Two-dimensional crystals of Escherichia coli RNA polymerase holoenzyme on positively charged lipid layers

A small bioactive glycoside inhibits epsilon toxin and prevents cell death

Clostridium perfringens epsilon toxin (Etx) is categorized as the third most lethal bioterrorism agent by the Centers for Disease Control and Prevention (CDC), with no therapeutic counter measures available for humans. Here, we have developed a high-affinity inhibitory compound by synthesizing and evaluating the structure activity relationship (SAR) of a library of diverse glycosides (numbered 1-12). SAR of glycoside-Etx heptamers revealed exceptionally strong H-bond interactions of glycoside-4 with a druggable pocket in the oligomerization and β-hairpin region of Etx. Analysis of its structure suggested that glycoside-4 might self-aggregate to form a robust micelle-like supra-molecular complex due to its linear side-chain architecture, which was authenticated by fluorescence spectroscopy. Further, this micelle hinders the Etx monomer-monomer interaction required for oligomerization, validated by both surface plasmon resonance (SPR) and immunoblotting. This phenomenon in turn leads to blockage of pore formation. Downstream evaluation revealed that glycoside-4 effectively blocked cell death of Etx-treated cultured primary cells and maintained cellular homeostasis via disrupting oligomerization, blocking pore formation, restoring calcium homeostasis, stabilizing the mitochondrial membrane and impairing high mobility group box 1 (HMGB1) translocation from nucleus to cytoplasm. Furthermore, a single dosage of glycoside-4 protected the Etx-challenged mice and restored normal function to multiple organs. This work reports for the first time a potent, nontoxic glycoside with strong ability to occlude toxin lethality, representing it as a bio-arm therapeutic against Etx-based biological threat.

Odd RNA polymerases or the A(B)C of eukaryotic transcription

Pioneering studies on eukaryotic transcription were undertaken with the bacterial system in mind. Will the bacterial paradigm apply to eukaryotes? Are there promoter sites scattered in the eukaryotic genome, and sigma-like proteins? Why three forms of RNA polymerase in eukaryotic cells? Why are they structurally so complex, in particular RNA polymerases I and III, compared to the bacterial enzyme? These questions and others that were raised along the way are evoked in this short historical survey of odd RNA polymerases studies, with some emphasis on the contribution of these studies to our global understanding of eukaryotic transcription systems. This article is part of a Special Issue entitled: Transcription by Odd Pols.

Two-dimensional crystallisation of soluble protein complexes

This method aims at providing structural information on protein or nucleoprotein complexes by high-resolution electron microscopy. The objective is to promote the self-assembly of the macromolecules into two-dimensional crystals in order to use electron crystallography methods. When combined with observations in the frozen hydrated states and dedicated image processing software these methods can provide detailed 3-D models of the complex. The 2-D crystals of soluble nucleoprotein complexes are formed on lipid monolayers spread at the air-water interface. The macromolecule of interest is targeted to the monolayer by either electrostatic or ligand-induced interactions with the hydrophilic head group of the lipid. Upon interaction with the lipids, the nucleoprotein complex is concentrated at the vicinity of the lipid layer whose in-plane mobility facilitates the contacts between macromolecules and the formation of ordered arrays.

7A 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 7A resolution, one of the highest resolution projection structures obtained with lipid monolayer crystals to date.

Self-assembled hydrophobin protein films at the air-water interface: structural analysis and molecular engineering

Hydrophobins are amphiphilic proteins produced by filamentous fungi. They function in a variety of roles that involve interfacial interactions, as in growth through the air-water interface, adhesion to surfaces, and formation of coatings on various fungal structures. In this work, we have studied the formation of films of the class II hydrophobin HFBI from Trichoderma reesei at the air-water interface. Analysis of hydrophobin aqueous solution drops showed that a protein film is formed at the air-water interface. This elastic film was clearly visible, and it appeared to cause the drops to take unusual shapes. Because adhesion and formation of coatings are important biological functions for hydrophobins, a closer structural analysis of the film was made. The method involved picking up the surface film onto a solid substrate and imaging the surface by atomic force microscopy. High-resolution images were obtained showing both the hydrophilic and hydrophobic sides of the film at nanometer resolution. It was found that the hydrophobin film had a highly ordered structure. To study the orientation of molecules and to obtain further insight in film formation, we made variants of HFBI that could be site specifically conjugated. We then used the avidin-biotin interaction as a probe. On the basis of this work, we suggest that the unusual interfacial properties of this type of hydrophobins are due to specific molecular interactions which lead to an ordered network of proteins in the surface films that have a thickness of only one molecule. The interactions between the proteins in the network are likely to be responsible for the unusual surface elasticity of the hydrophobin film.

