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Structural Dynamics of tRNA A Fluorescence Relaxation Study of tRNA Pheyeast

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Chemical Relaxation in Molecular Biology

Part of the book series: Molecular Biology Biochemistry and Biophysics ((MOLECULAR,volume 24))

Abstract

From the X-ray diffraction studies of KIM et al. (1974) and ROBERTUS et al. (1974) a detailed picture of the crystal structure of phenylalanine-tRNA from yeast (tRNA Pheyeast ) has emerged. The finding that most of the hydrogen bonds between loop and stem regions which stabilize the tertiary structure of tRNAphe involve bases of the invariable parts of the primary sequences of tRNA suggests a similarity of the tertiary structure of all tRNAs. It is generally assumed that the crystal structure is predominant also in solution. The support for this assumption is mainly based on the accessibility of nucleotides to chemical modification, and has been reviewed by RICH and RAJBHANDARY (1976). Experiments in which the binding of oligonucleotides to tRNA was investigated, however, indicate interaction between oligonucleotides and complementdry sequences particularly in the D-loop (UHLENBECK, 1972; CAMERON and UHLENBECK, 197 3) and the anticodon-loop (UHLENBECK, 1972; EISINGER and SPAHR, 1973) which are not accessible in the crystal lattice. Studies of the solution structure of tRNA applying spectroscopic techniques such as low-angle X-ray diffraction (KRIGBAUM and GOODWIN, 1966; CONNORS et al., 1969; PILZ et al., 1970) and NMR (LIGHTFOOT et al., 1973; SHULMAN et al., 1973; DANIEL and COHN, 19 75; REID et al., 1975; REID and ROBILLARD, 1975; KEARNS, 1976) were up to now not able to decide whether conformations differing from the crystal structure are present in solution.

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References

  • BEARDSLEY, D., TAO, T., CANTOR, Ch.R.: Studies on the conformation of the anticodon loop of phenylalanine transfer ribonucleic acid Effect of environment on the fluorescence of the Y-base. Biochemistry 9, 3524 (1970)

    Article  PubMed  CAS  Google Scholar 

  • CAMERON, V., UHLENBECK, O.C.: Removal of Y-37 from tRNAPhe yeast alters oligomer binding to two loops. Biochem. Biophys. Res. Comm. 50, 635 (1973)

    Article  PubMed  CAS  Google Scholar 

  • CHEN, M.C., GIEGE, R., LORD, R.C., RICH, A.: Raman spectra and structure of yeast phenylalanine transfer RNA in the crystalline state and in solution. Biochemistry 14, 4385 (1975)

    Article  PubMed  CAS  Google Scholar 

  • CHUANG, T.J., EISENTHAL, K.B.: Theory of fluorescence depolarization by anisotropic rotational diffusion. J. Chem. Phys. 57, 5094 (1972)

    Article  CAS  Google Scholar 

  • COLE, P.E., YANG, S.K., CROTHERS, D.M.: Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry 11, 4358 (1972)

    Article  PubMed  CAS  Google Scholar 

  • CONNORS, R.G., LABANAUSKAS, M., BEEMAN, W.W.: Structural studies on transfer RNA: The molecular conformation in solution. Science 166, 1528 (1969)

    Article  PubMed  CAS  Google Scholar 

  • DANIEL, Jr. W.E., COHN, M.: Proton nuclear magnetic resonance of spin-labelled Escherichia coli tRNAMet f1. Proc. Nat. Acad. Sci. (Wash.) 72, 2582 (1975)

    Article  CAS  Google Scholar 

  • EHRENBERG, M., RIGLER, R.: Polarized fluorescence and rotational Brownian motion. Chem. Phys. Lett. 14, 539 (1972)

    Article  CAS  Google Scholar 

  • EHRENBERG, M., RIGLER, R.: Fluorescence correlation spectroscopy applied to rotational diffusion of macromolecules. Quart. Rev. Biophys. 9, 69 (1976)

    Article  CAS  Google Scholar 

  • EHRENBERG, M., RIGLER, R., WINTERMEYER, W.: On the structure and conformational dynamics of fluorescence labelled tRNAPhe Yeast in solution. In preparation (1977)

    Google Scholar 

  • EIGEN, M.: Kinetics of reaction control and information transfer in enzymes and nucleic acids. In: Fast Reactions and Primary Process in Chemical Kinetics. CLAESSON, S. (ed.), p. 333. Stockholm: Almquist and Wiksell 1967

