Two-dimensional Crystallization Of Membrane Proteins Research Articles

Inducing two-dimensional crystallization of membrane proteins by dialysis for electron crystallography.

Electron crystallography is an electron cryo-microscopy (cryo-EM) method that is particularly suitable for structure-function studies of small membrane proteins, which are crystallized in two-dimensional (2D) arrays for subsequent cryo-EM data collection and image processing. This approach allows for structural analysis of membrane proteins in a close-to-native, phospholipid bilayer environment. The process of growing 2D crystals from purified membrane proteins by dialysis detergent removal is described in this chapter. A short section covers screening for and identifying 2D crystals by transmission electron microscopy, and in the last section, optimization of the purification to obtain crystals of higher quality is discussed.

Automated screening of 2D crystallization trials using transmission electron microscopy: A high-throughput tool-chain for sample preparation and microscopic analysis

We have built and extensively tested a tool-chain to prepare and screen two-dimensional crystals of membrane proteins by transmission electron microscopy (TEM) at room temperature. This automated process is an extension of a new procedure described recently that allows membrane protein 2D crystallization in parallel (Iacovache et al., 2010). The system includes a gantry robot that transfers and prepares the crystalline solutions on grids suitable for TEM analysis and an entirely automated microscope that can analyze 96 grids at once without human interference. The operation of the system at the user level is solely controlled within the MATLAB environment: the commands to perform sample handling (loading/unloading in the microscope), microscope steering (magnification, focus, image acquisition, etc.) as well as automatic crystal detection have been implemented. Different types of thin samples can efficiently be screened provided that the particular detection algorithm is adapted to the specific task. Hence, operating time can be shared between multiple users. This is a major step towards the integration of transmission electron microscopy into a high throughput work-flow.

Automated electron microscopy for evaluating two-dimensional crystallization of membrane proteins

Membrane proteins fulfill many important roles in the cell and represent the target for a large number of therapeutic drugs. Although structure determination of membrane proteins has become a major priority, it has proven to be technically challenging. Electron microscopy of two-dimensional (2D) crystals has the advantage of visualizing membrane proteins in their natural lipidic environment, but has been underutilized in recent structural genomics efforts. To improve the general applicability of electron crystallography, high-throughput methods are needed for screening large numbers of conditions for 2D crystallization, thereby increasing the chances of obtaining well ordered crystals and thus achieving atomic resolution. Previous reports describe devices for growing 2D crystals on a 96-well format. The current report describes a system for automated imaging of these screens with an electron microscope. Samples are inserted with a two-part robot: a SCARA robot for loading samples into the microscope holder, and a Cartesian robot for placing the holder into the electron microscope. A standard JEOL 1230 electron microscope was used, though a new tip was designed for the holder and a toggle switch controlling the airlock was rewired to allow robot control. A computer program for controlling the robots was integrated with the Leginon program, which provides a module for automated imaging of individual samples. The resulting images are uploaded into the Sesame laboratory information management system database where they are associated with other data relevant to the crystallization screen.

Synthesis of a hemifluorinated amphiphile designed for self-assembly and two-dimensional crystallization of membrane protein

The work reported herein deals with the synthesis and the preliminary physical–chemical analysis of new hemifluorinated surfactant made up of one fluorinated chain linked to a tricarboxylic acid polar head which is able to complex a Ni atom and should favor the two-dimensional crystallization of membrane proteins. Such a compound forms a Langmuir film which is a fluid at 20 °C and not perturbed by the presence of hydrocarbon detergent in aqueous solution.

7 Å projection map of the S-layer protein sbpA obtained with trehalose-embedded monolayer crystals

Two-dimensional crystallization on lipid monolayers is a versatile tool to obtain structural information of proteins by electron microscopy. An inherent problem with this approach is to prepare samples in a way that preserves the crystalline order of the protein array and produces specimens that are sufficiently flat for high-resolution data collection at high tilt angles. As a test specimen to optimize the preparation of lipid monolayer crystals for electron microscopy imaging, we used the S-layer protein sbpA, a protein with potential for designing arrays of both biological and inorganic materials with engineered properties for a variety of nanotechnology applications. Sugar embedding is currently considered the best method to prepare two-dimensional crystals of membrane proteins reconstituted into lipid bilayers. We found that using a loop to transfer lipid monolayer crystals to an electron microscopy grid followed by embedding in trehalose and quick-freezing in liquid ethane also yielded the highest resolution images for sbpA lipid monolayer crystals. Using images of specimens prepared in this way we could calculate a projection map of sbpA at 7 Å resolution, one of the highest resolution projection structures obtained with lipid monolayer crystals to date.