Structure analysis of soluble proteins using electron crystallography

Electron crystallography as a structural determination technique has grown dramatically in use over recent years. Improvements in microscopes, equipment, practical techniques, computation facilities and image processing methods are reflected in the increasing number of near-atomic resolution structures that have been published. In this review we shall summarize the techniques involved in structure determination of soluble proteins using electron crystallography. Many soluble protein structures have been investigated in this manner over the past two decades. Here we present several examples where a variety of approaches have been used to gradually increase the information obtained.

Arresting pore formation of a cholesterol-dependent cytolysin by disulfide trapping synchronizes the insertion of the transmembrane beta-sheet from a prepore intermediate

Perfringolysin O (PFO), a member of the cholesterol-dependent cytolysin family of pore-forming toxins, forms large oligomeric complexes comprising up to 50 monomers. In the present study, a disulfide bridge was introduced between cysteine-substituted serine 190 of transmembrane hairpin 1 (TMH1) and cysteine-substituted glycine 57 of domain 2 of PFO. The resulting disulfide-trapped mutant (PFO(C190-C57)) was devoid of hemolytic activity and could not insert either of its transmembrane beta-hairpins (TMHs) into the membrane unless the disulfide was reduced. Both the size of the oligomer formed on the membrane and its rate of formation were unaffected by the oxidation state of the Cys(190)-Cys(57) disulfide bond; thus, the disulfide-trapped PFO was assembled into a prepore complex on the membrane. The conversion of this prepore to the pore complex was achieved by reducing the C190-C57 disulfide bond. PFO(C190-C57) that was allowed to form the prepore prior to the reduction of the disulfide exhibited a dramatic increase in the rate of PFO-dependent hemolysis and the membrane insertion of its TMHs when compared with toxin that had the disulfide reduced prior mixing the toxin with membranes. Therefore, the rate-limiting step in pore formation is prepore assembly, not TMH insertion. These data demonstrate that the prepore is a legitimate intermediate during the insertion of the large transmembrane beta-sheet of the PFO oligomer. Finally, the PFO TMHs do not appear to insert independently, but instead their insertion is coupled.

Two-dimensional crystallization of streptavidin: in pursuit of the molecular origins of structure, morphology, and thermodynamics

The streptavidin two-dimensional (2D) crystallization model has served as a paradigm for molecular self-assembly at interfaces. We have developed quantitative Brewster angle microscopy for the in situ measurement of spatially resolved relative protein surface densities. This allows investigation of both the thermodynamics and morphologies of 2D crystal growth. For crystal structure analysis, we employ TEM on grown crystals transferred to solid substrates. Comparison of results between commercially available streptavidin, recombinant streptavidin, and site-directed streptavidin mutants has provided insight into the protein protein and protein-lipid interactions that underlie 2D crystallization.

Self-assembly of soluble proteins on functionalized lipid layers: a tentative correlation between the fluidity properties of the lipid film and protein ordering

New series of amphiphilic structures are designed to exhibit various fluidity properties when spread at the air-water interface. The influence of the molecular structure of these lipids on the process of two-dimensional (2D) crystallization of the B subunit of DNA gyrase, a soluble protein, is investigated in terms of size of the crystals produced, protein ordering, and crystallization kinetics. Whereas no difference is observed concerning the mean size of the protein 2D crystals obtained on the different lipid supports, the ultimate protein ordering observable by electron microscopy using the negative-staining technique is more regularly attained with some of these new lipids. The most interesting point results from large discrepancies in crystallization kinetics as highly-ordered protein 2D crystals form within 6-24 h depending on the lipid layer structure. Thus, these new lipids reveal of special interest when studying proteins that suffer from extended incubation time at 4 degrees C or higher temperature and lose their functionality.

