Structural constraints for the Crh protein from solid-state NMR experiments

Journal of Biomolecular NMR

Volumn 40, Issue 4, 2008, Pages 239-250

  Gardiennet, Carole ^a   Loquet, Antoine ^a   Etzkorn, Manuel ^b   Heise, Henrike ^b   Baldus, Marc ^b   Böckmann, Anja ^a  

^a UNIVERSITÉ DE LYON   (France)

^b MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

3D Protein structure; Catabolite repression histidine containing phosphocarrier protein (Crh); Distance constraints; MAS; Solid state NMR spectroscopy

Indexed keywords

CATABOLITE REPRESSION HISTIDINE CONTAINING PHOSPHOCARRIER PROTEIN; CELL PROTEIN; DIMER; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; CRH PROTEIN, BACILLUS SUBTILIS; PHOSPHOPROTEIN; PROTON;

ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DIMERIZATION; MAGNETIC SEPARATION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POLARIZATION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SOLID STATE; CHEMICAL STRUCTURE; CHEMISTRY; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; PROTEIN CONFORMATION;

BACTERIAL PROTEINS; DIMERIZATION; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PHOSPHOPROTEINS; PROTEIN CONFORMATION; PROTONS;

EID: 49449100490     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-008-9229-3     Document Type: Article

References (49)

