15N magnetic relaxation study of backbone dynamics of the ribosome-associated cold shock response protein Yfia of Escherichia coli

• Autorzy: Zhukov I. , Bayer P. , Scholermann B. , Ejchart A.
• Języki publikacji: EN

Abstrakty

EN

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 over all 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 milli second 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.

Słowa kluczowe

PL

spectroscopy; NMR method; stress adaptation; stress factor; protein Y; anisotropic overall molecular diffusion; disordered polypeptide chain motion; ribosome-associated cold shock response; Escherichia coli; amino acid residue; backbone dynamics

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2007
• Tom: 54
• Numer: 4
• Opis fizyczny: p.769-775,fig.,ref

Twórcy

autor

Zhukov I.

• Polish Academy of Sciences, A.Pawinskiego 5A, Warsaw, Poland

autor

Bayer P.

autor

Scholermann B.

autor

Ejchart A.

Bibliografia

• 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, Guntert P, Wuthrich K (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 5:1-10.
• Brutscher B, Bruschweiler 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 T1 and T2 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.