Synthesis of new fluidity-enhanced amphiphilic compounds for soluble protein two-dimensional crystallization purpose

The synthesis of new amphiphilic compounds is described. The structures are rationally designed for soluble protein two-dimensional (2D) crystallization purpose. Special attention is devoted to fluidity properties expected of resulting monolayers. A series of 13 compounds was prepared containing unsaturated, branched or fluorinated alkyl chains. Structures are either symmetrical or dissymmetrical and present a hydroxyl group as polar head, eventually complemented with two other 'secondary' hydrophilic functions.

Synthesis of Enzymatically Stable Analogues of GDP for Binding Studies with Transducin, the G-Protein of the Visual Photoreceptor

The synthesis of five enzymatically stable analogues of guanosine diphosphate (GDP) has been carried out. The pyrophosphate moiety was mimicked in turn by the malonate, the acetophosphonate, the phosphonoacetate, the methylene-bis-phosphonate, and the imidodiphosphate groups. All the compounds were prepared via the synthesis of a transient fully protected nucleoside diphosphate analogue, and the final deprotection step was achieved by catalytic hydrogenolysis. The biological properties of the compounds have been evaluated toward transducin, the G-protein of the visual photoreceptor. Three guanosine imidodiphosphate derivatives bearing a linker at different positions on the sugar and on the base were then prepared and evaluated, giving some insight into the GDP binding site of transducin.

Lipid nanotubes as substrates for helical crystallization of macromolecules

A general approach for crystallization of proteins in a fast and simple manner would be of immense interest to biologists studying protein structure-function relationships. Here, we describe a method that we have developed for promoting the formation of helical arrays of proteins and macromolecular assemblies. Electron micrographs of the arrays are suitable for helical image analysis and three-dimensional reconstruction. We show that hydrated mixtures of the glycolipid galactosylceramide (GalCer) and derivatized lipids or charged lipids form unilamellar nanotubules. The tubules bind proteins in a specific manner via high affinity ligands on the polar head groups of the lipid or via electrostatic interactions. By doping the GalCer with a novel nickel-containing lipid, we have been able to form helical arrays of two histidine-tagged proteins. Similarly, doping with a biotinylated lipid allows crystallization of streptavidin. Finally, three proteins with affinity for positively or negatively charged lipid layers formed helical arrays on appropriately charged tubules. The generality of this method may allow a wide variety of proteins to be crystallized on lipid nanotubes under physiological conditions.

Automated correlation and averaging of three-dimensional reconstructions obtained by electron tomography

We have developed a least-squares refinement procedure that in an automated way performs three-dimensional alignment and averaging of objects from multiple reconstructions. The computer implementation aligns the three-dimensional structures by a two-step procedure that maximizes the density overlap for all objects. First, an initial average density is built by successive incorporation of individual objects, after a global search for their optimal three-dimensional orientations. Second, the initial average is subsequently refined by excluding individual objects one at a time, realigning them with the reduced average containing all other objects and including them into the average again. The refinement is repeated until no further change of the average occurs. The resulting average model is therefore minimally biased by the order in which the individual reconstructions are incorporated into the average. The performance of the procedure was tested using a synthetic data set of randomly oriented objects with Poisson-distributed noise added. The program managed well to align and average the objects at the signal/noise ratio 1.0. The increase in signal/noise ratio was in all investigated cases almost equal to the expected square root of the number of objects. The program was also successfully tested on a set of authentic three-dimensional reconstructions from an in situ specimen containing Escherichia coli 70S ribosomes, where the immediate environment of the reconstructed objects may also contain variable amounts of other structures.

Electron density projection map of the botulinum neurotoxin 900-kilodalton complex by electron crystallography

The 900-kDa botulinum neurotoxin complex serotype A has been crystallized by the lipid-layer two-dimensional crystallization technique. Based on the binding characteristics of the hemagglutinating portion of the complex, a number of ganglioside/ lipid mixtures were tested but only lactosyl ceramide/1-palmityl-2-oleoyl-sn-glycero-3-phosphocholine was found to crystallize the complex. The optimum lipid mixture contained 75 mass % lactosyl ceramide and 25 mass % 1-palmityl-2-oleoyl-sn-glycero-3-phosphocholine. Using protein concentrations from 5 to 500 micrograms/ml and pH and 5 acetate buffer, we have obtained crystals that diffract to better than 15 A when prepared in negative stain. A projection map with a resolution of 30 A was calculated with unit cell dimensions of a = b = 157 A and P3 symmetry. The complex is triangular in shape with six distinct lobes observed. Additionally, six smaller structures protrude from the triangular core.

