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Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data

  • Alexander Grishaev
  • Jinfa Ying
  • Marella D. Canny
  • Arthur Pardi
  • Ad Bax
Article

Abstract

A procedure is presented for refinement of a homology model of E. coli tRNAVal, originally based on the X-ray structure of yeast tRNAPhe, using experimental residual dipolar coupling (RDC) and small angle X-ray scattering (SAXS) data. A spherical sampling algorithm is described for refinement against SAXS data that does not require a globbic approximation, which is particularly important for nucleic acids where such approximations are less appropriate. Substantially higher speed of the algorithm also makes its application favorable for proteins. In addition to the SAXS data, the structure refinement employed a sparse set of NMR data consisting of 24 imino N–HN RDCs measured with Pf1 phage alignment, and 20 imino N–HN RDCs obtained from magnetic field dependent alignment of tRNAVal. The refinement strategy aims to largely retain the local geometry of the 58% identical tRNAPhe by ensuring that the atomic coordinates for short, overlapping segments of the ribose-phosphate backbone and the conserved base pairs remain close to those of the starting model. Local coordinate restraints are enforced using the non-crystallographic symmetry (NCS) term in the XPLOR-NIH or CNS software package, while still permitting modest movements of adjacent segments. The RDCs mainly drive the relative orientation of the helical arms, whereas the SAXS restraints ensure an overall molecular shape compatible with experimental scattering data. The resulting structure exhibits good cross-validation statistics (jack-knifed Q free = 14% for the Pf1 RDCs, compared to 25% for the starting model) and exhibits a larger angle between the two helical arms than observed in the X-ray structure of tRNAPhe, in agreement with previous NMR-based tRNAVal models.

Keywords

NMR RDC Refinement Rigid body SAXS tRNA 

Abbreviations

MSA

Magnetic susceptibility anisotropy

NCS

Non-crystallographic symmetry

RDC

Residual dipolar coupling

SAXS

Small angle X-ray scattering

rms

Root mean square

Notes

Acknowledgments

This work was supported by the Intramural Research Program of the NIDDK, NIH, and by the Intramural AIDS-Targeted Antiviral Program of the Office of the Director, NIH and NIH grant AI33098 (AP).

Supplementary material

10858_2008_9267_MOESM1_ESM.doc (126 kb)
MOESM1 (DOC 126 kb)

