In-cell NMR of intrinsically disordered proteins in prokaryotic cells

Methods in Molecular Biology

Volumn 895, Issue , 2012, Pages 19-31

  Ito, Yutaka ^a   Mikawa, Tsutomu ^b   Smith, Brian O ^c  

^a TOKYO METROPOLITAN UNIVERSITY   (Japan)

^b RIKEN   (Japan)

^c UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

Escherichia coli; Heteronuclear multidimensional NMR; In cell NMR; Protein dynamics; Protein structure; Rapid NMR measurement

Indexed keywords

RECOMBINANT PROTEIN;

ARTICLE; BIOSYNTHESIS; CHEMISTRY; CULTURE TECHNIQUE; ESCHERICHIA COLI; ISOTOPE LABELING; METABOLISM; NUCLEAR MAGNETIC RESONANCE; PROKARYOTIC CELL; PROTEIN CONFORMATION;

CULTURE TECHNIQUES; ESCHERICHIA COLI; ISOTOPE LABELING; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROKARYOTIC CELLS; PROTEIN CONFORMATION; RECOMBINANT PROTEINS;

EID: 84865331940     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-927-3_2     Document Type: Article

References (51)

1. Serber Z, Dotsch V (2001) In-cell NMR spectroscopy. Biochemistry 40:14317-14323
2. Serber Z, Corsini L, Durst F, Dötsch V (2005) In-cell NMR spectroscopy. Method Enzymol 394:17-41
3. Serber Z, Selenko P, Hänsel R, Reckel S, Löhr F, Ferrell JE, Wagner G, Dötsch V (2006) Investigating macromolecules inside cultured and injected cells by in-cell NMR spectroscopy. Nat Protoc 1:2701-2709
4. Burz DS, Dutta K, Cowburn D, Shekhtman A (2006) Mapping structural interactions using in-cell NMR spectroscopy (STINT-NMR). Nat Methods 3:91-93
5. Burz DS, Dutta K, Cowburn D, Shekhtman A (2006) In-cell NMR for protein-protein interactions (STINT-NMR). Nat Protoc 1:146-152
6. Reckel S, Hänsel R, Löhr F, Dötsch V (2007) In-cell NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 51:91-101
7. Selenko P, Wagner G (2007) Looking into live cells with in-cell NMR spectroscopy. J Struct Biol 158:244-253
8. Pielak GJ, Li C, Miklos AC, Schlesinger AP, Slade KM, Wang GF, Zigoneanu IG (2009) Protein nuclear magnetic resonance under physiological conditions. Biochemistry 48:226-234
9. Ellis RJ (2001) Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci 26:597-604
10. Serber Z, Keatinge-Clay AT, Ledwidge R, Kelly AE, Miller SM, Dötsch V (2001) Highresolution macromolecular NMR spectroscopy inside living cells. J Am Chem Soc 123:2446-2447
11. Serber Z, Ledwidge R, Miller SM, Dötsch V (2001) Evaluation of parameters critical to observing proteins inside living Escherichia coli by in-cell NMR spectroscopy. J Am Chem Soc 123:8895-8901
12. Wieruszeski JM, Bohin A, Bohin JP, Lippens G (2001) In vivo detection of the cyclic osmoregulated periplasmic glucan of Ralstonia solanacearum by high-resolution magic angle spinning NMR. J Magn Reson 151:118-123
13. Selenko P, Serber Z, Gade B, Ruderman J, Wagner G (2006) Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes. Proc Natl Acad Sci USA 103:11904-11909
14. Sakai T, Tochio H, Tenno T, Ito Y, Kokubo T, Hiroaki H, Shirakawa M (2006) In-cell NMR spectroscopy of proteins inside Xenopus laevis oocytes. J Biomol NMR 36:179-188
15. Bodart JF,Wieruszeski JM, Amniai L, Leroy A, Landrieu I, Rousseau-Lescuyer A, Vilain JP, Lippens G (2008) NMR observation of Tau in Xenopus oocytes. J Magn Reson 192:252-257
16. Inomata K, Ohno A, Tochio H, Isogai S, Tenno T, Nakase I, Takeuchi T, Futaki S, Ito Y, Hiroaki H, Shirakawa M (2009) Highresolution multi-dimensional NMR spectroscopy of proteins in human cells. Nature 458:106-109
17. Ogino S, Kubo S, Umemoto R, Huang S, Nishida N, Shimada I (2009) Observation of NMR signals from proteins introduced into living Mammalian cells by reversible membrane permeabilization using a pore-forming toxin, streptolysin O. J Am Chem Soc 131:10834-10835
18. Burz DS, Shekhtman A (2008) In-cell biochemistry using NMR spectroscopy. PLoS One 3:e2571
19. Augustus AM, Reardon PN, Spicer LD (2009) MetJ repressor interactions with DNA probed by in-cell NMR. Proc Natl Acad Sci USA 106:5065-5069
20. Li C, Charlton LM, Lakkavaram A, Seagle C, Wang G, Young GB, Macdonald JM, Pielak GJ (2008) Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: implications for in-cell NMR spectroscopy. J Am Chem Soc 130:6310-6311
21. Charlton LM, Barnes CO, Li C, Orans J, Young GB, Pielak GJ (2008) Residue-level interrogation of macromolecular crowding effects on protein stability. J Am Chem Soc 130:6826-6830
22. Xie J, Thapa R, Reverdatto S, Burz DS, Shekhtman A (2009) Screening of small molecule interactor library by using in-cell NMR spectroscopy (SMILI-NMR). J Med Chem 52:3516-3522
