Singlet energy transfer studies of the arrangement of proteins in the 30 S Escherichia coli ribosome

Topography of ribosomes and initiation complexes from rat liver as revealed by atomic force microscopy

Atomic force microscopy (AFM) was used to image ribosomes and ribosomal subunits (60S, 40S and native 40S ribosomal subunits) isolated from rat liver. A variety of topographic images were obtained directly and found to be consistent with models established by other biophysical methods. In addition, the ternary complex of eIF-2 x GTP x Met-tRNA(i) and the 43S preinitiation complex have been discerned by AFM directly. Detailed information about the binding sites for eIF-1A, eIF-2, eIF-3, and Met-tRNA(i) on the 40S ribosomal subunit was derived from the AFM images. Finally, factors which may give rise to artifactual images, namely, convolution of the AFM tip on ribosomes, surface tension collapse effect and dehydration, are discussed. This work demonstrates that AFM is useful for imaging ribosomes and translational complexes and provides valuable information that can be used to complement other well-established techniques.

Assembly of the Escherichia coli 30S ribosomal subunit reveals protein-dependent folding of the 16S rRNA domains

Protein-nucleic acid interactions involved in the assembly process of the Escherichia coli 30S ribosomal subunit were quantitatively analyzed by high-resolution scanning transmission electron microscopy. The in vitro reconstituted ribonucleoprotein (core) particles were characterized by their morphology, mass, and radii of gyration. During the assembly of the 30S subunit, the 16S rRNA underwent significant conformational changes that were governed by the cooperative interactions of the ribosomal proteins. The sequential association of the first 12 proteins with the 16S rRNA resulted in the formation of core particles containing up to three mass centers at distinct stages of the assembly process. These globular mass centers may correspond to the three major domains (5', central, and 3') of the 16S rRNA. Through the subsequent interactions of the late assembly proteins with the 16S rRNA, two of the three domains merge, yielding the basic structural traits of the native 30S subunit. The fine morphological features of the native 30S subunit became distinctly resolved only after the addition of the full complement of proteins. The fully reconstituted 30S subunits are active in polyphenylalanine synthesis assays. Visualization of the assembly mechanism of the E. coli 30S ribosomal subunit revealed domain-specific folding of the 16S rRNA through the formation of distinct intermediate core particles hitherto not observed.

Structural elements in RNA

This chapter describes the RNA structural characteristics that have emerged so far. Folded RNA molecules are stabilized by a variety of interactions, the most prevalent of which are stacking and hydrogen bonding between bases. Many interactions among backbone atoms also occur in the structure of tRNA, although they are often ignored when considering RNA structure because they are not as well-characterized as interactions among bases. Backbone interactions include hydrogen bonding and the stacking of sugar or phosphate groups with bases or with other sugar and phosphate groups. The interactions found in a three-dimensional RNA structure can be divided into two categories: secondary interactions and tertiary interactions. This division is useful for several reasons. Secondary structures are routinely determined by a combination of techniques discussed in chapter, whereas tertiary interactions are more difficult to determine. Computer algorithms that generate RNA structures can search completely through possible secondary structures, but the inclusion of tertiary interactions makes a complete search of possible structures impractical for RNA molecules even as small as tRNA. The division of RNA structure into building blocks consisting of secondary or tertiary interactions makes it easier to describe RNA structures. In those cases in which RNA studies are incomplete, the studies of DNA are described with the rationalization that RNA structures may be analogous to DNA structures, or that the techniques used to study DNA could be applied to the analogous RNA structures. The chapter focuses on the aspects of RNA structure that affect the three-dimensional shape of RNA and that affect its ability to interact with other molecules.