Electron crystallography of macromolecular periodic arrays on phospholipid monolayers

Electron crystallography has the potential of yielding structural information equivalent to x-ray diffraction. The major difficulty has been preparing specimens with the required structural order and size for diffraction and imaging in the electron microscope. 2D crystallization on phospholipid monolayers is capable of fulfilling both of these requirements. Crystals can form as a result of specific interactions with a protein's ligand or an analog, suitably linked to a lipid tail; or on a surface of complementary head-group charge. With such choices, the availability of a suitable lipid is limited only by synthetic chemistry. Ultimately, it is the quality and regularity of the protein-protein interactions that determine the crystalline order, as it is with any protein crystal. In the case of streptavidin, the monolayer crystal diffracts beyond 2.5 A. A 3 A projection map reconstructed from electron diffraction amplitudes and phases from images shows density which can be interpreted as beta-sheets and clusters of side chains. It remains to be shown that the monolayer crystals are flat and diffract as well at high tilt angle as untilted. Technological issues such as charging must be resolved. With parallel advances in data collection and processing, electron crystallography of monolayer macromolecular crystals will eventually take its place beside x-ray crystallography and NMR as a routine and efficient structural technique.

Protein arrays: concepts and subjects

To adapt proteins, the materials in life, for use as materials in science and technology, we focused not only on the biological aspects (functional aspects) but also on the material aspects as matter (structural and physical aspects). Engineering with protein arrays will develop under such consideration and advance toward stable devices made of protein molecules. The protein arrays with 2D crystalline order provide a primary model of macroscopic protein-based devices. The combination of protein engineering, the leading edge of life science, and array engineering, the leading edge of materials science, will provide clues to the controlled integration of protein molecules to a form of functional supramolecules on proper surfaces.

Two-dimensional crystallization of rabbit C-reactive protein on lipid monolayers

Two-dimensional (2D) crystals of rabbit C-reactive protein (CRP) have been obtained by protein binding on lipid monolayers at the air/water interface. Two different types of crystalline arrays of CRP were obtained, by specific binding and non-specific adsorption to the lipids. Electron crystallographic analysis of the negatively stained specimens showed that the unit cell parameters of the CRP 2D crystals formed by specific binding were a=81 angstroms, b=78 angstroms, gamma=118.35 degrees, and those formed by nonspecific adsorption were a=74 angstroms, b=67 angstroms, gamma=95.5 degrees, both with the layer group p1. Projection maps were obtained at a resolution of 26 angstroms and 22 angstroms respectively. They showed that only the monomers of the CRP were packed in the 2D arrays and the orientations of the monomers on the lipid monolayers were different in the two types of crystals. By comparing the two projection maps, a preliminary shape of the CRP monomer has been derived. A model of the pentameric structure of the oligomeric CRP has been proposed.

Two-dimensional protein crystallization via metal-ion coordination by naturally occurring surface histidines

A powerful and potentially general approach to the targeting and crystallization of proteins on lipid interfaces through coordination of surface histidine residues to lipid-chelated divalent metal ions is presented. This approach, which should be applicable to the crystallization of a wide range of naturally occurring or engineered proteins, is illustrated here by the crystallization of streptavidin on a monolayer of an iminodiacetate-Cu(II) lipid spread at the air-water interface. This method allows control of the protein orientation at interfaces, which is significant for the facile production of highly ordered protein arrays and for electron density mapping in structural analysis of two-dimensional crystals. Binding of native streptavidin to the iminodiacetate-Cu lipids occurs via His-87, located on the protein surface near the biotin binding pocket. The two-dimensional streptavidin crystals show a previously undescribed microscopic shape that differs from that of crystals formed beneath biotinylated lipids.

Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme

The structure of E. coli core RNA polymerase (RNAP) has been determined to approximately 23 A resolution by three-dimensional reconstruction from electron micrographs of flattened helical crystals. The structure reveals extensive conformational changes when compared with the previously determined E. coli RNAP holoenzyme structure, but resembles the yeast RNAPII structure. While each of these structures contains a thumb-like projection surrounding a channel 25 A in diameter, the E. coli RNAP holoenzyme thumb defines a deep but open groove on the molecule, whereas the thumb of E. coli core and yeast RNAPII form part of a ring that surrounds the channel. This may define promoter-binding and elongation conformations of RNAP, as E. coli holoenzyme recognizes promoter sites on double-stranded DNA, while both E. coli core and yeast RNAPII are elongating forms of the polymerase and are incapable of promoter recognition.

Epitaxial growth of protein crystals from two-dimensional crystals on lipid layers

Two-dimensional crystals of proteins formed on lipid layers effectively nucleate the epitaxial growth of three-dimensional protein crystals. Crystals suitable for X-ray crystallography can be grown in this way more rapidly, and using substantially lower concentrations of protein and precipitants, than when using conventional methods.

Formation of two-dimensional complexes of F-actin and crosslinking proteins on lipid monolayers: demonstration of unipolar alpha-actinin-F-actin crosslinking

A method is described for forming two-dimensional (2-D) paracrystalline complexes of F-actin and bundling/gelation proteins on positively charged lipid monolayers. These arrays facilitate detailed structural studies of protein interactions with F-actin by eliminating superposition effects present in 3-D bundles. Bundles of F-actin have been produced using the glycolytic enzymes aldolase and glyceraldehyde-3-phosphate dehydrogenase, the cytoskeletal protein erythrocyte adducin as well as smooth muscle alpha-actinin from chicken gizzard. All of the 2-D bundles formed contain F-actin with a 13/6 helical structure. F-actin-aldolase bundles have an interfilament spacing of 12.6 nm and a superlattice arrangement of actin filaments that can be explained by expression of a local twofold axis in the neighborhood of the aldolase. Well ordered F-actin-alpha-actinin 2-D bundles have an interfilament spacing of 36 nm and contain crosslinks 33 nm in length angled approximately 25-35 degrees to the filament axis. Images and optical diffraction patterns of these bundles suggest that they consist of parallel, unipolar arrays of actin filaments. This observation is consistent with an actin crosslinking function at adhesion plaques where actin filaments are bound to the cell membrane with uniform polarity.

Langmuir-Blodgett films

The controlled transfer of organized monolayers of amphiphilic molecules from the airwater interface to a solid substrate was the first molecular-scale technology for the creation of new materials. However, the potential benefits of the technology envisioned by Langmuir and Blodgett in the 1930s have yet to be fully realized. Problems of reproducibility and defects and the lack of basic understanding of the packing of complex molecules in thin films have continued to thwart practical applications of Langmuir-Blodgett films and devices made from such films. However, modern high-resolution x-ray diffraction and scanning probe microscopy have proven to be ideal tools to resolve many of the basic questions involving thin organic films. Here, studies are presented of molecular order and organization in thin films of fatty acid salts, the prototypical system of Katharine Blodgett. Even these relatively simple systems present liquid, hexatic, and crystalline order; van der Waals and strained layer epitaxy on various substrates; wide variations in crystal symmetry and interfacial area with counterions; modulated superstructures; and coexisting lattice structures. The wide variety of possible structures presents both a challenge and an opportunity for future molecular design of organic thin-film devices.

High-resolution electron crystallography of protein molecules

Electron diffraction data and high-resolution images can now be used to obtain accurate, three-dimensional density maps of biological macromolecules. These density maps can be interpreted by building an atomic-resolution model of the structure into the experimental density. The Cowley-Moodie formalism of dynamical diffraction theory has been used to validate the use of kinematic diffraction theory (strictly, the weak phase object approximation) in producing such 3D density maps. Further improvements in the preparation of very flat (planar) specimens and in the retention of diffraction to a resolution of 0.2 nm or better could result in electron crystallography becoming as important a technique as X-ray crystallography currently is for the field of structural molecular biology.