    Google Scholar 

  • EIGEN, M.: New looks and outlooks on physical enzymology. Quart. Rev. Biophys. 1, 3 (1968)

    Article  CAS  Google Scholar 

  • EISINGER, J., FEUER, B., YAMANE, T.: Luminiscence and binding studies on tRNAphe. Proc. Nat. Acad. Sci. (Wash.) 65, 638 (1970)

    Article  CAS  Google Scholar 

  • EISINGER, J., LAMOLA, A.A.: In: Excited States of Protein and Nucleic Acids. STEINER, R.F., WEINRYB, I. (eds.), p. 189. New York: Plenum Press 1971

    Google Scholar 

  • EISINGER, J., SPAHR, P.F.: Binding of complementary pentanucleo- tides to the anticodon loop of transfer RNA. J. Mol. Biol. 73, 131 (1973)

    Article  PubMed  CAS  Google Scholar 

  • FRESCO, J.A., ADAMS, A., ASCIONE, R., HENLEY, D., LINDAHL, T.: Tertiary structure in transfer ribonucleic acids. Cold Spring Harbor Symp. Quant. Biol. 31, 527 (1966)

    CAS  Google Scholar 

  • GARTLAND, W.W., SUEOKA, N.: Two interconvertible forms of trypto- phanyl sRNA in E. coli Proc. Nat. Acad. Sci. (Wash.) 55., 948 (1966)

    Article  Google Scholar 

  • GRINVALD, A., STEINBERG, I.Z.: On the analysis of fluorescence decay kinetics by the method of last-squares. Analyt. Biochem. 59, 583 (1974)

    Article  PubMed  CAS  Google Scholar 

  • HÄNGGI, U.J., STREECK, R.E., VOIGT, H.P., ZACHAU, H.G.: Phosphorylation od dephosphorylated tRNA and oligonucleotides by polynucleotide kinease. Biochem. Biophys. Acta 217, 287 (1970)

    Google Scholar 

  • HIRSH, D.: Tryptophan transfer RNA as the UGA suppressor. J. Mol. Biol. 58, 439 (1971)

    Article  PubMed  CAS  Google Scholar 

  • HIRSH, D., GOLD, L.: Translation of the UGA triplet in vitro by tryptophan transfer RNAs. J. Mol. Biol. 58, 459 (1971)

    Article  PubMed  CAS  Google Scholar 

  • KAN, L.S., TS’0, P.O.P., SPRINZL, M., Van der HAAR, F., CRAMER, F.: Biophys. J. 16, 11a (1976)

    Google Scholar 

  • KEARNS, D.R.: High-resolution nuclear magnetic resonance investigations of the structure of tRNA in solution: In: Progress in Nucleic Acid Research and Molecular Biology. COHN, W.E. (ed.), Vol. 18, p. 91. New York: Academic Press 1976

    Google Scholar 

  • KIM, S.H., LANGLOIS, R., CANTOR, Ch.: Conformation of anticodon loop of yeast tRNAphe in solution and in crystals as monitored by the Y-base fluorescence. Abstracts, EMBO Workshop on tRNA structure and function, Israel: Nof Ginossar 1975

    Google Scholar 

  • KIM, S.H., QUIGLEY, G., SUDDATH, F.L., RICH, A.: High-resolution X-ray diffraction patterns of crystalline transfer RNA that show helical regions. Proc. Nat. Acad. Sci. (Wash.) 68, 841 (1971)

    Article  CAS  Google Scholar 

  • KIM, S.H., SUDDATH, F.L., QUIGLEY, G.J., McPHERSON, A., SUSSMAN, J.L., WANG, A.H.J., SEEMAN, N.C., RICH, A.: Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science, N.Y. 185, 435 (1974)

    Article  CAS  Google Scholar 

  • KIRSCHNER, K., EIGEN, M., BITTMANN, R., VOIGT, B.: The binding of NAD to yeast D-glyceraldehyde-3-phosphate dehydrogenase: Temperature jump relaxation studies on H:he mechanism of an allosteric enzyme. Proc. Nat. Acad. Sci. (Wash.) 56, 1661 (1966)

    Article  CAS  Google Scholar 

  • KRAUSS, G., RIESNER, D., MAASS, G.: Mechanism of discrimination between cognate and non-cognate tRNAs by phenylalanyl-tRNA synthetase from yeast. Europ. J. Biochem. 68, 81 (1976)