Distances as degrees of freedom

Tertiary contact distance information of varying resolution for large biological molecules abounds in the literature. The results provided herein develop a framework by which information of this type can be used to reduce the allowable configuration space of a macromolecule. The approach combines graph theory and distance geometry. Large molecules are represented as simple, undirected graphs, with atoms, or groups, as vertices, and distances between them as edges. It is shown that determination of the exact structure of a molecule in three dimensions only requires the specification of all the distances in a single tetrahedron, and four distances to every other atom. This is 4N-10 distances which is a subset of the total N(N-1)/2 unique distances in a molecule consisting of N atoms. This requirement for only 4N-10 distances has serious implications for distance geometry implementations in which all N(N-1)/2 distances are specified by bounded random numbers. Such distance matrices represent overspecified systems which when solved lead to non-obvious distribution of any error caused by inherent contradictions in the input data. It is also shown that numerous valid subsets of 4N-10 distances can be constructed. It is thus possible to tailor a subset of distances using all known distances as degrees of freedom, and thereby reduce the configuration space of the molecule. Simple algebraic relationships are derived that relate sets of distances, and complicated rotations are avoided. These relationships are used to construct minimum, complete sets of distances necessary to specify the exact structure of the entire molecule in three dimensions from incomplete distance information, and to identify sets of inconsistent distances. The method is illustrated for the flexible structural types present in large ribosomal RNAs: 1.) A five-membered ring; 2.) a chemically bonded chain with its ends in contact (i.e., a hairpin loop); 3.) the spatial orientation of two separate molecules, and; 4.) an RNA helix that can have variation in individual base pairs, giving rise to global deviation from standardized helical forms.

Positions of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit of Escherichia coli

Neutron scattering distance data are presented for 33 protein pairs in the 30 S ribosomal subunit from Escherichia coli, along with the methods used for measuring distances between its exchangeable components. When combined with prior data, these new results permit the positioning of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit, completing the mapping of its proteins by neutron scattering. Comparisons with other data suggest that the neutron map is a reliable guide to the quaternary structure of the 30 S subunit.

A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli

The relative positions of the centers of mass of the 21 proteins of the 30S ribosomal subunit from Escherichia coli have been determined by triangulation using neutron scattering data. The resulting map of the quaternary structure of the small ribosomal subunit is presented, and comparisons are made with structural data from other sources.

Structure of ribosome-bound messenger RNA as revealed by enzymatic accessibility studies

Digestion with ribonuclease T2 has been used to study the size of poly(U) protected by ribosome binding. Several different preparations of ribosomes all appear to cover 49 nucleotides of message; however, there are two partially accessible internal nuclease cleavage sites, which yield, ultimately, fragments 20, 16 and 13 nucleotides in length. Curiously, the site between fragments of length 20 and 16 is accessible to RNase T2 but not to the several much smaller RNases. Arguments based on the quantitative pattern of cleavage and comparisons with previous studies lead to the conclusion that the 20-mer is the 5' fragment, while 13-mer (which is lost the moment it is cleaved from the 16-mer) is the 3' fragment. Both ribosome-bound tRNAs appear to contact only the 16-mer. The presence of the two internal cleavage sites fits nicely with recent electron microscopic data suggesting that mRNA forms a loop around the 30 S subunit.

Location of protein S4 on the small ribosomal subunit of E. coli and B. stearothermophilus with protein- and hapten-specific antibodies

In spite of considerable effort there is still serious disagreement in the literature about the question of whether epitopes of ribosomal protein S4 are accessible for antibody binding on the intact small ribosomal subunit. We have attempted to resolve this issue using three independent approaches: (i) a re-investigation of the exposure and the location of epitopes of ribosomal protein S4 on the surface of the 30S subunit and 30S core particles of the E. coli ribosome, including rigorous controls of antibody specificity, (ii) a similar investigation of protein S4 from Bacillus stearothermophilus and (iii) the labelling of residue Cys-31 of E. coli S4 with a fluorescein derivative the accessibility of which towards a fluorescein-specific antibody was demonstrated directly by fluorimetry. In each of the three cases the antigen (E. coli S4, B. stearothermophilus S4 or fluorescein) was found to reside on the small lobe.

Positions of proteins S14, S18 and S20 in the 30 S ribosomal subunit of Escherichia coli

A map of the 30 S ribosomal subunit is presented giving the positions of 15 of its 21 proteins. The components located in the map are S1, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S14, S15, S18 and S20.

