15N magnetic relaxation study of backbone dynamics of the ribosome-associated cold shock response protein Yfia of Escherichia coli
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In the solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli in the free state two structural segments can be distinguished: a well structured, rigid N-terminal part displaying a βαβββα topology and a flexible C-terminal tail comprising last 20 amino-acid residues. The backbone dynamics of Yfia protein was studied by 15N nuclear magnetic relaxation at three magnetic fields and analyzed using model-free approach. The overall diffusional tumbling of the N-terminal part is strongly anisotropic with a number of short stretches showing increased mobility either on a subnanosecond time scale, or a micro- to millisecond time scale, or both. In contrast, the unstructured polypeptide chain of the C-terminal part, which cannot be regarded as a rigid structure, shows the predominance of fast local motions over slower ones, both becoming faster closer to the C-terminus.
- Agafonov DE, Kolb VA, Nazimov IV, Spirin AS (1999) A protein residing at the subunit interface of the bacterial ribosome. Proc Natl Acad Sci USA 96: 12345-12349.
- Agafonov DE, Kolb VA, Spirin AS (2001) Ribosome-associated protein that inhibits translation at the aminoacyl-tRNA binding stage. EMBO Rep 2: 399-402.
- Alexandrescu AT, Shortle D (1994) Backbone dynamics of a highly disordered 131 residue fragment of staphylococcal nuclease. J Mol Biol 242: 527-546.
- Barbato G, Ikura M, Kay LE, Pastor RW, Bax A (1992) Backbone dynamics of calmodulin studied by ^15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible. Biochemistry 31: 5269-5278.
- Bartels C, Xia T, Billeter M, Güntert P, Wüthrich K (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 5: 1-10.
- Brutscher B, Brüschweiler R, Ernst RR (1997) Backbone dynamics and structural characterization of the partially folded A state of ubiquitin by ^1H, ^13C, and ^15N nuclear magnetic resonance spectroscopy. Biochemistry 36: 13043-13053.
- Buevich AV, Shinde UP, Inouye M, Baum J (2001) Backbone dynamics of the natively unfolded pro-peptide of subtilisin by heteronuclear NMR relaxation studies. J Biomol NMR 20: 233-249.
- Case DA (1999) Calculations of NMR dipolar coupling strengths in model peptides. J Biomol NMR 15: 95-102.
- Cavanagh J, Fairbrother WJ, Palmer III AG, Skelton NJ (1996) Protein NMR spectroscopy. Principles and practice; pp 290-297. Academic Press, San Diego, London.
- Clore GM, Driscoll PC, Wingfield PT, Gronenborn AM (1990) Analysis of backbone dynamics of interleukin-1β using two-dimensional inverse detected heteronuclear ^15N-^1H NMR spectroscopy. Biochemistry 29: 7387-7401.
- Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) A multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6: 277-293.
- Farrow NA, Muhamdiram R, Singer AU, Paskal SM, Kay CM, Gish G, Shoelton SE, Pawson T, Forman-Kay JD, Kay LE (1994) Backbone dynamics of a free and a phosphopeptide-complexed Src homology 2 domain studied by ^15N NMR relaxation. Biochemistry 33: 5984-6003.
- Johnson CH, Kruft V, Subramanian AR (1990) Identification of a plastid-specific ribosomal protein in the 30S subunit of chloroplast ribosomes and isolation of the cDNA clone encoding its cytoplasmic precursor. J Biol Chem 265: 12790-12795.
- Kalinin A, Rak A, Scherbakov D, Bayer P (2002) ^1H, ^13C and ^15N resonance assignments of the ribosome-associated cold shock response protein Yfia of Escherichia coli. J Biomol NMR 23: 335-336.
- Kay LE (2005) NMR studies of protein structure and dynamics. J Magn Reson 173: 193-207.
- Kay LE, Keifer P, Saarinen T (1992a) Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J Am Chem Soc 114: 10663-10665.
- Kay LE, Nicholson LK, Delaglio F, Bax A, Torchia DA (1992b) Pulse schemes for removal of the effects of cross-correlation between dipolar and chemical-shift anisotropy relaxation mechanisms on the measurement of heteronuclear T_1 and T_2 values in proteins. J Magn Reson 97: 359-375.
- Korzhnev DM, Billeter M, Arseniev AS, Orekhov Y (2001) NMR studies of Brownian tumbling and internal motions in proteins. Prog NMR Spectr 38: 197-266.
- Lipari G, Szabo A (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. J Am Chem Soc 104: 4546-4570.
- Ochsenbein F, Neumann JM, Guittet E, van Heijenoort C (2002) Dynamic characterization of residual and non-native structures in a partially folded protein by ^15N NMR relaxation using a model based on a distribution of correlation times. Protein Sci 11: 957-964.
- Palmer AG (2004) NMR characterization of the dynamics of biomolecules. Chem Rev 104: 3623-3640.
- Parsons L, Eisenstein E, Orban J (2001) Solution structure of HI0257, a bacterial ribosome binding protein. Biochemistry 40: 10979-10986.
- Peng JW, Wagner G (1995) Frequency spectrum of NH bonds in eglin c from spectral density mapping at multiple fields. Biochemistry 34: 16733-16752.
- Press WH, Flannery BP, Teukolsky SA, Vetterling WT (1986) Numerical recipes. The art of scientific computing; pp 529-538. Cambridge University Press, Cambridge.
- Rak A, Kalinin A, Shcherbakov D, Bayer P (2002) Solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli. Biochem Biophys Res Commun 299: 710-714.
- Shaka A, Baker PB, Freeman R (1985) Computer-optimized decoupling scheme for wideband applications at low-level operation. J Magn Reson 64: 547-552.
- Stone MJ, Fairbrother WJ, Palmer III AG, Reizer J, Saier Jr. MH, Wright PE (1992) Backbone dynamics of the Bacillus subtilis glucose permease IIA domain determined from ^15N NMR relaxation measurements. Biochemistry 31: 4394-4406.
- Tjandra N, Kuboniwa H, Bax A (1995) Rotational dynamics of calcium-free calmodulin studied by ^15N-NMR relaxation measurements. Eur J Biochem 230: 1014-1024.
- Tjandra N, Szabo A, Bax A (1996a) Protein backbone dynamics and ^15N chemical shift anisotropy from quantitative measurement of relaxation interference effects. J Am Chem Soc 118: 6986-6991.
- Tjandra N, Wingfield P, Stahl S, Bax A (1996b) Anisotropic rotational diffusion of perdeuterated HIV protease from ^15N NMR relaxation measurements at two magnetic fields. J Biomol NMR 8: 273-284.
- Vila-Sanjurjo A, Schuwirth BS, Hau CW, Cate JHD (2004) Structural basis for the control of translation initiation during stress. Nat Struct Mol Biol 11: 1054-1059.
- Ward IM, Klein PG (1996) Polymer physics. In Encyclopedia of nuclear magnetic resonance. Grant DM, Harris RK, eds, pp 3693-3706, Wiley, Chichester.
- Woessner DE (1962) Nuclear spin relaxation in ellipsoid undergoing rotational Brownian motion. J Chem Phys 37: 647-654.
- Ye K, Serganov A, Hu W, Garber M, Patel DJ (2002) Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold. Eur J Biochem 269: 5182-5191.
- Zhukov I, Ejchart A (1999) Factors improving the accuracy of determination of ^15N relaxation parameters in proteins. Acta Biochim Polon 46: 665-671.
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