1. M Billeter W Braun K Wuthrich 1982 Sequential resonance assignments in protein H-1 nuclear magnetic-resonance spectra - computation of sterically allowed proton proton distances and statistical-analysis of proton proton distances in single-crystal protein conformations J Mol Biol 155 321 346 10.1016/0022-2836(82)90008-0
2. A Böckmann 2006 Structural and dynamic studies of proteins by high resolution solid state NMR C R Chim 9 381 392
3. Böckmann A, McDermott AE (2002) Assignments and prospects for structure determination of solid proteins using MAS and isotopic enrichment. In: Grant DM, Harris RK (eds)The encyclopedia of NMR. Wiley, London
4. A Böckmann A Lange A Galinier S Luca N Giraud M Juy H Heise R Montserret F Penin M Baldus 2003 Solid-state NMR sequential resonance assignments and conformational analysis of the 2 × 10.4 kDa dimeric form of the Bacillus subtilis protein Crh J Biomol NMR 27 323 339 10.1023/A:1025820611009 (Pubitemid 37322106)
5. A Böckmann M Juy E Bettler L Emsley A Galinier F Penin A Lesage 2005 Water-protein hydrogen exchange in the micro-crystalline protein Crh as observed by solid state NMR spectroscopy J Biomol NMR 32 195 207 10.1007/s10858-005-8073-y (Pubitemid 41258800)
6. M Carravetta X Zhao A Böckmann MH Levitt 2003 Coherence transfer selectivity in two-dimensional solid-state NMR Chem Phys Lett 376 515 523 10.1016/S0009-2614(03)00944-8 2003CPL...376..515C
7. F Castellani B van Rossum A Diehl M Schubert K Rehbein H Oschkinat 2002 Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy Nature 420 98 102 10.1038/nature01070 2002Natur.420...98C (Pubitemid 35291447)
8. V Chevelkov K Faelber A Schrey K Rehbein A Diehl B Reif 2007 Differential line broadening in MAS solid-state NMR due to dynamic interference J Am Chem Soc 129 10195 200 10.1021/ja072024c (Pubitemid 47312961)
9. V Chevelkov AV Zhuravleva Y Xue B Reif NR Skrynnikov 2007 Combined analysis of (15)N relaxation data from solid- and solution-state NMR spectroscopy J Am Chem Soc 129 12594 12595 10.1021/ja073234s (Pubitemid 350004432)
10. G DePaëpe N Giraud A Lesage P Hodgkinson A Böckmann L Emsley 2003 Transverse dephasing optimized solid-state NMR spectroscopy J Am Chem Soc 125 13938 13939 10.1021/ja037213j (Pubitemid 37420881)
11. L Duma S Hediger B Brutscher A Böckmann L Emsley 2003 Resolution enhancement in multidimensional solid-state NMR of 13C-labeled proteins using spin-state selection J Am Chem Soc 125 11816 11817 10.1021/ja036893n (Pubitemid 37175405)
12. RL Dunbrack FE Cohen 1997 Bayesian statistical analysis of protein side-chain rotamer preferences Protein Sci 6 1661 1681 10.1002/pro.5560060807
13. M Ernst A Detken A Böckmann BH Meier 2003 NMR spectra of a micro-crystalline protein at 30 kHz MAS J Am Chem Soc 125 15807 15810 10.1021/ja0369966 (Pubitemid 37553697)
14. M Etzkorn A Böckmann A Lange M Baldus 2004 Probing molecular interfaces using 2D magic-angle-spinning NMR on protein mixtures with different uniform labeling J Am Chem Soc 126 14746 14751 10.1021/ja0479181 (Pubitemid 39532154)
15. A Favier B Brutscher M Blackledge A Galinier J Deutscher F Penin D Marion 2002 Solution structure and dynamics of Crh, the Bacillus subtilis catabolite repression HPr J Mol Biol 317 131 144 10.1006/jmbi.2002.5397 (Pubitemid 34722205)
16. M Fossi F Castellani M Nilges H Oschkinat BJ van Rossum 2005 SOLARIA: a protocol for automated cross-peak assignment and structure calculation for solid-state magic-angle spinning NMR spectroscopy Angew Chem Int Ed Engl 44 6151 6154 10.1002/anie.200501884 (Pubitemid 41394102)
17. BM Fung AK Khitrin K Ermolaev 2000 An improved broadband decoupling sequence for liquid crystals and solids J Magn Reson 142 97 101 10.1006/jmre.1999.1896 2000JMagR.142...97F
18. A Galinier J Haiech MC Kilhoffer M Jaquinod J Stulke J Deutscher I Martin-Verstraete 1997 The Bacillus subtilis crh gene encodes a Hpr-like protein involved in carbon catabolite repression Proc Natl Acad Sci USA 94 8439 8444 10.1073/pnas.94.16.8439 1997PNAS...94.8439G (Pubitemid 27335057)
19. N Giraud A Böckmann A Lesage F Penin M Blackledge L Emsley 2004 Site-specific backbone dynamics from a crystalline protein by solid-state NMR spectroscopy J Am Chem Soc 126 11422 11423 10.1021/ja046578g (Pubitemid 39244942)
20. N Giraud M Blackledge M Goldman A Böckmann A Lesage F Penin L Emsley 2005 Quantitative analysis of backbone dynamics in a crystalline protein from nitrogen-15 spin-lattice relaxation J Am Chem Soc 127 18190 18201 10.1021/ja055182h (Pubitemid 43038482)
21. N Giraud J Sein G Pintacuda A Böckmann A Lesage M Blackledge L Emsley 2006 Observation of heteronuclear overhauser effects confirms the 15N-1H dipolar relaxation mechanism in a crystalline protein J Am Chem Soc 128 12398 12399 10.1021/ja064037g (Pubitemid 44476613)
22. N Giraud M Blackledge A Böckmann L Emsley 2007 The influence of nitrogen-15 proton driven spin diffusion on the measurement of nitrogen-15 longitudinal relaxation times J Magn Reson 184 51 61 10.1016/j.jmr.2006.09.015 2007JMagR.184...51G (Pubitemid 46049039)
23. A Grommek BH Meier M Ernst 2006 Distance information from proton-driven spin diffusion under MAS Chem Phys Lett 427 404 409 10.1016/j.cplett.2006.07.005 2006CPL...427..404G (Pubitemid 44189332)
