidt‐Krey I. Cryo‐EM in the Study of Membrane Transport Proteins. Compr Physiol 2012; 2:283-93. [DOI: 10.1002/cphy.c110028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Plasencia I, Survery S, Ibragimova S, Hansen JS, Kjellbom P, Helix-Nielsen C, Johanson U, Mouritsen OG. Structure and stability of the spinach aquaporin SoPIP2;1 in detergent micelles and lipid membranes. PLoS One 2011; 6:e14674. [PMID: 21339815 PMCID: PMC3038850 DOI: 10.1371/journal.pone.0014674] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 12/23/2010] [Indexed: 12/13/2022] Open
Abstract
Background SoPIP2;1 constitutes one of the major integral proteins in spinach leaf plasma membranes and belongs to the aquaporin family. SoPIP2;1 is a highly permeable and selective water channel that has been successfully overexpressed and purified with high yields. In order to optimize reconstitution of the purified protein into biomimetic systems, we have here for the first time characterized the structural stability of SoPIP2;1. Methodology/Principal Finding We have characterized the protein structural stability after purification and after reconstitution into detergent micelles and proteoliposomes using circular dichroism and fluorescence spectroscopy techniques. The structure of SoPIP2;1 was analyzed either with the protein solubilized with octyl-β-D-glucopyranoside (OG) or reconstituted into lipid membranes formed by E. coli lipids, diphytanoylphosphatidylcholine (DPhPC), or reconstituted into lipid membranes formed from mixtures of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPE), 1-palmitoyl-2oleoyl-phosphatidylethanolamine (POPE), 1-palmitoyl-2-oleoyl-phosphatidylserine (POPS), and ergosterol. Generally, SoPIP2;1 secondary structure was found to be predominantly α-helical in accordance with crystallographic data. The protein has a high thermal structural stability in detergent solutions, with an irreversible thermal unfolding occurring at a melting temperature of 58°C. Incorporation of the protein into lipid membranes increases the structural stability as evidenced by an increased melting temperature of up to 70°C. Conclusion/Significance The results of this study provide insights into SoPIP2;1 stability in various host membranes and suggest suitable choices of detergent and lipid composition for reconstitution of SoPIP2;1 into biomimetic membranes for biotechnological applications.
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Affiliation(s)
- Inés Plasencia
- Department of Physics and Chemistry, MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
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Cymer F, Schneider D. A single glutamate residue controls the oligomerization, function, and stability of the aquaglyceroporin GlpF. Biochemistry 2010; 49:279-86. [PMID: 20000688 DOI: 10.1021/bi901660t] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Like many other alpha-helical membrane proteins, the monomeric Escherichia coli aquaglyceroporin GlpF associates within cellular membranes and forms higher-order oligomeric structures. A potential impact of the oligomeric state on the protein function remains enigmatic. We have analyzed the role of residues W42 and E43 in the oligomerization of the E. coli GlpF protein in vitro and in vivo. In contrast to W42, the polar glutamate residue at position 43 appears to be critical for oligomerization. While other polar residues can substitute for the function of E43, replacement of E43 with alanine results in a greatly reduced GlpF oligomerization propensity. The reduced interaction propensity of GlpF E43A correlates with an impaired in vivo function as well as a decreased in vivo stability. Therefore, E43 is critical for the proper oligomerization of GlpF, and protein oligomerization appears to be crucial for the channel function as well as for the in vivo stability of the protein.
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Affiliation(s)
- Florian Cymer
- Institut für Biochemie und Molekularbiologie, ZBMZ, Albert-Ludwigs-Universität Freiburg,Stefan-Meier-Strasse 17, 79104 Freiburg, Germany
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Schenk AD, Hite RK, Engel A, Fujiyoshi Y, Walz T. Electron crystallography and aquaporins. Methods Enzymol 2010; 483:91-119. [PMID: 20888471 DOI: 10.1016/s0076-6879(10)83005-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Electron crystallography of two-dimensional (2D) crystals can provide information on the structure of membrane proteins at near-atomic resolution. Originally developed and used to determine the structure of bacteriorhodopsin (bR), electron crystallography has recently been applied to elucidate the structure of aquaporins (AQPs), a family of membrane proteins that form pores mostly for water but also other solutes. While electron crystallography has made major contributions to our understanding of the structure and function of AQPs, structural studies on AQPs, in turn, have fostered a number of technical developments in electron crystallography. In this contribution, we summarize the insights electron crystallography has provided into the biology of AQPs, and describe technical advancements in electron crystallography that were driven by structural studies on AQP 2D crystals. In addition, we discuss some of the lessons that were learned from electron crystallographic work on AQPs.