Two-dimensional crystallization of catalase on a monolayer film of poly(1-benzyl-L-histidine) spread at the air/water interface

Two-dimensional (2D) crystals of beef liver catalase were prepared by adsorption to a film of synthetic polypeptide, poly(1-benzyl-L-histidine) (PBLH), spread at the air/water interface. The crystallization experiments were carried out in the pH range of 4.8-6.4 for catalase solutions at low concentration (10 micrograms/ml). The pH-dependence suggested an electrostatic interaction in the binding of catalase to the PBLH film. At lower pH, small crystals were formed at a low binding rate, and at higher pH the binding was rapid and densely-packed 2D arrays with poor crystallinity were formed. To stimulate crystal growth, a thermal treatment was applied. One-shot heating of the interfacial catalase-PBLH film to 35-40 degrees C was remarkably effective to form larger 2D crystals. The structure of catalase 2D crystals has been analyzed by Fourier filtering of the transmission electron micrographs. The crystal form is a new one, containing four catalase molecules in the unit cell with lattice parameters of alpha = 187 A, b = 225 A and gamma = 92.8 degrees.

2D crystallization: from art to science

The techniques as well as the principles of the 2D crystallization of membrane and water-soluble proteins for electron crystallography are reviewed. First, the biophysics of the interactions between proteins, lipids and detergents is surveyed. Second, crystallization of membrane proteins in situ and by reconstitution methods is discussed, and the various factors involved are addressed. Third, we elaborate on the 2D crystallization of water-soluble proteins, both in solution and at interfaces, such as lipid monolayers, mica, carbon film or mercury surfaces. Finally, techniques and instrumentations that are required for 2D crystallization are described.

Specimen flatness of thin crystalline arrays: influence of the substrate

The extreme degree of specimen flatness (i.e. planarity) required for high-resolution electron diffraction and electron microscopy at high tilt angles cannot be realized with thin, sheet-like crystals of biological macromolecules, just on the basis of the intrinsic stiffness of the specimen itself. In an effort to improve the rate of success at which suitably flat specimens are prepared, this paper analyzes several different factors that can either limit or enhance the specimen flatness. If specimens are adsorbed (by attractive forces) to a support film, such as evaporated carbon, which itself is not flat to atomic dimensions, quantitative calculations show that it is quite likely that the specimen will be too wrinkled to be used for high-resolution studies. Adsorption to an air-water interface is more likely to result in the necessary degree of flatness. Repulsive interactions, which might be used to "sandwich" a specimen between two interfaces, are estimated to be too "soft", i.e. too long-range in character, to be effective. Finally, if only one edge of a specimen sticks firmly to a substrate, then surface tension forces can pull the specimen taut over the surface of the substrate, so that the specimen itself can be more flat than the surface of the substrate upon which it is deposited. A second, important consideration in many studies is the fact that cooling the specimen to low temperature can result in specimen wrinkling, because of the fact that the biological crystal has a much larger coefficient of thermal expansion than that of the evaporated carbon film. In this case one expects that cooling-induced wrinkling might be reduced by using a metal support grid which has a smaller thermal coefficient than that of the carbon film. The validity of this qualitative idea is supported by experiments which show that cooling-induced wrinkling of glucose-embedded purple membrane can be prevented if molybdenum grids are used rather than copper.

Electrodeposition procedure of E. coli RNA polymerase onto gold and deposition of E. coli RNA polymerase onto mica for observation with scanning force microscopy

Molecules of the transcriptional enzyme E. coli RNA polymerase (RNAP) have been deposited using three different deposition methods: (1) passive adsorption onto gold, (2) electrochemical adsorption onto gold and (3) adsorption onto mica. In all cases SFM imaging was straightforward and reliable, and surface coverage by the protein varied with deposition conditions as expected. To determine the nature of the electrochemical treatment on the gold substrate, cyclic voltammetry was performed with various chemical solutions. Finally, a comparison is made between the SFM images of RNAP obtained with these methods and STM images obtained earlier. Both STM and SFM show strikingly similar results; however, heights and widths of individual molecules differ.