    Article  PubMed  CAS  Google Scholar 

  • KRIGBAUM, W.R., GOODWIN, R.W.: Small-angle X-ray study of transfer RNA. Science 154, 423 (1966)

    Google Scholar 

  • KURLAND, Ch.: Prospects of ribosome structure and function. In: Protein Synthesis. WEISSBACH, H., PESTKA, S. (eds.). New York: Academic Press 1975

    Google Scholar 

  • KURLAND, C.G., RIGLER, R., EHRENBERG, M., BLOMBERG, C.: Allosteric mechanism for codon-dependent tRNA selection on ribo- somes. Proc. Nat. Acad. Sci. (Wash.) 72, 4248 (1975)

    Article  CAS  Google Scholar 

  • LADNER, J.E., FINCH, J.T., KLUG, A., CLARK, B.F.C.: High-resolu- tion X-ray diffraction studies on a pure species of transfer RNA. J. Mol. Biol. 72, 99 (1972)

    Article  PubMed  CAS  Google Scholar 

  • LIGHTFOOT, D.R., WONG, K.L., KEARNS, D.R., REID, B.R., SHULMAN, R.G.: Assignment of the low field proton nuclear magnetic resonance spectrum of yeast phenylalanine transfer RNA to specific base pairs. J. Mol. Biol. 78, 71 (1973)

    Article  PubMed  CAS  Google Scholar 

  • LINDAHL, T., ADAMS, A., FRESCO, J.R.: Renaturation of transfer ribonucleic acids through site binding of magnesium. Proc. Nat. Acad. Sci. (Wash.) 55, 941 (1966)

    Article  CAS  Google Scholar 

  • LUCAS-LENARD, J., LIPMANN, F.: Protein biosynthesis. In: Annual Review of Biochemistry. SNELL, E.E., BOYER, P.D., SINSHEIMER, R.L. (eds.). Vol. 40, p. 409. Palo Alto, Calif.: Annual Reviews Inc. 1971

    Google Scholar 

  • LYNCH, D.C., SCHIMMEL, P.R.: Cooperative binding of magnesium to transfer ribonucleic acid studied by a fluorescent probe. Biochemistry 13, 1841 (1974)

    Article  PubMed  CAS  Google Scholar 

  • MARQUARDT, D.W.: An algorithm for least-squares estimation of non-linear parameters. J. Soc. Ind. Appl. Math. 11, 431 (1963)

    Article  Google Scholar 

  • MEETER, D.A.: Non-Linear Least-Squares (Gaushaus). Univ. Wisconsin Computing Center, 1964

    Google Scholar 

  • MEMMING, R.: Theorie der Fluoreszenzpolarization für nicht kugel- summetrische Moleküle. Z. Physik. Chem. N.F. (Frankfurt) 28, 168 (1961)

    Article  CAS  Google Scholar 

  • OLSON, T., FOURNIER, M.J., LANGLEY, K.H., FORD, N.C.: Detection of a major conformational change in transfer ribonucleic acid by laser light scattering. J. Mol. Biol. 102, 193 (1976)

    Article  PubMed  CAS  Google Scholar 

  • PILZ, I., KRATKY, O., CRAMER, R., van der HAAR, F., SCHLIMME, E.: On the conformation of phenylalanine specific transfer RNA. Studies on size and shape of the molecule by X-ray small angle scattering. Europ. J. Biochem. 15, 401 (1970)

    Article  PubMed  CAS  Google Scholar 

  • RAJBHANDARY, U.L., CHANG, S.H., STUART, A., FAULKNER, R.D., HOSKINSON, R.M., KHORANA, H.G.: Studies on polynucleotides, LXVIII. The primary structure of yeast phenylalanine transfer RNA. Proc. Nat. Acad. Sci. (Wash.) 57, 751 (1967)

    Article  CAS  Google Scholar 

  • REID, B.R., RIBEIRO, N.S., GOULD, G., ROBILLARD, G., HILBERS, C.W., SHULMAN, R.G.: Tertiary hydrogen bonds in the solution structure of transfer RNA. Proc. Nat. Acad. Sci. (Wash.) 72, 2049 (1975)

    Article  CAS  Google Scholar 

  • REID, B.R., RÖBILLARD, G.T.: Demonstration and origin of six tertiary base pair resonances in the NMR spectrum of E. coli tRNAval 1. Nature (London) 257, 287 (1975)

    Article  CAS  Google Scholar 

  • RENAUD, M., BOLLACK, C., BEFORT, N., EBEL, J.P.: (1971) cited by ZACHAU et al. (1972)