24. P Güntert YQ Qian G Otting M Müller W Gehring K Wüthrich 1991 Structure determination of the Antp (C39 - - S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS and GLOMSA J Mol Biol 217 531 540 10.1016/0022-2836(91)90755-U (Pubitemid 121003299)
25. S Hediger BH Meier RR Ernst 1995 Adiabatic passage Hartmann-Hahn cross polarization in NMR under magic angle sample spinning Chem Phys Lett 240 449 456 10.1016/0009-2614(95)00505-X 1995CPL...240..449H
26. H Heise K Seidel M Etzkorn S Becker M Baldus 2005 3D NMR spectroscopy for resonance assignment and structure elucidation of proteins under MAS: novel pulse schemes and sensitivity consideration J Magn Reson 173 64 74 10.1016/j.jmr.2004.11.020 2005JMagR.173...64H (Pubitemid 40206418)
27. M Hologne K Faelber A Diehl B Reif 2005 Characterization of dynamics of perdeuterated proteins by MAS solid-state NMR J Am Chem Soc 127 11208 11209 10.1021/ja051830l (Pubitemid 41176858)
28. M Hologne Z Chen B Reif 2006 Characterization of dynamic processes using deuterium in uniformly 2H,13C,15N enriched peptides by MAS solid-state NMR J Magn Reson 179 20 28 10.1016/j.jmr.2005.10.014 2006JMagR.179...20H
29. M Hong K Jakes 1999 Selective and extensive 13C labeling of a membrane protein for solid-state NMR investigations J Biomol NMR 14 71 74 10.1023/A:1008334930603 (Pubitemid 29258287)
30. CP Jaroniec BA Tounge J Herzfeld RG Griffin 2001 Frequency selective heteronuclear dipolar recoupling in rotating solids: accurate (13)C-(15)N distance measurements in uniformly (13)C,(15)N-labeled peptides J Am Chem Soc 123 3507 3519 10.1021/ja003266e (Pubitemid 32884585)
31. M Juy F Penin A Favier A Galinier R Montserret R Haser J Deutscher A Böckmann 2003 Dimerization of Crh by reversible 3D domain swapping induces structural adjustments to its monomeric homologue HPr J Mol Biol 332 767 776 10.1016/S0022-2836(03)00918-5 (Pubitemid 37101365)
32. V Ladizhansky RG Griffin 2004 Band selective carbonyl to aliphatic side chain distance measurements J Am Chem Soc 126 948 958 10.1021/ja037138c (Pubitemid 38114379)
33. A Lange S Luca M Baldus 2002 Structural constraints from proton-mediated rare-spin correlation spectroscopy in rotating solids J Am Chem Soc 124 9704 9705 10.1021/ja026691b (Pubitemid 34906915)
34. A Lange K Seidel L Verdier S Luca M Baldus 2003 Analysis of proton-proton transfer dynamics in rotating solids and their use for 3D structure determination J Am Chem Soc 125 12640 12648 10.1021/ja034555g (Pubitemid 37254778)
35. A Lange S Becker K Seidel K Giller O Pongs M Baldus 2005 A concept for rapid protein-structure determination by solid-state NMR spectroscopy Angew Chem Int Ed Engl 44 2 5
36. A Lesage A Böckmann 2003 Water-protein interactions in microcrystalline Crh measured by 1H-13C solid-state NMR spectroscopy J Am Chem Soc 125 13336 13337 10.1021/ja036720y (Pubitemid 37352102)
37. A Lesage L Emsley F Penin A Böckmann 2006 Investigation of dipolar-mediated water-protein interactions in microcrystalline Crh by solid-state NMR spectroscopy J Am Chem Soc 128 8246 8255 10.1021/ja060866q (Pubitemid 43967769)
38. SC Lovell JM Word JS Richardson DC Richardson 2000 The penultimate rotamer library Proteins 40 389 408 10.1002/1097-0134(20000815)40:3<389::AID- PROT50>3.0.CO;2-2 (Pubitemid 30624447)
39. JL Markley A Bax Y Arata CW Hilbers R Kaptein BD Sykes PE Wright K Wüthrich 1998 Recommendations for the presentation of NMR structures of proteins and nucleic acids Eur J Biochem 256 1 15 10.1046/j.1432-1327.1998. 2560001.x
40. Marulanda D, Tasayco ML, Cataldi M, Arriaran V, Polenova T (2005) Resonance assignments and secondary structure analysis of E. coli Thioredoxin by magic angle spinning solid-state NMR spectroscopy. J Phys Chem B 18135-18145
41. G Metz XL Wu SO Smith 1994 Ramped-amplitude cross-polarization in magic-angle-spinning Nmr J Magn Reson Ser A 110 219 227 10.1006/jmra.1994.1208
42. M Nilges 1995 Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities J Mol Biol 245 645 660 10.1006/jmbi.1994.0053
43. F Penin A Favier R Montserret B Brutscher J Deutscher D Marion A Galinier 2001 Evidence for a dimerisation state of the Bacillus subtilis catabolite repression HPr-like protein, Crh J Mol Microbiol Biotechnol 3 429 432
44. GN Ramachandran C Ramakrishnan V Sasisekharan 1963 Stereochemistry of polypeptide chain configurations J Mol Biol 7 95
45. B Reif Y Xue V Agarwal MS Pavlova M Hologne A Diehl YE Ryabov NR Skrynnikov 2006 Protein side-chain dynamics observed by solution- and solid-state NMR: comparative analysis of methyl 2H relaxation data J Am Chem Soc 128 12354 12355 10.1021/ja062808a (Pubitemid 44476592)
46. Seidel K, Etzkorn M, Heise H, Becker S, Baldus M (2005) High-resolution solid-state NMR studies on uniformly [(13)C,(15)N]-labeled ubiquitin. Chembiochem 6(9):1638-1647
47. L Sonnenberg S Luca M Baldus 2004 Multiple-spin analysis of chemical-shift-selective (13C, 13C) transfer in uniformly labeled biomolecules J Magn Reson 166 100 110 10.1016/j.jmr.2003.10.014 2004JMagR.166..100S
48. Y Xue MS Pavlova YE Ryabov B Reif NR Skrynnikov 2007 Methyl rotation barriers in proteins from 2H relaxation data. Implications for protein structure J Am Chem Soc 129 6827 6838 10.1021/ja0702061 (Pubitemid 46847525)
49. SG Zech AJ Wand AE McDermott 2005 Protein structure determination by high-resolution solid-state NMR spectroscopy: application to microcrystalline ubiquitin J Am Chem Soc 127 8618 8626 10.1021/ja0503128 (Pubitemid 40868243)