Two-dimensional Crystallization of Membrane Proteins

Two-dimensional Crystallization of Membrane Proteins

Radiation damage to protein specimens from electron beam imaging and diffraction: a mini-review of anti-damage approaches, with special reference to synchrotron X-ray crystallography

Recent research progress using X-ray cryo-crystallography with the photon beams from third-generation synchrotron sources has resulted in recognition that this intense radiation commonly damages protein samples even when they are held at 100 K. Other structural biologists examining thin protein crystals or single particle specimens encounter similar radiation damage problems during electron diffraction and imaging, but have developed some effective countermeasures. The aim of this concise review is to examine whether analogous approaches can be utilized to alleviate the X-ray radiation damage problem in synchrotron macromolecular crystallography. The critical discussion of this question is preceded by presentation of background material on modern technical procedures with electron beam instruments using 300-400 kV accelerating voltage, low-dose exposures for data recording, and protection of protein specimens by cryogenic cooling; these practical approaches to dealing with electron radiation damage currently permit best resolution levels of 6 A (0.6 nm) for single particle specimens, and of 1.9 A for two-dimensional membrane protein crystals. Final determination of the potential effectiveness and practical value of using such new or unconventional ideas will necessitate showing, by experimental testing, that these produce significantly improved protection of three-dimensional protein crystals during synchrotron X-ray diffraction.

High-Resolution AFM of Membrane Proteins Directly Incorporated at High Density in Planar Lipid Bilayer

The heterologous expression and purification of membrane proteins represent major limitations for their functional and structural analysis. Here we describe a new method of incorporation of transmembrane proteins in planar lipid bilayer starting from 1 pmol of solubilized proteins. The principle relies on the direct incorporation of solubilized proteins into a preformed planar lipid bilayer destabilized by dodecyl- β-maltoside or dodecyl- β-thiomaltoside, two detergents widely used in membrane biochemistry. Successful incorporations are reported at 20°C and at 4°C with three bacterial photosynthetic multi-subunit membrane proteins. Height measurements by atomic force microscopy (AFM) of the extramembraneous domains protruding from the bilayer demonstrate that proteins are unidirectionally incorporated within the lipid bilayer through their more hydrophobic domains. Proteins are incorporated at high density into the bilayer and on incubation diffuse and segregate into protein close-packing areas. The high protein density allows high-resolution AFM topographs to be recorded and protein subunits organization delineated. This approach provides an alternative experimental platform to the classical methods of two-dimensional crystallization of membrane proteins for the structural analysis by AFM. Furthermore, the versatility and simplicity of the method are important intrinsic properties for the conception of biosensors and nanobiomaterials involving membrane proteins.

電子線で今何ができるか１．電子線結晶構造解析の最先端 電子回折法による膜タンパク質の二次元結晶構造解析

Here applications of electron crystallography to the structural analysis of membrane proteins at high resolution are described. Methods to grow two-dimensional crystals of membrane proteins for the structural analysis and the sample preparation methods for cryo-electron microscopy are discussed. About the sample preparation, we developed a new technique, in which the crystals are put between two sheets of carbon film, to reduce the beam-induced image movement by electron microscopy from tilted specimens. Two structures of the membrane proteins, a proton pump and a water channel, were shown as two examples of electron crystallographic structural analysis of membrane proteins.

In Situ FTIR ATR Spectroscopy of the Preparation of an Oriented Monomolecular Film of Porin Omp32 on an Internal Reflecting Element by Dialysis

The development of a reproducible technique for the preparation of oriented porin Omp32 monolayers on an attenuated total reflection (ATR) internal reflection element (IRE) was the principal aim of this work. A procedure earlier applied for two-dimensional crystallization of membrane proteins [Paul, A.; Engelhardt, H.; Jakubowski, U.; Baumeister, W. Biophys. J. 1992, 61, 172−188] could be successfully adapted. Layer formation was performed in a spectroscopic dialysis cell in the presence of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) micelles by the removal of the detergent (n-octylpolyoxyethylene, OPOE). This setup enabled in situ monitoring of the monolayer formation by means of the Fourier transform infrared (FTIR) single beam sample reference ATR technique. The time course of OPOE and sodium azide extraction by dialysis and the formation of the protein/lipid layer on top of the IRE was evaluated from corresponding time-dependent absorbance changes in the IR spectra. Both OPOE and azide featured a first-order kinetics, whereas the synchronous adsorption of porin to the Ge IRE resulted in a sigmoidal time behavior. At the beginning of the dialysis, the concentration of OPOE was just above the critical micellar concentration (cmc) which is about 0.25%. As the cmc was reached by dialysis, Omp32 adsorption was accelerated, reaching saturation after about 5 h. Quantitative analysis of the Omp32/lipid layer gave strong evidence for a well-ordered monolayer with the barrel axis of the Omp32 trimer being approximately oriented perpendicular to the supporting IRE. Two to six DMPC molecules were detected per Omp32 monomer.