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Affiliation(s)
- Andreas D Schenk
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
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Ubarretxena-Belandia I, Stokes DL. Present and future of membrane protein structure determination by electron crystallography. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2010; 81:33-60. [PMID: 21115172 DOI: 10.1016/b978-0-12-381357-2.00002-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This chapter describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins.
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Affiliation(s)
- Iban Ubarretxena-Belandia
- Department of Structural and Chemical Biology, Mt. Sinai School of Medicine, New York, New York, USA
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7
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Abstract
Selected applications of free energy calculations to the realm of membrane proteins are reviewed. The theoretical underpinnings of these calculations are described, focusing on free energy perturbation and the use of thermodynamic integration to determine free energy changes along well-delineated order parameters. Current strategies for improving the reliability of free energy calculations, while making them somewhat more affordable are outlined. Application of the free energy methodology to understand the structure and function of membrane proteins is illustrated in three concrete examples: The binding of an agonist ligand to a G protein-coupled receptor, the assisted transport of a small permeant through a membrane channel, and the recognition and association of transmembrane alpha-helical domains.
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Membrane fatty acids adaptive profile in the simultaneous presence of arsenic and toluene in Bacillus sp. ORAs2 and Pseudomonas sp. ORAs5 strains. Extremophiles 2008; 12:343-9. [PMID: 18305894 DOI: 10.1007/s00792-008-0147-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Accepted: 12/17/2007] [Indexed: 10/22/2022]
Abstract
Bacillus sp. ORAs2 and Pseudomonas sp. ORAs5, two arsenic-resistant bacterial strains previously isolated from sediments of the Orbetello Lagoon, Italy, were tested for their adaptation to mixed contaminants on the level of membrane fatty acid composition. The two bacterial strains were characterized by high levels of arsenic resistance, and Pseudomonas sp. ORAs5 was also shown to be solvent-tolerant. The bacterial strains were exposed to mixtures of two toxic compounds: arsenic at fixed concentrations and toluene in variable amounts or, alternatively, toluene at constant values along with arsenic added at variable concentrations. Both strains react to the contaminants by changing the composition of their membrane fatty acids. Bacillus sp. strain ORAs2 showed a correlation between growth rate decreases and fatty acids degree of saturation increases in both cases, although pointedly in the presence of 1, 2, and 3 mM of toluene and different additions of arsenic, counteracting membranes fluidity induced by toxic compounds. In Pseudomonas sp. ORAs5, adaptive changes in membrane composition was observed both in terms of increases in the degree of saturation and in the trans/cis ratio of unsaturated fatty acids in the presence of varying toluene and constant arsenic concentrations, whereas only minor changes occurred with increasing arsenic and constant toluene concentrations. Thus, on the level of membrane composition, Bacillus sp. ORAs2 showed a higher potential for adaptation to the presence of mixed pollutants, suggesting its probable suitability for bioremediation purposes.
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Galka JJ, Baturin SJ, Manley DM, Kehler AJ, O’Neil JD. Stability of the Glycerol Facilitator in Detergent Solutions. Biochemistry 2008; 47:3513-24. [DOI: 10.1021/bi7021409] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jamie J. Galka
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simon J. Baturin
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Darren M. Manley
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Angela J. Kehler
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Joe D. O’Neil
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
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Borgnia MJ, Shi D, Zhang P, Milne JLS. Visualization of alpha-helical features in a density map constructed using 9 molecular images of the 1.8 MDa icosahedral core of pyruvate dehydrogenase. J Struct Biol 2005; 147:136-45. [PMID: 15193642 DOI: 10.1016/j.jsb.2004.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2003] [Revised: 02/03/2004] [Indexed: 11/26/2022]
Abstract
Strategies to achieve the highest resolutions in structures of protein complexes determined by cryo-electron microscopy generally involve averaging information from large numbers of individual molecular images. However, significant limitations are posed by heterogeneity in image quality and in protein conformation that are inherent to large data sets of images. Here, we demonstrate that the combination of iterative refinement and stringent molecular sorting is an effective method to obtain substantial improvements in map quality of the 1.8 MDa icosahedral catalytic core of the pyruvate dehydrogenase complex from Bacillus stearothermophilus. From a starting set of 42,945 images of the core complex, we show that using only the best 139 particles in the data set produces a map that is superior to those constructed with greater numbers of images, and that the location of many of the alpha-helices in the structure can be unambiguously visualized in a map constructed from as few as 9 particles.
