Three-Dimensional Organization of the 30S Ribosomal Proteins from
            <i>Escherichia coli</i>
            , I. Preliminary Classification of the Proteins

Craven, Gary R.; Gupta, Vatsala J.

doi:10.1073/pnas.67.3.1329

Cited by 50 publications

(6 citation statements)

References 16 publications

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“…As can be seen, the proteins of the 30S ribosome are remarkably resistant to either trypsin or chymotrypsin attack under the same conditions that TP30 is completely digested. Some proteins in the 30S particle are sensitive as has been previously detailed (Craven & Gupta, 1970; Chang & Flaks, 1970; Spitnik-Elson & Breiman, 1971; Crichton & Whittmann, 1971; Rummel & Noller, 1973). We interpret these results to mean that the macromolecular interactions inherent in the structure of the ribosome effectively protect the resistant proteins from proteolytic cleavage.…”

Section: Resultssupporting

confidence: 63%

“…Preparation of 30S Ribosomal Subunits and Purification of Ribosomal Proteins. Ribosomes were isolated from E. coli MRE 600, and 30S ribosomal subunits were purified from 70S ribosomes by zonal centrifugation as described by Craven & Gupta (1970). Ribosomal proteins were extracted from the purified 30S subunits with 67% acetic acid and further 0006-2960/79/0418-1275S01.00/0 © 1979 American Chemical Society fractionated by phosphocellulose column chromatography (Mannex-P,, high capacity) following the procedure described by Hardy et al (1969).…”

Section: Methodsmentioning

confidence: 99%

“…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.…”

mentioning

confidence: 99%

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

Changchien¹,

Craven²

1979

Biochemistry

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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.

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Section: Resultssupporting

confidence: 63%

Section: Methodsmentioning

confidence: 99%

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

Changchien¹,

Craven²

1979

Biochemistry

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“…One such problem is the folding of the ribosomal RNAs in functional ribosomes. Numerous studies have been employed to determine the spatial location of the ribosomal proteins including partial reconstitution studies (1,2), protection from chemical probes and enzymatic digestion (3)(4)(5), chemical crosslinking (6), immune electron microscopy (7,8) and most informatively, neutron diffraction (9). The rRNA itself can be partially folded as a result of predictive studies of secondary (10)(11)(12) and tertiary (13,14) structure as well as a variety of experiments that reveal protected and exposed regions.…”

Section: Introductionmentioning

confidence: 99%

Explicit Distance Geometry: Identification of all the Degrees of Freedom in a Large RNA Molecule

Hadwiger

Fox

1991

Journal of Biomolecular Structure and Dynamics

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An alternative approach to distance geometry ("explicit" distance geometry) is being developed for problems, such as the modeling of RNA folding in the ribosome, where relatively few distances are known. The approach explicitly identifies minimal sets of additional distances that can be added to a distance matrix in order to calculate structures that are consistent with all the known information without distorting the original input data. These additional distances are bounded to the extent possible by the known distances. These explicitly added distances can be treated as degrees of freedom and used to explore the full range of alternative foldings consistent with the original input in an organized way. The present paper establishes that it is practical to explicitly determine such degrees of freedom for even very large RNAs. To demonstrate the feasibility of the approach tRNA was represented as a simple undirected graph containing all relevant information represented in the usual cloverleaf secondary structure and nine base-base tertiary interactions. Using a three atom representation for each residue a total of 206 degrees of freedom are explicitly identified. To accomplish this a graph theoretic approach was used in which a minimal covering cycle basis was determined.

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“…A number of chemical and enzymic agents have been used to explore the topography of ribosomal subunits from Escherichia coli (Craven & Gupta, 1970;Chang & Flaks, 1970;Gavrilova & Spirin, 1974). Most of these are rather specific, however, and only react with a few of the 'surface' proteins of the particles (Wittmann & St6ffler, 1972).…”

mentioning

confidence: 99%

Enzymic iodination of eukaryotic ribosomal subunits. Characterization and analysis by two-dimensional gel electrophoresis

Leader

1975

Biochemical Journal

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1. Conditions are described for the enzymic iodination of ribosomal subunits from rat liver. The reaction is relatively insensitive to broad changes in the concentration of KCl, allowing subunits to be studied under conditions which minimize their dimerization. 2. Mixtures of extracted ribosomal proteins were iodinated with (125)I, the proteins separated by two-dimensional gel electrophoresis and the radioactivity in each protein was determined. Thus 19 out of 23 of the proteins of the small subunit and 25 out of 33 of the proteins of the large subunit were labelled. Iodination should therefore be a suitable method for studying the topography of the ribosomal proteins of rat liver. 3. When the intact 40S subunit (rather than the extracted mixture of proteins) was iodinated, 18 of the 19 proteins were still labelled. However five of these were labelled less strongly than before. When the intact 60S subunit was iodinated, 17 of the 25 proteins were still labelled, although six of these were labelled less strongly. 4. These results show that in rat liver most of the ribosomal proteins of both subunits are at least partially at the surface of the particles. They are also consistent with the idea that the proportion of the ribosomal proteins in the interior of the particle may be greater for the 60S subunit than for the 40S subunit.

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Three-Dimensional Organization of the 30S Ribosomal Proteins from Escherichia coli , I. Preliminary Classification of the Proteins

Cited by 50 publications

References 16 publications

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

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

Explicit Distance Geometry: Identification of all the Degrees of Freedom in a Large RNA Molecule

Enzymic iodination of eukaryotic ribosomal subunits. Characterization and analysis by two-dimensional gel electrophoresis

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