A new technique to co-localise membrane proteins with Homer/vesl

The minimal requirements were defined as necessary for cluster formation of the group 1 metabotropic glutamate receptor (mGluR), which is regulated by the Homer/vesl family of scaffolding proteins [Curr. Opin. Neurobiol. 10 (2000) 370]. Cluster formation of G-protein-coupled receptors (GPCRs) plays a fundamental role in signal transduction, particularly at the neuronal synapse. To understand the interaction of mGluR with PSD-Zip45, a Homer/vesl family member, we designed a series of chimeric receptor proteins, consisting of C-terminal mGluR1α sequences that were fused to endothelin B receptors (ET BRs). In vitro and in vivo studies revealed that an extended 20 amino acid long C-terminal mGluR1α peptide, including the proline-rich core motif PPXXF, is sufficient to induce clustering of chimeric ET BR/mGluR1α receptors by PSD-Zip45. This result is especially important because it constitutes the basis for a new approach to form two-dimensional crystals of membrane proteins in situ, which may render unstable membrane proteins amenable to electron crystallographic structure determination.

Two-dimensional crystals: a powerful approach to assess structure, function and dynamics of membrane proteins

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.

Use of Octyl β-Thioglucopyranoside in Two-Dimensional Crystallization of Membrane Proteins

A great interest exists in producing and/or improving two-dimensional (2D) crystals of membrane proteins amenable to structural analysis by electron crystallography. Here we report on the use of the detergent n-octyl β-d-thioglucopyranoside in 2D crystallization trials of membrane proteins with radically different structures including FhuA from the outer membrane of Escherichia coli, light-harvesting complex II from Rubrivivax gelatinosus, and Photosystem I from cyanobacterium Synechococcus sp. We have analyzed by electron microscopy the structures reconstituted after detergent removal from lipid–detergent or lipid–protein–detergent micellar solutions containing either only n-octyl β-d-thioglucopyranoside or n-octyl β-d-thioglucopyranoside in combination with other detergents commonly used in membrane protein biochemistry. This allowed the definition of experimental conditions in which the use of n-octyl β-d-thioglucopyranoside could induce a considerable increase in the size of reconstituted membrane structures, up to several micrometers. An other important feature was that, in addition to reconstitution of membrane proteins into large bilayered structures, this thioglycosylated detergent also was revealed to be efficient in crystallization trials, allowing the proteins to be analyzed in large coherent two-dimensional arrays. Thus, inclusion of n-octyl β-d-thioglucopyranoside in 2D crystallization trials appears to be a promising method for the production of large and coherent 2D crystals that will be valuable for structural analysis by electron crystallography and atomic force microscopy.

Two-Dimensional Crystallization on Lipid Layer: A Successful Approach for Membrane Proteins

A considerable interest exists currently in designing innovative strategies to produce two-dimensional crystals of membrane proteins that are amenable to structural analysis by electron crystallography. We have developed a protocol for crystallizing membrane protein that is derived from the classical lipid-layer two-dimensional crystallization at the air/water interface used so far for soluble proteins. Lipid derivatized with a Ni2+-chelating head group provided a general approach to crystallizing histidine-tagged transmembrane proteins. The processes of protein binding and two-dimensional crystallization were analyzed by electron microscopy, using two prototypic membrane proteins: FhuA, a high-affinity receptor from the outer membrane of Escherichia coli, and the F0F1-ATP synthase from thermophilic Bacillus PS3. Conditions were found to avoid solubilization of the lipid layer by the detergent present with the purified membrane proteins and thus to allow binding of micellar proteins to the functionalized lipid head groups. After detergent removal using polystyrene beads, membrane sheets of several hundreds of square micrometers were reconstituted at the interface. High protein density in these membrane sheets allowed further formation of planar two-dimensional crystals. We believe that this strategy represents a new promising alternative to conventional dialysis methods for membrane protein 2D crystallization, with the additional advantage of necessitating little purified protein.

Surface crystallisation of the plasma membrane H +-ATPase on a carbon support film for electron crystallography

Large two-dimensional crystals of H +-ATPase, a 100 kDa integral membrane protein, were grown directly onto the carbon surface of an electron microscope grid. This procedure prevented the fragmentation that is normally observed upon transfer of the crystals from the air-water interface to a continuous carbon support film. Crystals grown by this method measure ∼5 μm across and have a thickness of ∼240Å. They are of better quality than the monolayers previously obtained at the air-water interface, yielding structure factors to at least 8Åin-plane resolution by electron image processing. Unlike most other two-dimensional crystals of membrane proteins they do not contain a lipid bilayer, but consist of detergent-protein micelles of H +-ATPase hexamers tightly packed on a trigonal lattice. The crystals belong to the two-sided plane group p321 ( a= b=165Å), containing two layers of hexamers related by an in-plane axis of 2-fold symmetry. The protein is in contact with the carbon surface through its large, hydrophilic 70 kDa cytoplasmic portion, yet due to the presence of detergent in the crystallizing buffer, the hydrophobicity of the carbon surface does not appear to affect crystal formation. Surface crystallisation may be a useful method for other proteins which form fragile two-dimensional crystals, in particular if conditions for obtaining three-dimensional crystals are known, but their quality or stability is insufficient for X-ray structure determination.