23. Sakakibara D, Sasaki A, Ikeya T, Hamatsu J, Hanashima T, Mishima M, Yoshimasu M, Hayashi N, Mikawa T, Walchli M, Smith BO, Shirakawa M, Guntert P, Ito Y (2009) Protein structure determination in living cells by in-cell NMR spectroscopy. Nature 458:102-105
24. Dedmon MM, Patel CN, Young GB, Pielak GJ (2002) FlgM gains structure in living cells. Proc Natl Acad Sci USA 99:12681-12684
25. Williams SP, Haggie PM, Brindle KM (1997) 19F NMR measurements of the rotational mobility of proteins in vivo. Biophys J 72:490-498
26. Ikeya T, Sasaki A, Sakakibara D, Shigemitsu Y, Hamatsu J, Hanashima T, Mishima M, Yoshimasu M, Hayashi N, Mikawa T, Nietlispach D, Walchli M, Smith BO, Shirakawa M, Guntert P, Ito Y (2010) NMR protein structure determination in living E. coli cells using nonlinear sampling. Nat Protoc 5:1051-1060
27. McIntosh LP, Dahlquist FW (1990) Biosynthetic incorporation of 15N and 13C for assignment and interpretation of nuclear magnetic resonance spectra of proteins. Q Rev Biophys 23:1-38
28. Serber Z, Straub W, Corsini L, Nomura AM, Shimba N, Craik CS, de Montellano PO, Dötsch V (2004) Methyl groups as probes for proteins and complexes in in-cell NMR experiments. J Am Chem Soc 126:7119-7125
29. Rosen MK, Gardner KH,Willis RC, Parris WE, Pawson T, Kay LE (1996) Selective methyl group protonation of perdeuterated proteins. J Mol Biol 263:627-636
30. Li C,Wang GF,Wang Y, Creager-Allen R, Lutz EA, Scronce H, Slade KM, Ruf RA, Mehl RA, Pielak GJ (2010) Protein 19F NMR in Escherichia coli. J Am Chem Soc 132:321-327
31. Jones DH, Cellitti SE, Hao X, Zhang Q, Jahnz M, Summerer D, Schultz PG, Uno T, Geierstanger BH (2010) Site-specific labeling of proteins with NMR-active unnatural amino acids. J Biomol NMR 46:89-100
32. Schanda P, Brutscher B (2005) Very fast twodimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. J Am Chem Soc 127:8014-8015
33. Schanda P, Van Melckebeke H, Brutscher B (2006) Speeding up three-dimensional protein NMR experiments to a few minutes. J Am Chem Soc 128:9042-9043
34. Barna JCJ, Laue ED, Mayger MR, Skilling J, Worrall SJP (1987) Exponential sampling, an alternative method for sampling in twodimensional NMR experiments. J Magn Reson 73:69-77
35. Schmieder P, Stern AS, Wagner G, Hoch JC (1994) Improved resolution in triple-resonance spectra by nonlinear sampling in the constanttime domain. J Biomol NMR 4:483-490
36. Rovnyak D, Frueh DP, Sastry M, Sun ZYJ, Stern AS, Hoch JC, Wagner G (2004) Accelerated acquisition of high resolution tripleresonance spectra using non-uniform sampling and maximum entropy reconstruction. J Magn Reson 170:15-21
37. Laue ED, Mayger MR, Skilling J, Staunton J (1986) Reconstruction of phase sensitive 2D NMR spectra by maximum entropy. J Magn Reson 68:14-29
38. Hoch JC, Stern AS (1996) NMR data processing. Wiley-Liss, New York
39. Jaravine V, Ibraghimov I, Orekhov VY (2006) Removal of a time barrier for high-resolution multidimensional NMR spectroscopy. Nat Methods 3:605-607
40. Marion D (2005) Fast acquisition of NMR spectra using Fourier transform of nonequispaced data. J Biomol NMR 32:141-150
41. Kazimierczuk K, Zawadzka A, Kozminski W, Zhukov I (2006) Random sampling of evolution time space and Fourier transform processing. J Biomol NMR 36:157-168
42. Kraulis PJ (1989) ANSIG: a program for the assignment of protein 1H 2D NMR spectra by interactive computer graphics. J Magn Reson 84:627-633
43. Kraulis PJ, Domaille PJ, Campbell-Burk SL, Van Aken T, Laue ED (1994) Solution structure and dynamics of Ras p21-GDP determined by heteronuclear three-and fourdimensional NMR spectroscopy. Biochemistry 33:3515-3531
44. Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59:687-696
45. Johnson BA, Blevins RA (1994) NMR View: a computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603-614
46. Johnson BA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278:313-352
47. 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 6:1-10
48. Güntert P (2003) Automated NMR protein structure calculation. Prog Nucl Magn Reson Spectrosc 43:105-125
49. Linge JP, O'Donoghue SI, Nilges M (2001) Automated assignment of ambiguous nuclear overhauser effects with ARIA. Methods Enzymol 339:71-90
50. Panchal SC, Bhavesh NS, Hosur RV (2001) Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins. J Biomol NMR 20:135-147
51. Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku Y, Miki K, Masui R, Kuramitsu S (2000) Structural genomics projects in Japan. Nat Struct Biol 7 Suppl: 943-945