    Google Scholar 

  • RIALDI, G., LEVY, J., BILTONEN, R.: Thermodynamic studies of transfer ribonucleic acids. I. Magnesium binding to yeast phenylalanine transfer ribonucleic acid. Biochemistry VI, 2472 (1972)

    Google Scholar 

  • RICH, A., RAJBHANDARY, U.L.: Transfer RNAß Molecular structure, sequence and properties. In: Annual Review of Biochemistry. SNELL, E.E., BOYER, P.D., MEISTER, A., SINSHEIMER, R.L. (eds.). Vol. 45, p. 805. Palo Alto, Calif.: Annual Reviews Inc. 1976

    Google Scholar 

  • RICHTER, D.L., ERDMANN, V.A., SPRINZL, M.: Specific recognition of G-T-W-C loop (loop IV) of tRNA by 50S ribosomale subunits from E.coli. Nature (New Biol.) 246, 132 (1973)

    CAS  Google Scholar 

  • RIESNER, D., MAASS, G., THIEBE, R., PHILIPPSEN, P., ZACHAU, H.G.: The conformational transitions in yeast tRNAphe as studied with tRNAphe fragments. Europ. J. Biochem. 36, 76 (1973)

    Article  PubMed  CAS  Google Scholar 

  • RIESNER, D., PINGOUD, A., BOEHME, D., PETERS, F., MAASS, G.: Distinct steps in the specific binding of tRNA to aminoacyl- tRNA synthetase. Temperature-jump studies on the serine-spe- cific system from yeast and the tyrosine-specific system form Escherichia coli. Europ. J. Biochem. 68, 71 (1976)

    Article  PubMed  CAS  Google Scholar 

  • RIGLER, R., EHRENBERG, M.: Molecular interactions and structure as analysed by fluorescence relaxation spectroscopy. Quart. Rev. Biophys. 6, 139 (1973)

    Article  CAS  Google Scholar 

  • RIGLER, R., EHRENBERG, M.: Fluorescence relaxation spectroscopy in the analysis of macromolecular structure and motion. Quart. Rev. Biophys. 9, 1 (1976)

    Google Scholar 

  • RIGLER, R., PACHMANN, U., HIRSCH, R., ZACHAU, H.G.: On the interaction of seryl-tRNA synthetase with tRNASer. A contribution to the problem of synthetase-tRNA recognition. Europ. J. Biochem. 65, 307 (1976)

    Article  PubMed  CAS  Google Scholar 

  • RIGLER, R., RABL, C.R., JOVIN, T.M.: A temperature jump apparatus for fluorescence measurements. Rev. Sci. Instrumen. 45, 580 (1974)

    Article  CAS  Google Scholar 

  • ROBERTUS, J.D., LADNER, J.E., FINCH, F.T., RHODES, D., BROWN, R.S., CLARK, B.F., KLUG, A.: Structure of yeast phenyl-alanine tRNA at 3 8 resolution. Nature (London) 250, 546 (1974)

    Article  CAS  Google Scholar 

  • ROBISON, B., ZIMMERMANN, T.P.: Cation dependence of the transfer reaction catalyzed by phenylalanine transfer ribonucleic acid synthetase from Baker1s yeast. J. Biol. Chem. 246, 4664 (1971)

    PubMed  CAS  Google Scholar 

  • ROBISON, B., ZIMMERMANN, T.P.: A conformational study of yeast phenylalanine transfer ribonucleic acid. J. Biol. Chem. 246, 110 (1971)

    PubMed  CAS  Google Scholar 

  • RÖMER, R., HACH, R.: tRNA conformation and magnesium binding. A study of yeast phenylalanine-specific tRNA by a fluorescent indicator and differential melting curves. Europ. J. Biochem. 55, 271 (1975)

    Article  PubMed  Google Scholar 

  • RÖMER, R., RIESNER, D., MAASS, G.: Resolution of five conformational transitions in phenylalanine specific tRNA from yeast. FEBS Lett. 10, 352 (1970)

    Article  PubMed  Google Scholar 

  • SANDER, C., TS’O, P.O.: Interaction of nucleic acids VIII. Binding of magnesium ions by nucleic acids. J. Mol. Biol. 55, 1 (1971)

    Article  PubMed  CAS  Google Scholar 

  • SCHWARZ, U., LÃœHRMANN, R., GASSEN, H.G.: On the mRNA-induced conformational change of AA-tRNA exposing the T-f-C-G sequence for binding to the 50S ribosomal sub unit.. Biophys. Biochem. Res. Comm. 56, 807 (1974)