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Affiliation(s)
- Mario J Borgnia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Stroud RM, Nollert P, Miercke L. The glycerol facilitator GlpF its aquaporin family of channels, and their selectivity. ADVANCES IN PROTEIN CHEMISTRY 2003; 63:291-316. [PMID: 12629974 DOI: 10.1016/s0065-3233(03)63011-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Robert M Stroud
- Department of Biochemistry and Biophysics, School of Medicine, University of California, San Francisco, California 94143, USA
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Stahlberg H, Engel A, Philippsen A. Assessing the structure of membrane proteins: combining different methods gives the full picture. Biochem Cell Biol 2003; 80:563-8. [PMID: 12440697 DOI: 10.1139/o02-160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The rotor stoichiometry of F-ATPases has been revealed by the combined approaches of X-ray diffraction (XRD), electron crystallography, and atomic force microscopy (AFM). XRD showed the rotor from the yeast mitochondrial F-ATPase to contain 10 subunits. AFM was used to visualize the tetradecameric chloroplast rotors, and electron crystallography and AFM together revealed the rotors from Ilyobacter tartaricus to be composed of 11 subunits. While biochemical methods had determined an approximate stoichiometric value, precise measurements and new insights into a species-dependent rotor stoichiometry became available by applying the three structural tools together. The structures of AQP1, a water channel, and G1pF, a glycerol channel, were determined by electron crystallography and XRD. The combination of both of these structural tools with molecular dynamics simulations gave a differentiated description of the mechanisms determining the selectivity of water and glycerol channels. This illustrates that the combination of different methods in structural biology reveals more than each method alone.
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Engel A, Stahlberg H. Aquaglyceroporins: channel proteins with a conserved core, multiple functions, and variable surfaces. INTERNATIONAL REVIEW OF CYTOLOGY 2002; 215:75-104. [PMID: 11952238 DOI: 10.1016/s0074-7696(02)15006-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Membrane channels for water and small nonionic solutes are required for osmoregulation in bacteria, plants, and animals. Aquaporin-1, the water channel of human erythrocytes, is the first channel demonstrated to conduct water, by expression in Xenopus oocytes. Phylogenetic analyses reveal the existence of two clusters of subfamilies, the aquaporins (AQPs) and glycerol facilitators (GLPs). Sequence-based structure prediction provided a model comprising six membrane-spanning helices, while sequence analyses suggested strategic residues that are important for structure and function. The surface topography of several AQPs has been mapped by atomic force microscopy, revealing different features that correlate with differences in the loops connecting transmembrane helices. The 3D structures of AQP1 and GlpF have been determined by electron cryomicroscopy. The 3.8-A density map allowed the first atomic model of AQP1 to be built, taking into account data from sequence analyses. This model provides some insight into the permeation of water through a channel that blocks the passage of protons. GIpF has been resolved to 6.9 A, revealing helices that are similar to those of AQP1. Homology modeling shows the channel region of these distant aquaglyceroporins to be similar, as confirmed by the 2.2-A structure of GlpF from X-ray crystallography.
