J. Piefke

Crystallization of Escherichia coli ribosomes

The knowledge of the structure of the ribosome is an essential requirement to reveal its role at the molecular level in the process of protein biosynthesis. This information is being obtained by a battery of chemical, physical, immunological and genetic methods (for reviews see [1]). Important methods for the study of the three-dimensional structure of the ribosomes are X-ray crystallography and image reconstruction. Two-dimensional ordered sheets of ribosomes from a few eukaryotic species are found under special conditions in vivo [2-4] or in cell homogenates [5]. Small two-dimensional arrays of E. coli ribosomal subunits were obtained in vitro [6,7]. The first three-dimensional crystals of ribosomal particles were obtained in vitro from the large subunit of the Bacillus stearothermophilus ribosome [8,9]. These have been characterized by three-dimensional image reconstruction studies [10]. Here we report the in vitro crystallization of E. coli ribosomes. We have obtained ordered threedimensional microcrystals. After washing and redissolving, the crystalline ribosomes sediment with a coefficient of 70 S in a sucrose gradient and are biologically active in the poly(U) in vitro system. Electron micrographs of thin sections of the crystals show regular arrangement of the ribosomes, and their optical diffraction patterns extend out to about 6.5 nm. Thus three-dimensional image reconstruction studies can be carried out. 2. MATERIALS AND METHODS

Crystals of complexes mimicking protein biosynthesis are suitable for crystallographic studies.

A complex of 70S ribosomes from Thermus thermophilus together with an average of 1.5-1.8 equivalents of PhetRNA(Phe) and a short mRNA chain, composed of 35 +/- 5 uridines, was crystallized under the conditions used for the growth of crystals of isolated ribosomes from the same source. Considering the reproducibility of their growth, their internal order and their shape, the crystals of the complex are superior to those of isolated ribosomes. In accord with previous three-dimensional reconstruction and modeling experiments, we conclude that the complex is less flexible and that an average population of complexes is more homogeneous than that of isolated 70S ribosomes. The crystals of the complex diffract to higher than 15 A resolution and can be irradiated with synchrotron X-ray beam at cryo-temperatures for days without noticeable decay. Since the crystals of the complex are apparently isomorphous with these of the isolated 70S ribosomes (P4(1)2(1)2; a = b = 526; c = 315 A), they should provide tool for phasing as well as for locating the mRNA and tRNA binding sites.

Characterization of single crystals of the large ribosomal particles from Bacillus stearothermophilus

Single, three-dimensional crystals of the 50 S ribosomal subunit from Bacillus stearothermophilus (strain NCA) have been characterized using a synchrotron X-ray source. The crystals are orthorhombic with unit cell dimensions: a = 350 A, b = 670 A, c = 905 A, and contain at least one 2-fold screw axis. With cooling to -2 degrees C, the large crystals (1.0 mm X 0.2 mm X 0.1 mm) diffract to 15 to 18 A resolution and are stable in the synchrotron beam for several hours. Despite the large cell dimensions, the reflections are readily resolved when the X-ray diffraction patterns are densitometered with a 25 microns faster.

Three-dimensional image reconstruction from ordered arrays of 70S ribosomes

A better understanding of the molecular mechanism of protein biosynthesis still awaits a reliable model for the ribosomal particle. We describe here the application of a diffraction technique, namely three-dimensional image reconstruction from two-dimensional sheets of 70S ribosomes from Bacillus stearothermophilus at 47 A resolution. The three-dimensional model obtained by these studies shows clearly the two subunits, the contact points between them, an empty space large enough to accommodate the components of protein biosynthesis, the location of regions rich in RNA and a possible binding site for mRNA. The tunnel within the 50S particle which may provide the path taken by the nascent polypeptide chain in partially resolved.

Two-dimensional crystalline sheets of Bacillus stearothermophilus 50S ribosomal subunits containing a nascent polypeptide chain

Polylysine chains were synthesized on Bacillus stearothermophilus ribosomes in a poly(A)-programmed in vitro system. After separation of the ribosomal subunits by sucrose gradient centrifugation, the polylysine chains (in contrast to the polyphenylalanine chains synthesized in a poly(U) system) reproducibly remained attached to the large ribosomal subunit. It was possible to produce two-dimensional crystalline sheets from the large ribosomal subunits containing the polylysine chains. These sheets are an essential prerequisite for three-dimensional reconstruction studies aiming to show that the tunnel in the large ribosomal subunit provides a path for the nascent polypeptide chain.

The growth of ordered two-dimensional sheets of 70 S ribosomes from Bacillus stearothermophilus

Well ordered two‐dimensional sheets of intact 70 S ribosomes from Bacillus stearothermophilus have been obtained in vitro using salt‐alcohol mixtures. These sheets consist of relatively small unit cells with dimensions of 200 ± 20 Å and 400 ± 30 Å. Diffraction patterns of electron micrographs of these sheets stained with uranyl acetate contain features to 42 Å resolution.

A compact three-dimensional crystal form of the large ribosomal subunit from Bacillus stearothermophilus

A new form of well‐ordered three‐dimensional crystals of intact 50 S ribosomal subunits from Bacillus stearothermophilus have been obtained. Electron micrographs of positively stained sections of these crystals revealed that the ribosomal particles are packed closely. The cell parameters have been determined. Representative electron micrographs and their computed contoured filtered images are shown.

Crystallographic, biochemical and genetic studies on halophilic ribosomes

Summary Ribosomal particles from Haloarcula marismortui were crystallized. The best crystals, diffracting to 2.9 A resolution and yielding crystallographic data of reasonable quality were grown from the large ribosomal subunits. Attempts at crystallization of functional ribosomal complexes are in progress, benefiting from experience gained from crystals of ribosomes of an extreme thermophilic bacterium, Thermus thermophilus . For obtaining phase information, a monofunctional reagent was prepared from an undecagold cluster, by attaching to it a chemically reactive handle, specific for sulfhydryl moieties. Heavy atom derivatives were prepared by binding this cluster to exposed sulfhydryls prior to the crystallization. Cores of halophilic ribosomal particles, lacking four ribosomal proteins, were prepared using dioxane. All detached proteins could be fully reconstituted. However, blocking the -SH group of one of them (HmaL11), prevented its incorporation into the core particles. The so obtained depleted 50S subunits crystallize under the same conditions as native ones and show apparent isomorphism with them. Most of the genes of several r-proteins were cloned. These are being used for sequencing as well as for providing new locations for binding heavy atom clusters by genetic insertion of cysteines on the ribosomal surface, according to accessibility data, obtained either chemically or by limited proteolysis. A nucleoprotein complex of protein HmaL1 and a fragment of the 23S rRNA was isolated from ribosomes. Chimeric complexes were reconstituted with E. coli ribosomal components, indicating rather high homolgy, despite the evolution distance.

The growth of ordered two-dimensional sheets of ribosomal particles from salt-alcohol mixtures

A procedure for the in vitro growth of well-ordered two-dimensional sheets from ribosomal particles using salts and salt-alcohol mixtures has been developed. Employing this procedure, ordered two-dimensional sheets of the wild type as well as of mutated 50 S ribosomal subunits from Bacillus stearothermophilus can readily be obtained. These sheets, stained with uranyl acetate or gold-thioglucose, are suitable for three-dimensional image reconstruction. They consist of relatively small unit cells with dimensions of 160 +/- 15 and 365 +/- 20 A. Diffraction patterns of electron micrographs of these sheets contain features to 25 A resolution.