    Article  CAS  Google Scholar 

  • SCHWARZ, U., MENZEL, H.M., GASSEN, H.G.: Codon-dependent rearrangement of the three-dimensional structure of phenylalanine tRNA, exposing the T-W-C-G sequence for binding to the 50S ribosomal subunit. Biochemistry 15, 1484 (1976)

    Article  Google Scholar 

  • SHULMAN, R.G., HILBERS, C.W., KEARNS, D.R., REID, B.R., WONG, Y.P.: Ring-current shifts in the 300 MHz nuclear magnetic resonance spectra of six purified transfer RNA molecules. J. Mol. Biol. 78, 57 (1973)

    Article  PubMed  CAS  Google Scholar 

  • TAKASAKI, Y., IMAHORI, K.: CD and fluorescence studies of tRNAphe from Baker’s yeast. J. Biochem. 74, 513 (1973)

    PubMed  CAS  Google Scholar 

  • THANG, M.N., BELTCHEV, B., GRUNBER-GMANAGO, M.: Phosphorolysis of tRNA. Multiple conformational states of tRNA in solution. Europ. J. Biochem. 19, 184 (1971)

    Article  PubMed  CAS  Google Scholar 

  • THANG, M.N., GUSCHLBAUER, W., ZACHAU, H.G., GRUNBERG-MANAGO, M.: Degradation of transfer ribonucleic acid by polynucleotide phosphorylase. I. Mechanism of phosphorolysis and structure of tRNA. J. Mol. Biol. 26, 403 (1967)

    Article  Google Scholar 

  • UHLENBECK, O.C.: Complementary oligonucleotide binding to transfer RNA. J. Mol. Biol. 65, 25 (1972)

    Article  PubMed  CAS  Google Scholar 

  • WATANABE, K., IMAHORI, K.: The conformation difference between tRNAmet f from E. coli. Biochem. Biophys. Res. Comm. 45, 488 (1971)

    Article  CAS  Google Scholar 

  • WINTERMEYER, W., ZACHAU, H.G.: Replacement of the Y base, dihydro- uracil and 7-methyl-guanine in tRNA by artificial odd bases. FEBS Lett. 18, 214 (1971)

    Article  PubMed  CAS  Google Scholar 

  • WINTERMEYER, W., ZACHAU, H.G.: Replacement of odd bases in tRNA by fluorescent dyes. In: Methods of Enzymology. COLOWICK, S.P., KAPLAN, N.O. (eds.)vol XX1X, pp. 667–673. New York: Academic Press 1974

    Google Scholar 

  • WINTERMEYER, W., ZACHAU, H.G.: Characterization of fluorescent derivatives of yeast tRNA in the ribosomal system. Mol. Biol. (Russian) 9, 63; (English) 9, 49 (1975)

    Google Scholar 

  • WINTERMEYER, W., ROBERTSON, J.M., ZACHAU, H.G.: Fluorescence studies on tRNA conformation and ribosome interaction. Proc. Conf. Synthesis Structure and Chemistry of tRNAs and Their Components. WIEWIOROWSKI, M. (ed.). Poland: Poznan 1976

    Google Scholar 

  • ZACHAU, H.G., STREECK, R.E., HANGGI, U.J.: Conformational states of transfer ribonucleic acids. In: Gene Expression and Its Regulation. KENNEY, F.T., HAMKALO, B.A., FAVELUKES, G., AUGUST, J.T. (eds.). New York: Plenum Publishing Corp. 1972

    Google Scholar 

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  1. R. Rigler
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  2. M. Ehrenberg
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  3. W. Wintermeyer
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Editors and Affiliations

  1. Department of Chemical Immunology, The Weizmann Institute of Science, Rehovot, Israel

    Israel Pecht

  2. Department of Medical Biophysics, Karolinska Institutet, S-10401, Stockholm 60, Sweden

    Rudolf Rigler

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Rigler, R., Ehrenberg, M., Wintermeyer, W. (1977). Structural Dynamics of tRNA A Fluorescence Relaxation Study of tRNA Pheyeast . In: Pecht, I., Rigler, R. (eds) Chemical Relaxation in Molecular Biology. Molecular Biology Biochemistry and Biophysics, vol 24. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-81117-3_6

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  • DOI: https://doi.org/10.1007/978-3-642-81117-3_6

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