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Affiliation(s)
- Andreas Engel
- M. E. Müller-Institute for Microscopic Structural Biology, Biozentrum, University of Basel, Switzerland
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Mukhopadhyay R, Rosen BP, Phung LT, Silver S. Microbial arsenic: from geocycles to genes and enzymes. FEMS Microbiol Rev 2002; 26:311-25. [PMID: 12165430 DOI: 10.1111/j.1574-6976.2002.tb00617.x] [Citation(s) in RCA: 386] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Arsenic compounds have been abundant at near toxic levels in the environment since the origin of life. In response, microbes have evolved mechanisms for arsenic resistance and enzymes that oxidize As(III) to As(V) or reduce As(V) to As(III). Formation and degradation of organoarsenicals, for example methylarsenic compounds, occur. There is a global arsenic geocycle, where microbial metabolism and mobilization (or immobilization) are important processes. Recent progress in studies of the ars operon (conferring resistance to As(III) and As(V)) in many bacterial types (and related systems in Archaea and yeast) and new understanding of arsenite oxidation and arsenate reduction by respiratory-chain-linked enzyme complexes has been substantial. The DNA sequencing and protein crystal structures have established the convergent evolution of three classes of arsenate reductases (that is classes of arsenate reductases are not of common evolutionary origin). Proposed reaction mechanisms in each case involve three cysteine thiols and S-As bond intermediates, so convergent evolution to similar mechanisms has taken place.
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Affiliation(s)
- Rita Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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de Groot BL, Grubmüller H. Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF. Science 2001; 294:2353-7. [PMID: 11743202 DOI: 10.1126/science.1066115] [Citation(s) in RCA: 201] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
"Real time" molecular dynamics simulations of water permeation through human aquaporin-1 (AQP1) and the bacterial glycerol facilitator GlpF are presented. We obtained time-resolved, atomic-resolution models of the permeation mechanism across these highly selective membrane channels. Both proteins act as two-stage filters: Conserved fingerprint [asparagine-proline-alanine (NPA)] motifs form a selectivity-determining region; a second (aromatic/arginine) region is proposed to function as a proton filter. Hydrophobic regions near the NPA motifs are rate-limiting water barriers. In AQP1, a fine-tuned water dipole rotation during passage is essential for water selectivity. In GlpF, a glycerol-mediated "induced fit" gating motion is proposed to generate selectivity for glycerol over water.
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Affiliation(s)
- B L de Groot
- Theoretical Molecular Biophysics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Levy D, Chami M, Rigaud JL. Two-dimensional crystallization of membrane proteins: the lipid layer strategy. FEBS Lett 2001; 504:187-93. [PMID: 11532452 DOI: 10.1016/s0014-5793(01)02748-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Due to the difficulty to crystallize membrane proteins, there is a considerable interest to intensify research topics aimed at developing new methods of crystallization. In this context, the lipid layer crystallization at the air/water interface, used so far for soluble proteins, has been recently adapted successfully to produce two-dimensional (2D) crystals of membrane proteins, amenable to structural analysis by electron crystallography. Besides to represent a new alternative strategy, this approach gains the advantage to decrease significantly the amount of material needed in incubation trials, thus opening the field of crystallization to those membrane proteins difficult to surexpress and/or purify. The systematic studies that have been performed on different classes of membrane proteins are reviewed and the physico-chemical processes that lead to the production of 2D crystals are addressed. The different drawbacks, advantages and perspectives of this new strategy for providing structural information on membrane proteins are discussed.
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Affiliation(s)
- D Levy
- Institut Curie, Section de Recherche, UMR-CNRS 168 and LRC-CEA 8, 11 Rue Pierre et Marie Curie, 75231 Cedex 05, Paris, France
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Stahlberg H, Fotiadis D, Scheuring S, Rémigy H, Braun T, Mitsuoka K, Fujiyoshi Y, Engel A. Two-dimensional crystals: a powerful approach to assess structure, function and dynamics of membrane proteins. FEBS Lett 2001; 504:166-72. [PMID: 11532449 DOI: 10.1016/s0014-5793(01)02746-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Electron crystallography and atomic force microscopy allow the study of two-dimensional membrane protein crystals. While electron crystallography provides atomic scale three-dimensional density maps, atomic force microscopy gives insight into the surface structure and dynamics at sub-nanometer resolution. Importantly, the membrane protein studied is in its native environment and its function can be assessed directly. The approach allows both the atomic structure of the membrane protein and the dynamics of its surface to be analyzed. In this way, the function-related conformational changes can be assessed, thus providing a detailed insight on the molecular mechanisms of essential biological processes.
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Affiliation(s)
- H Stahlberg
- M.E.Müller-Institute for Structural Biology, University of Basel, Switzerland
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