Two-dimensional and epitaxial crystallization of a mutant form of yeast RNA polymerase II

A mutant form of yeast RNA polymerase II that lacks the fourth and seventh largest subunits, referred to as pol II delta 4/7, crystallized on positively charged lipid layers. Both single-layered (two-dimensional) crystals and several multi-layered crystal forms were obtained. The two-dimensional crystals, preserved in negative stain, diffracted strongly to about 1/20 A-1 and more weakly to 1/13 A-1 resolution. A projection map computed from averaged Fourier transforms revealed four pol II delta 4/7 complexes per unit cell and further revealed a cleft on the surface of the complex similar to that previously observed in the structure of Escherichia coli RNA polymerase. One of the multi-layered crystal forms, preserved in negative stain, diffracted strongly beyond 1/15 A-1 resolution. Coherent diffraction from the multi-layered crystal is indicative of protein-protein interactions between layers and ordering in the third dimension.

Structural analysis of two-dimensional arrays of cholera toxin B-subunit

Two-dimensional arrays of cholera toxin B-subunit (CTB) have been obtained by specific interaction with lipid films, as described by Ludwig et al. (1986). The relationship between two types of array, of either rectangular or hexagonal geometry, was analyzed using crystallographic methods of electron image analysis. Our results showed that the type of array obtained was highly dependent on the negative stain used and that both arrays presented related lattice parameters, indicating that they originated from a common unstained structure. Image analysis of hexagonal arrays at 17 A resolution revealed variable CTB projected structures, ranging from annularly symmetric particles to highly asymmetric particles, very distinct from the pentameric structure resolved from rectangular crystals. The present data suggest that hexagonal arrays result from an imperfect staining of CTB rectangular crystals. The staining distortion is such that the stain layer does not match faithfully the pentameric protein distribution whereas the regular organization of the specimen is maintained.

Three-dimensional structure of yeast RNA polymerase II at 16 A resolution

The structure of yeast RNA polymerase II has been determined by three-dimensional reconstruction from electron micrographs of two-dimensional crystals at approximately 16 A resolution. The most prominent feature of the structure is an arm of protein density surrounding a channel about 25 A in diameter, similar to that found previously for E. coli RNA polymerase. The 25 A-diameter channel bifurcates on one face of the protein, connecting with a 25 A-wide groove and with a channel about half as wide. The 25 A channel and groove, and the narrow channel, may bind double- and single-stranded nucleic acids, respectively. A finger of protein density projecting from the molecule adjacent to the arm-like feature may represent the C-terminal domain of the largest subunit. These results provide a structural basis for analyses of the transcription process and its regulation.

Improved transfer of two-dimensional crystals from the air/water interface to specimen support grids for high-resolution analysis by electron microscopy

Electron crystallographic analysis of two-dimensional crystals grown on lipid layers at the air/water interface has been limited by loss or damage during transfer of the crystals to an electron microscope support grid. Two methods of transfer are described which are applicable on a small scale (10 microliters of protein solution) and which give greatly improved results for streptavidin crystals on biotinylated lipid layers. In the first method, a hydrophobic grid surface was produced by coating a carbon support film with a thin layer of SiO2, followed by alkylation with dimethyloctadecylchlorosilane. The transfer efficiency of protein crystals approached 50% coverage of the alkylated grid surface. The degree of order of crystals transferred to the alkylated grid surface and preserved in negative stain was significantly improved over that of crystals transferred directly to a carbon support film. In the second method, crystals at the air/water interface were transferred to a holey carbon support film. The efficiency of transfer across the holes was virtually 100% as nearly every hole was completely covered with crystals. After preservation of the crystals in 1% glucose and cooling to liquid nitrogen temperature, electron diffraction was obtained that extended to 1/2.8 A-1 resolution. This demonstrates that two-dimensional crystals grown on lipid layers at the air/water interface can be sufficiently well-ordered, even after transfer to a support grid, to yield high-resolution structural information.

Two-dimensional crystals of streptavidin on biotinylated lipid layers and their interactions with biotinylated macromolecules

Streptavidin forms two-dimensional crystals when specifically bound to layers of biotinylated lipids at the air/water interface. The three-dimensional structure of streptavidin determined from the crystals by electron crystallography corresponds well with the structure determined by x-ray crystallography. Comparison of the electron and x-ray crystallographic structures reveals the occurrence of free biotin-binding sites on the surface of the two-dimensional crystals facing the aqueous solution. The free biotin-binding sites could be specifically labeled with biotinylated ferritin. The streptavidin/biotinylated lipid system may provide a general approach for the formation of two-dimensional crystals of biotinylated macromolecules.