References

  1. Al-Hashimi HM, Valafar H, Terrell M, Zartler ER, Eidsness MK, Prestegard JH (2000) Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings. J Magn Reson 143:402–406CrossRefADSGoogle Scholar
  2. Allain FHT, Varani G (1997) How accurately and precisely can RNA structure be determined by NMR? J Mol Biol 267:338–351CrossRefGoogle Scholar
  3. Bailor MH, Musselman C, Hansen AL, Gulati K, Patel DJ, Al-Hashimi HM (2007) Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings. Nat Protoc 2:1536–1546CrossRefGoogle Scholar
  4. Bhatnagar J, Freed JH, Crane BR (2007) Rigid body refinement of protein complexes with long-range distance restraints from pulsed dipolar ESR. Meth Enzymol 423:117–133CrossRefGoogle Scholar
  5. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921CrossRefGoogle Scholar
  6. Cai ML, Williams DC, Wang GS, Lee BR, Peterkofsky A, Clore GM (2003) Solution structure of the phosphoryl transfer complex between the signal-transducing protein IIA(Glucose) and the cytoplasmic domain of the glucose transporter IICBGlucose of the Escherichia coli glucose phosphotransferase system. J Biol Chem 278:25191–25206CrossRefGoogle Scholar
  7. Chou JJ, Li SP, Klee CB, Bax A (2001) Solution structure of Ca2+-calmodulin reveals flexible hand-like properties of its domains. Nat Struct Biol 8:990–997CrossRefGoogle Scholar
  8. Clore GM, Bewley CA (2002) Using conjoined rigid body/torsion angle simulated annealing to determine the relative orientation of covalently linked protein domains from dipolar couplings. J Magn Reson 154:329–335CrossRefADSGoogle Scholar
  9. Clore GM, Kuszewski J (2003) Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation. J Am Chem Soc 125:1518–1525CrossRefGoogle Scholar
  10. Davis IW, Murray LW, Richardson JS, Richardson DC (2004) MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 32:W615–W619CrossRefGoogle Scholar
  11. Dingley AJ, Masse JE, Peterson RD, Barfield M, Feigon J, Grzesiek S (1999) Internucleotide scalar couplings across hydrogen bonds in Watson-Crick and Hoogsteen base pairs of a DNA triplex. J Am Chem Soc 121:6019–6027CrossRefGoogle Scholar
  12. D’Souza V, Dey A, Habib D, Summers MF (2004) NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus. J Mol Biol 337:427–442CrossRefGoogle Scholar
  13. Fraser RDB, Macrae TP, Suzuki E (1978) Improved method for calculating contribution of solvent to X-ray-diffraction pattern of biological molecules. J Appl Crystallogr 11:693–694CrossRefGoogle Scholar
  14. Gabel F, Simon B, Sattler M (2006) A target function for quaternary structural refinement from small angle scattering and NMR orientational restraints. Eur Biophys J Biophys Lett 35:313–327Google Scholar
  15. Getz M, Sun XY, Casiano-Negroni A, Zhang Q, Al-Hashimi HM (2007) NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings. Biopolymers 86:384–402CrossRefGoogle Scholar
  16. Grishaev A, Wu J, Trewhella J, Bax A (2005) Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data. J Am Chem Soc 127:16621–16628CrossRefGoogle Scholar
  17. Grishaev A, Tugarinov V, Kay LE, Trewhella J, Bax A (2008) Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints. J Biomol NMR 40:95–106CrossRefGoogle Scholar
  18. Jain NU, Wyckoff TJO, Raetz CRH, Prestegard JH (2004) Rapid analysis of large protein-protein complexes using NMR-derived orientational constraints: the 95 kDa complex of LpxA with acyl carrier protein. J Mol Biol 343:1379–1389CrossRefGoogle Scholar
  19. Koch MHJ, Vachette P, Svergun DI (2003) Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q Rev Biophys 36:147–227CrossRefGoogle Scholar
  20. Kuszewski J, Gronenborn AM, Clore GM (1997) Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids. J Magn Reson 125:171–177CrossRefADSGoogle Scholar
  21. Latham MP, Hanson P, Brown DJ, Pardi A (2008) Comparison of alignment tensors generated for native tRNA(Val) using magnetic fields and liquid crystalline media. J Biomol NMR 40:83–94CrossRefGoogle Scholar
  22. Lipfert J, Doniach S (2007) Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu Rev Biophys Biomol Struct 36:307–327CrossRefGoogle Scholar
  23. Lipfert J, Chu VB, Bai Y, Herschlag D, Doniach S (2007a) Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling. J Appl Crystallogr 40:S229–S234CrossRefGoogle Scholar
  24. Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S (2007b) Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J Mol Biol 365:1393–1406CrossRefGoogle Scholar
