Escherichia coli ribosome

Protein molecules extracted from Escherichia coli ribosomes were examined by viscosity, sedimentation, and diffusion experiments for characterization with respect to molecular weight, hydration, and ellipticity. These dataf are examined in this and the following problem. Use Fig. 9.4a to estimate the axial ratio of the molecules, assuming a solvation of 0.26 g water (g protein)"V At 20°C, [r ] = 27.7 cm g" and P2 = 1.36 for aqueous solutions of this polymer. 

ACTH, adrenocorticotrophic hormone Met, methionine Met(O), methionine sulfoxide DTT, dithiothreitol L7, L12, Escherichia coli ribosomal proteins Met(0)-L12, L12 containing Met(O) residues a-l-PI, a-1-proteinase inhibitor Met(0)-a-l-PI, a-l-PI... 

Arnold, R. J. Reilly, J. P. Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry. Anal. Biochem. 1999, 269,105-112. 

Kaji, A. (1968). Techniques for measuring specific sRNA binding to Escherichia coli ribosomes. Methods Enzymol. 12B, 692—699. 

Cover, J.A., Lambert, J.M., Norman, C.M., and Traut, R.R. (1981) Identification of proteins at the subunit interface of the Escherichia coli ribosome by cross-linking with dimethyl 3,3 -dithiobis(propionimi date). Biochemistry 20, 2843-2852. 

Huang, K.-H., Fainclough, R.H., and Cantor, C.R. (1975) Singlet energy transfer studies of the arrangement of proteins in the 30S Escherichia coli ribosome./. Mol. Biol. 97, 443. 

Odom Jr., O.W., Robins, D.J., Lynch, J., Dottavio-Martin, D., Kramer, G., and Hardesty, B. (1980) Distances between 3 ends of ribosomal ribonucleic acids reassembled into Escherichia coli ribosomes. 

Politz, S.M., Noller, H.F., and McWhirter, P.D. (1981) Ribonucleic acid-protein cross-linking in Escherichia coli ribosomes (4-azidophenyl) glyoxal, a novel heterobifunctional reagent. Biochemistry 20, 372-378. 

StarkH, RodninaM, Rinke-Appel J, BrimacombeR, WintermeyerW, vanHeelM. Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 1997 389 403 105. 

B. Lux, D. Gerard, and G. Laustriat, Tyrosine fluorescence ofS8 and S15 Escherichia coli ribosomal proteins, FEBS Lett. 80, 66-70 (1977). 

Appendix Primary Structure of Escherichia coli Ribosomal Proteins... 

Xiong L, Korkhin Y, Mankin AS. (2005) Binding site of the bridged macrolides in the Escherichia coli ribosome. Antimicrob Agents Chemother 49 281-288. 

Gralla JD, Escherichia coli ribosomal RNA transcription Regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein. Mol Microbiol 55 973-977, 2005. 

Klaholz BP, Pape T, Zavialov AV, Myasnikov AG, Orlova EV, Vestergaard B, Ehrenberg M, van Heel M (2003) Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature 421 90-94... 

Jue, R., Lambert, J. M., Pierce, L. R., and Traut, R. R. (1978) Addition of sulfhydryl groups to Escherichia coli ribosomes by protein modification with 2-iminothiolane (methyl 4-mercap-tobutyrimidate). Biochemistry 17, 5399—5405. 

Ringquist, S., Jones, T., Snyder, E.E., Gibson, T., Boni, I. and Gold, L. (1995) High-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein SI comparison of natural and unnatural binding sites. Biochemistry, 34, 3640-3648. 

FIGURE 3.7 A cryo-EM map of the Escherichia coli ribosome (complexed with fMet-tRNAf Met and mRNA) where fMet = formylmethionine obtained from 73,000 particles at a resolution of 11.5 A. (a-d) Four views of the map, with the ribosome 30S subunit painted in yellow, the ribosome 50S subunit in blue, helix 44 of 16S RNA in red, and fMet-tRNA at the P site in green. Inset on top juxtaposes the experimental tRNA mass (green, on left) with the appearance of the X-ray structure of tRNA at 11 A resolution (on right). Arrows mark points at which tRNA contacts the surrounding ribosome mass. Landmarks h = head and sp = spur of the 30S subunit. CP = central protuberance LI = LI stalk and St = L7/L12 stalk base of the 50S subunit. 

Draper, D.E., von Hippel, P.H. (1979) Interaction of Escherichia coli Ribosomal Protein SI with Ribosomes, Proc. Natl. Acad. Sci. USA 76,1040-1044. 

S. N. Vladimirov, Z. Druzina, R. Wang, and B.S. Cooperman. 2000. Identification of 50S components neighboring 23S rRNA nucleotides A2448 and U2604 within the peptidyl transferase center of Escherichia coli ribosomes Biochemistry 39 183-193. (PubMed)... 

Information on the three-dimensional structure of RNA can be obtained by tethering cleavage agents to known positions and then by studying the fragments produced by the cleavage reactions. This has been used to study Escherichia coli ribosomal... 

Teraoka, H., and Nierhaus, K. H. (1978). Protein from Escherichia coli ribosomes involved in the binding of erythromycin. J. Mol. Biol, 126, 185-193. 

Femandez-Munoz, R., Monro, R. E., Torres-Pinedo, R., and Vazquez, D. (1971). Substrate-and antibiotic-binding sites at the peptidyltransferase center of Escherichia coli ribosomes. Studies on the chloramphenicol, lincomycin and erythromycin sites. Eur. J. Biochem. 23, 185-193. 

Moini, M. and Huang, H., Application of capillary electrophoresis/electrospray ionization-mass spectrometry to subcellular proteomics of Escherichia coli ribosomal proteins. Electrophoresis, 25, 1981-1987, 2004. 

---