Distance measurement by energy transfer. Ribosomal proteins L6, L10 and L11 of Escherichia coli

Ribosomal proteins L6, L11 and the complex [(L12)4 X L10] were labelled specifically at their respective single thiol groups, either with the acetylaminoethyl-dansyl or with the acetamidofluorescein fluorophore. The labelled proteins were then reconstituted, singly or in pairs, into ribosomal 50S subunits; the presence of the label had no observable effect on the composition, shape or activity of the reconstituted subunits. The distances between the labelled thiol groups were measured by a fluorescence energy transfer method detailed elsewhere [Epe, B. et al. (1983) Proc. Natl Acad. Sci. USA, 80, 2579-2583] and were found to be: for L6-L10, 60 A (6.0 nm); for L6-L11, 46 A (4.6 nm); for L10-L11, 56 A (5.6 nm). Reversal of the direction of energy transfer by exchanging labels gave duplicate distances which differed, on average, by about 4%. The distance between the fluorescent labels on L10 and L11 in the [23 S-RNA X L10 X L11 X (L12)4] ribonucleoprotein complex was the same as in the 50S subunit, but all three distances were greater in 50S subunits which had been reconstituted without the final activation step (incubation at 50 degrees C). This suggests a tightening of the L6/L10/L11 domain of the 50S subunit during the activation step.

Structural arrangement of the proteinase binding sites in human alpha 2-macroglobulin

Using singlet-singlet energy transfer measurements with labeled-chymotrypsin-alpha 2-macroglobulin complexes, we find that the two proteinase binding sites of alpha 2-macroglobulin are separated from each other by 44 A. The free thiol groups generated upon reaction of alpha 2-macroglobulin with trypsin or chymotrypsin react with thiopropyl Sepharose, indicating that they are located at the surface of the complexes. Singlet-singlet energy transfer experiments from labeled proteinases to labeled thiols of alpha 2-macroglobulin show that the thiol groups are in close contact with the proteinase molecules whether the latter are covalently or noncovalently bound to alpha 2-macroglobulin. In addition, they are remote from the association interface between the Mr = 360,000 halves of alpha 2-macroglobulin. Using the same approach we demonstrate that the active sites of chymotrypsin molecules are separated by a distance of at least 20 A from the thiols group of each alpha 2-macroglobulin subunit.

Immunoelectron microscopy of ribosomes carrying a fluorescence label in a defined position. Location of proteins S17 and L6 in the ribosome of Escherichia coli

By coupling fluorescein to a defined amino acid of a single ribosomal protein and incorporating this protein into the ribosome, we have obtained ribosomes labelled at a single, defined position. A fluorescein-specific antibody preparation was used to locate the fluorescein residues bound to the two cysteines at positions 58 and 63 of protein S17 and to the cysteine at position 86 of protein L6. This study demonstrates the advantages which accrue from the combination of electron microscopy and fluorimetry.

Structural arrangement in the alpha 2-macroglobulin--thrombin complex

The cysteine sulfhydryl groups of alpha 2-macroglobulin (alpha 2M) generated upon thrombin complex formation are in contact with the proteinase surface as evidenced by singlet--singlet energy transfer measurements from N-(iodoacetylaminoethyl)-5-naphthylamine-1-sulfonic acid-labeled thiol functions of alpha 2M to fluorescein isothiocyanate-labeled thrombin. The thrombin-alpha 2M binding is normally covalent, but the presence of hydroxylamine during the reaction leads to the formation of a non-covalent complex. The transfer energy determinations show that the alpha 2M binding sites of thrombin are quite similar, whatever covalent or non-covalent binding occurs.

Localization of the proteinase-induced thiol groups in alpha 2-macroglobulin

Free thiol groups released on proteolytic attack of alpha 2-macroglobulin by trypsin or chymotrypsin bind covalently to thiopropyl-Sepharose, indicating that they are located at the surface of the complexes. These cysteine sulfhydryl groups appear to be in contact with the alpha 2M-bound proteases from singlet-singlet energy transfer measurements between fluorescein isothiocyanate-labeled proteinases and N-(iodoacetylaminoethyl)-5-naphtylamine-1-sulfonic acid-labeled thiols in alpha 2-macroglobulin.