  25. Losonczi JA, Andrec M, Fischer MWF, Prestegard JH (1999) Order matrix analysis of residual dipolar couplings using singular value decomposition. J Magn Reson 138:334–342CrossRefADSGoogle Scholar
  26. Lukavsky PJ, Kim I, Otto GA, Puglisi JD (2003) Structure of HCVIRES domain II determined by NMR. Nat Struct Biol 10:1033–1038CrossRefGoogle Scholar
  27. Mollova ET, Hansen MR, Pardi A (2000) Global structure of RNA determined with residual dipolar couplings. J Am Chem Soc 122:11561–11562CrossRefGoogle Scholar
  28. Parsons LM, Grishaev A, Bax A (2008) The periplasmic domain of To1R from haemophilus influenzae forms a dimer with a large hydrophobic groove: NMR solution structure and comparison to SAXS data. Biochemistry 47:3131–3142CrossRefGoogle Scholar
  29. Putnam CD, Hammel M, Hura GL, Tainer JA (2007) X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 40:191–285Google Scholar
  30. Sass J, Cordier F, Hoffmann A, Rogowski M, Cousin A, Omichinski JG, Lowen H, Grzesiek S (1999) Purple membrane induced alignment of biological macromolecules in the magnetic field. J Am Chem Soc 121:2047–2055CrossRefGoogle Scholar
  31. Sass HJ, Musco G, Stahl SJ, Wingfield PT, Grzesiek S (2001) An easy way to include weak alignment constraints into NMR structure calculations. J Biomol NMR 21:275–280CrossRefGoogle Scholar
  32. Schwieters CD, Clore GM (2007) A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data. Biochemistry 46:1152–1166CrossRefGoogle Scholar
  33. Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:65–73CrossRefADSGoogle Scholar
  34. Shi HJ, Moore PB (2000) The crystal structure of yeast phenylalanine tRNA at 1.93 angstrom resolution: a classic structure revisited. RNA-Publ. RNA Soc 6:1091–1105CrossRefGoogle Scholar
  35. Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr 25:495–503CrossRefGoogle Scholar
  36. Svergun D, Barberato C, Koch MHJ (1995) CRYSOL—a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28:768–773CrossRefGoogle Scholar
  37. Svergun DI, Petoukhov MV, Koch MHJ (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80:2946–2953CrossRefGoogle Scholar
  38. Tang C, Iwahara J, Clore GM (2006) Visualization of transient encounter complexes in protein-protein association. Nature 444:383–386CrossRefADSGoogle Scholar
  39. Ulmer TS, Ramirez BE, Delaglio F, Bax A (2003) Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. J Am Chem Soc 125:9179–9191CrossRefGoogle Scholar
  40. Vermeulen A (2003) Determining nucleic acid global structure by application of NMR residual dipolar couplings. PhD, University of Colorado, BoulderGoogle Scholar
  41. Vermeulen A, Zhou H, Pardi A (2000) Determining DNA global structure and DNA bending by application of NMR residual dipolar couplings. J Am Chem Soc 122:9638–9647CrossRefGoogle Scholar
  42. Vermeulen A, McCallum SA, Pardi A (2005) Comparison of the global structure and dynamics of native and unmodified tRNA. Biochemistry 44:6024–6033CrossRefGoogle Scholar
  43. Wang GS, Louis JM, Sondej M, Seok YJ, Peterkofsky A, Clore GM (2000) Solution structure of the phosphoryl transfer complex between the signal transducing proteins HPr and IIA(Glucose) of the Escherichia coli phosphoenolpyruvate: sugar phosphotransferase system. EMBO J 19:5635–5649CrossRefGoogle Scholar
  44. Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285:1735–1747CrossRefGoogle Scholar
  45. Ying JF, Grishaev A, Latham MP, Pardi A, Bax A (2007) Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field. J Biomol NMR 39:91–96CrossRefGoogle Scholar
  46. Zhang Q, Sun XY, Watt ED, Al-Hashimi HM (2006) Resolving the motional modes that code for RNA adaptation. Science 311:653–656CrossRefADSGoogle Scholar
  47. Zuo XB, Wang JB, Foster TR, Schwieters CD, Tiede DM, Butcher SE, Wang YX (2008) Global molecular structure and interfaces: refining an RNA: RNA complex structure using solution X-ray scattering data. J Am Chem Soc 130:3292–3293CrossRefGoogle Scholar
  48. Zweckstetter M, Bax A (2002) Evaluation of uncertainty in alignment tensors obtained from dipolar couplings. J Biomol NMR 23:127–137CrossRefGoogle Scholar
  49. Zweckstetter M, Hummer G, Bax A (2004) Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophys J 86:3444–3460CrossRefGoogle Scholar

Copyright information

© US Government 2008

Authors and Affiliations

  1. 1.Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaUSA
  2. 2.Department of Chemistry and Biochemistry, 215 UCBUniversity of Colorado, BoulderBoulderUSA

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