An automatic Bio-Beads-supplying device for two-dimensional crystallization of membrane proteins

A simple device has been developed for the automatic supply of hydrophobic resin beads simultaneously to many sample solutions. The device enables the programmed removal of various types of nonionic detergents often used for two-dimensional crystallization of membrane proteins.

Electron Crystallography of Two-Dimensional Crystals of Membrane Proteins

Electron microscopy has become a powerful technique, along with X-ray crystallography and nuclear magnetic resonance spectroscopy, to study the three-dimensional structure of biological molecules. It has evolved into a number of methods dealing with a wide range of biological samples, with electron crystallography of two-dimensional crystals being so far the only method allowing data collection at near-atomic resolution. In this paper, we review the methodology of electron crystallography and its application to membrane proteins, starting with the pioneering work on bacteriorhodopsin, which led to the first visualization of the secondary structure of a membrane protein in 1975. Since then, improvements in instrumentation, sample preparation, and data analysis have led to atomic models for bacteriorhodopsin and light-harvesting complex II from higher plants. The structures of many more membrane proteins have been studied by electron crystallography and in this review examples are included where a resolution of better than 10 Å has been achieved. Indeed, in some of the given examples an atomic model can be expected in the near future. Finally, a brief outlook is given on current and future developments of electron crystallographic methods.

How to make tubular crystals by reconstitution of detergent-solubilized Ca2(+)-ATPase

In an attempt to better define the parameters governing reconstitution and two-dimensional crystallization of membrane proteins, we have studied Ca2(+)-ATPase from rabbit sarcoplasmic reticulum. This ion pump forms vanadate-induced crystals in its native membrane and has previously been reconstituted at high lipid-to-protein ratios for functional studies. We have characterized the reconstitution of purified Ca2(+)-ATPase at low lipid-to-protein ratios and discovered procedures that produce long, tubular crystals suitable for helical reconstruction. C12E8 (n-dodecyl-octaethylene-glycol monoether) was used to fully solubilize various mixtures of lipid and purified Ca2(+)-ATPase, and BioBeads were then used to remove the C12E8. Slow removal resulted in two populations of vesicles, and the proteoliposome population was separated from the liposome population on a sucrose density gradient. These proteoliposomes had a lipid-to-protein ratio of 1:2, and virtually 100% of molecules faced the outside of vesicles, as determined by fluorescein isothiocyanate labeling. Cycles of freeze-thaw caused considerable aggregation of these proteoliposomes, and, if phosphatidyl ethanolamine and phosphatidic acid were included, or if the bilayers were doped with small amounts of C12E8, vanadate-induced tubular crystals grew from the aggregates. Thus our procedure comprised two steps-reconstitution followed by crystallization-allowing us to consider mechanisms of bilayer formation separately from those of crystallization and tube formation.

Bio-Beads: An Efficient Strategy for Two-Dimensional Crystallization of Membrane Proteins

This work establishes the potential of Bio-Beads as a simple alternative to conventional dialysis for removing detergent and for obtaining 2D crystals of integral membrane proteins useful for structure analysis by electron crystallography. Kinetic and equilibrium aspects of removal of different detergents by adsorption onto hydrophobic Bio-Beads SM2 have been systematically investigated and extended to 2D crystallization of different prototypic membrane proteins, including: (a) Ca2+ATPase from sarcoplasmic reticulum; (b) melibiose permease fromEscherichia coli;(c) cytochromeb6ffromChlamydomonas reinhardtii.Different crystals could be produced from all protein preparations, with optical diffraction down to 20–25 Å in negative stain.

The micelle to vesicle transition of lipids and detergents in the presence of a membrane protein: towards a rationale for 2D crystallization

The assembly of two-dimensional membrane protein crystals in the presence of lipids was analyzed with quasielastic light scattering and electron microscopy. Mixtures of detergent-solubilized lipids and/or proteins were submitted to slow or rapid dilution while measuring the hydrodynamic radii of the aggregates. Lipids alone exhibited λ-shaped dilution curves with intermediate rod-shaped particles that converted into small vesicles. Depending on the protein-protein and protein-lipid interactions, detergent-solubilized protein-lipid mixtures showed a sharp transition from micelles to large, densely packed proteoliposomes. Electron microscopy revealed that formation of crystals occurred shortly after this phase transition.