PROTEIN-RNA INTERACTIONS IN BACTERIAL RIBOSOMES

ABSTRACT There are several ribosomal proteins which can bind specifically to the three ribosomal RNA's of E. coli. Some structural properties of these proteins and of the RNA are described together with the optimal conditions for binding. Evidence for conformational changes occurring in some proteins, and in the RNA's during binding, is also discussed. The partial localisation of protein binding sites on the 16S and 5S RNA's, and for one protein on the 23S RNA has been attained recently. However, relatively little is known about the regions of the protein which interact with the RNA. Although the nature of the specificity of the protein-RNA interactions is not yet understood, some experimental approaches which are in progress to elucidate the basis of this specificity are mentioned together with a discussion of the structural factors which may be important.

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Ribosomal proteins. XXVI. The number of specific protein binding sites on 16 s and 23 s RNA of Escherichia coli

Journal of Molecular Biology ◽

10.1016/0022-2836(71)90437-2 ◽

1971 ◽

Vol 62 (2) ◽

pp. 411-414 ◽

Cited By ~ 53

Author(s):

G. Stöffler ◽

L. Daya ◽

K.H. Rak ◽

R.A. Garrett

Keyword(s):

Escherichia Coli ◽

Protein Binding ◽

Binding Sites ◽

Ribosomal Proteins ◽

Specific Protein ◽

Protein Binding Sites

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Identification of (η6-arene)ruthenium(II) protein binding sites in E. coli cells by combined multidimensional liquid chromatography and ESI tandem mass spectrometry: specific binding of [(η6-p-cymene)RuCl2(DMSO)] to stress-regulated proteins and to helicases

JBIC Journal of Biological Inorganic Chemistry ◽

10.1007/s00775-007-0242-x ◽

2007 ◽

Vol 12 (6) ◽

pp. 883-894 ◽

Cited By ~ 39

Author(s):

Joanna Will ◽

Andreas Kyas ◽

William S. Sheldrick ◽

Dirk Wolters

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Tandem Mass Spectrometry ◽

Protein Binding ◽

Binding Sites ◽

Specific Binding ◽

Tandem Mass ◽

Protein Binding Sites ◽

E Coli

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Differential BUM-HMM: a robust statistical modelling approach for detecting RNA flexibility changes in high-throughput structure probing data

10.1101/2020.07.30.229179 ◽

2020 ◽

Author(s):

Paolo Marangio ◽

Ka Ying Toby Law ◽

Guido Sanguinetti ◽

Sander Granneman

Keyword(s):

Protein Binding ◽

High Throughput ◽

Conformational Changes ◽

Binding Sites ◽

Rna Structure ◽

Structural Changes ◽

High Throughput Sequencing ◽

Structural Information ◽

Protein Binding Sites ◽

Structure Probing

Combining RNA structure probing with high-throughput sequencing technologies has greatly enhanced our ability to analyze RNA structure at transcriptome scale. However, the high level of noise and variability encountered in these data call for the development of computational tools that robustly extract RNA structural information. Here we present diffBUM-HMM, a noise-aware model that enables accurate detection of RNA flexibility and conformational changes from high-throughput RNA structure-probing data. DiffBUM-HMM is compatible with a wide variety of high-throughput RNA structure probing data, taking into consideration biological variation, sequence coverage and sequence representation biases. We demonstrate that, compared to the existing approaches, diffBUM-HMM displays higher sensitivity while calling virtually no false positives. DiffBUM-HMM analysis of ex vivo and in vivo Xist SHAPE-MaP data detected many more RNA structural differences, involving mostly single-stranded nucleotides located at or near protein-binding sites. Collectively, our analyses demonstrate the value of diffBUM-HMM for quantitatively detecting RNA structural changes and reinforce the notion that RNA structure probing is a very powerful tool for identifying protein-binding sites.

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Protein-induced conformational changes in 16S rRNA during assembly of the Escherichia Coli 30S ribosomal subunit: A STEM study

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100128833 ◽

1987 ◽

Vol 45 ◽

pp. 910-911

Author(s):

M. Boublik ◽

V. Mandiyan ◽

J.F. Hainfeld ◽

J.S. Wall

Keyword(s):

16S Rrna ◽

Conformational Changes ◽

Ribosomal Proteins ◽

Structural Changes ◽

Ribosomal Subunit ◽

Compact Structure ◽

E Coli ◽

Freeze Dried ◽

16S Rna ◽

30S Subunit

The aim of this study is to understand the mechanism of 16S rRNA folding into the compact structure of the small 30S subunit of E. coli ribosome. The assembly of the 30S E. coli ribosomal subunit is a sequence of specific interactions of 16S rRNA with 21 ribosomal proteins (S1-S21). Using dedicated high resolution STEM we have monitored structural changes induced in 16S rRNA by the proteins S4, S8, S15 and S20 which are involved in the initial steps of 30S subunit assembly. S4 is the first protein to bind directly and stoichiometrically to 16S rRNA. Direct binding also occurs individually between 16S RNA and S8 and S15. However, binding of S20 requires the presence of S4 and S8. The RNA-protein complexes are prepared by the standard reconstitution procedure, dialyzed against 60 mM KCl, 2 mM Mg(OAc)2, 10 mM-Hepes-KOH pH 7.5 (Buffer A), freeze-dried and observed unstained in dark field at -160°.

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EVALUATION OF TISSUE STEROID BINDING IN VITRO

Acta Endocrinologica ◽

10.1530/acta.0.068s223 ◽

1971 ◽

Vol 68 (1_Suppl) ◽

pp. S223-S246 ◽

Cited By ~ 2

Author(s):

C. R. Wira ◽

H. Rochefort ◽

E. E. Baulieu

Keyword(s):

Protein Binding ◽

Binding Sites ◽

Experimental System ◽

Specific Protein ◽

Coupling Mechanism ◽

Target Tissue ◽

Protein Binding Sites ◽

Definition Of ◽

Hormone Specificity

ABSTRACT The definition of a RECEPTOR* in terms of a receptive site, an executive site and a coupling mechanism, is followed by a general consideration of four binding criteria, which include hormone specificity, tissue specificity, high affinity and saturation, essential for distinguishing between specific and nonspecific binding. Experimental approaches are proposed for choosing an experimental system (either organized or soluble) and detecting the presence of protein binding sites. Techniques are then presented for evaluating the specific protein binding sites (receptors) in terms of the four criteria. This is followed by a brief consideration of how receptors may be located in cells and characterized when extracted. Finally various examples of oestrogen, androgen, progestagen, glucocorticoid and mineralocorticoid binding to their respective target tissues are presented, to illustrate how researchers have identified specific corticoid and mineralocorticoid binding in their respective target tissue receptors.

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