Distance measurement by energy transfer: the 3' end of 16-S RNA and proteins S4 and S17 of the ribosome of Escherichia coli

Escherichia coli ribosomal proteins S4 and S17 were specifically labelled at their thiol groups with the acetylaminoethyl-dansyl and/or bimane fluorophores. Each formed a complex with 16-S RNA and, when the other 30-S ribosomal proteins were added, a complete 30-S subunit with at least partial activity. If the 3' end of the RNA was also labelled (with fluorescein) then the distance between the two fluorophores could be measured by Förster-type energy transfer. The result for S4 was 6.0 nm (60 A) in the ribonucleoprotein complex and 5.6 nm (56 A) in the 30-S subunit, and for S17 6.3 nm (63 A) in the complex and 6.2 nm (62 A) in the subunit. There is no evidence for a major change in the relative disposition of the 3' and 5' ends of the 16-S RNA during formation of the 30-S subunit. Sources of error are discussed, including the question of multiple labelling. In order to measure more accurately the extent of energy transfer a procedure based upon enzymic digestion was developed and is detailed in this paper.

Secondary structure of 16S ribosomal RNA

A secondary structure model for 16S ribosomal RNA which is based on available chemical, enzymatic, and comparative sequence data shows good agreement between constraints dictated by the model and a wide variety of experimental observations. The four major structural domains created by the base-pairing scheme correspond closely to RNA fragments isolated after nuclease digestion in the presence of bound ribosomal proteins. Functionally important sites appear to be located in unpaired regions and are phylogenetically highly conserved.

Effect of DNA length on the nucleosome low salt transition

The effect of DNA length on the low salt unfolding transition of nucleosomes has been studied by the use of fluorescently labeled histones. Nucleosomes were formed by the reconstitution of bulk DNA fragments averaging 173 and 250 base pairs in length. These nucleosomes exhibited a conformational change in a transition centered at about 7 mM ionic strength, very different from that observed for the standard 145 bp nucleosomes (1-3mM). In addition, the conformational change of the 173 and 250 bp nucleosomes involves twice as many ions as that of the 145 bp nucleosomes.

Analysis of protein--protein relationships in 30S ribosome assembly intermediates using protection from proteolytic digestion

Treatment of the intact bacterial ribosome with proteolytic enzymes results in little or no digestion of many of the component proteins [Craven, G. R., & Gupta, V. (1970) Proc. Natl. Acad. Sci. U.S.A. 67, 1329]. In contrast, when the proteins are released from the constraints of ribosome structure they become completely susceptible to proteolytic attack. We have attempted to exploit these observations in an effort to determine the precise steps in ribosome assembly which result in a conversion of the structures of the various proteins from a proteolysis sensitive to a resistant form. Thus, a total of 11 30S ribosome assembly intermediate complexes of proteins and 16S RNA were prepared and digested with trypsin or chymotrypsin. The kinetics of digestion of each protein in the complex were followed by polyacrylamide gel electrophoresis. By a comparison of the digestion pattern of two complexes differing only by the presence of a single protein, it was possible to deduce several specific protective effects of one protein on its neighbor in the complex. On the basis of these studies, we propose nine protein-protein protective effects. The possible relevance of these interrelationships to other well-established proximity relationships is discussed.

A new method for the purification of 30S ribosomal proteins from Escherichia coli using nondenaturing conditions

A new method for the purification of Escherichia coli (A19) 30S ribosomal proteins has been developed that avoids the use of denaturing conditions such as urea, acetic acid, and lyophilization. In this way the majority of the proteins from the small ribosomal subunit can be obtained in 5--100 mg quantities and at greater than or equal to 90% purity. This has been achieved by the initial "splitting" of the proteins into two main groups with LiCl followed by fractionating on ion-exchange and gel-filtration columns, in the absence of urea and in the presence of salt. The proteins prepared by this nondenaturing procedure were soluble at high ionic strength and less soluble, being aggregated, at low salt concentrations. This behavior was exactly the opposite of that exhibited by proteins prepared with methods using denaturing conditions. These new methods have enabled additional ribosomal RNA-binding proteins to be found and potential protein-proteins complexes to be isolated. Preliminary evidence that these proteins may retain a more native structure is presented.