In-cell NMR spectroscopy in escherichia coli

Methods in Molecular Biology

Volumn 831, Issue , 2012, Pages 261-271

  Robinson, Kirsten E ^a   Reardon, Patrick N ^a   Spicer, Leonard D ^a,b  

^a DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b DUKE UNIVERSITY   (United States)

Author keywords

Escherichia coli; Fast NMR spectroscopy; In cell NMR spectroscopy; Protein NMR spectroscopy

Indexed keywords

ESCHERICHIA COLI PROTEIN;

ARTICLE; CELL SURVIVAL; ESCHERICHIA COLI; METABOLISM; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE;

CELL SURVIVAL; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; XENOPUS LAEVIS;

EID: 84855896814     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-480-3_15     Document Type: Article

References (42)

1. Dobson, C. M. (2004) Chemical space and biology. Nature 432, 824-828. (Pubitemid 40037137)
2. Goto, S., Okuno, Y., Hattori, M., Nishioka, T., and Kanehisa, M. (2002) LIGAND: database of chemical compounds and reactions in biological pathways. Nucl. Acids Res. 30, 402-404. (Pubitemid 34679597)
3. Lander, E. S., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921. (Pubitemid 32165345)
4. Goodsell, D. S. (1991) Inside a living cell. Trends Biochem. Sci. 16, 203-206. (Pubitemid 121004436)
5. Ellis, R. J., and Minton, A. P. (2003) Cell biology: join the crowd. Nature 425, 27-28.
6. Hall, D., and Minton, A. P. (2003) Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges. Biochim. Biophys. Acta. 1649, 127-139. (Pubitemid 38234581)
7. Burz, D. S., Dutta, K., Cowburn, D., and Shekhtman, A. (2006) Mapping structural interactions using in-cell NMR spectroscopy (STINT-NMR). Nat. Methods 3, 91-93. (Pubitemid 43173306)
8. Reardon, P. N., and Spicer, L. D. (2005) Multidimensional NMR spectroscopy for protein characterization and assignment inside cells. J. Am. Chem. Soc. 127, 10848-10849. (Pubitemid 41129858)
9. Sakakibara, D., Sasaki, A., Ikeya, T., Hamatsu, J., Hanashima, T., Mishima, M., Yoshimasu, M., Hayashi, N., Mikawa, T., Walchli, M., Smith, B. O., Shirakawa, M., Guntert, P., and Ito, Y. (2009) Protein structure determination in living cells by in-cell NMR spectroscopy. Nature 458, 102-105.
10. 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, B. O., Shirakawa, M., Guntert, P., and Ito, Y. (2010) NMR protein structure determination in living E. coli cells using nonlinear sampling. Nat. Protoc. 5, 1051-1060.
11. Augustus, A. M., Reardon, P. N., and Spicer, L. D. (2009) MetJ repressor interactions with DNA probed by in-cell NMR. Proc. Natl. Acad. Sci. USA 106, 5065-5069.
12. Hubbard, J. A., MacLachlan, L. K., King, G. W., Jones, J. J., and Fosberry, A. P. (2003) Nuclear magnetic resonance spectroscopy reveals the functional state of the signalling protein CheY in vivo in Escherichia coli. Mol. Microbiol. 49, 1191-1200. (Pubitemid 37153490)
13. Xie, J., Thapa, R., Reverdatto, S., Burz, D. S., and Shekhtman, A. (2009) Screening of small molecule interactor library by using in-cell NMR spectroscopy (SMILI-NMR). J. Med. Chem. 52, 3516-3522.
14. Serber, Z., Keatinge-Clay, A. T., Ledwidge, R., Kelly, A. E., Miller, S. M., and Dotsch, V. (2001) High-resolution macromolecular NMR spectroscopy inside living cells. J. Am. Chem. Soc. 123, 2446-2447. (Pubitemid 32904788)
15. Serber, Z., Straub, W., Corsini, L., Nomura, A. M., Shimba, N., Craik, C. S., Ortiz de Montellano, P., and Dotsch, V. (2004) Methyl groups as probes for proteins and complexes in in-cell NMR experiments. J. Am. Chem. Soc. 126, 7119-7125. (Pubitemid 38855411)
16. Tugarinov, V., and Kay, L. E. (2003) Ile, Leu, and Val methyl assignments of the 723-residue malate synthase G using a new labeling strategy and novel NMR methods. J. Am. Chem. Soc. 125, 13868-13878. (Pubitemid 37386061)
17. Goto, N. K., Gardner, K. H., Mueller, G. A., Willis, R. C., and Kay, L. E. (1999) A robust and cost-effective method for the production of Val, Leu, Ile (delta 1) methyl-protonated 15N-, 13C-, 2H-labeled proteins. J. Biomol. NMR 13, 369-374. (Pubitemid 29210329)
18. Li, C., Wang, G. F., Wang, Y., Creager-Allen, R., Lutz, E. A., Scronce, H., Slade, K. M., Ruf, R. A., Mehl, R. A., and Pielak, G. J. (2010) Protein (19)F NMR in Escherichia coli. J. Am. Chem. Soc. 132, 321-327.
19. Serber, Z., Ledwidge, R., Miller, S. M., and Dotsch, 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. (Pubitemid 32884710)
20. Li, C., Charlton, L. M., Lakkavaram, A., Seagle, C., Wang, G., Young, G. B., Macdonald, J. M., and Pielak, G. J. (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. (Pubitemid 351706077)
21. Barnes, C. O., and Pielak, G. J. (2010) In-cell protein NMR and protein leakage, Proteins 79, 347-351.
22. Burz, D. S., and Shekhtman, A. (2008) In-cell biochemistry using NMR spectroscopy. PLoS One 3, e2571.
23. Dedmon, M. M., Patel, C. N., Young, G. B., and Pielak, G. J. (2002) FlgM gains structure in living cells. Proc. Natl. Acad. Sci. USA 99, 12681-12684.
24. McNulty, B. C., Young, G. B., and Pielak, G. J. (2006) Macromolecular crowding in the Escherichia coli periplasm maintains alpha-synuclein disorder. J. Mol. Biol. 355, 893-897. (Pubitemid 43012748)
25. Mandelshtam, V. A., Taylor, H. S., and Shaka, A. J. (1998) Application of the filter diagonalization method to one-and two-dimensional NMR spectra. J. Magn. Reson. 133, 304-312. (Pubitemid 128450646)
26. Kupce, E., and Freeman, R. (2003) Fast multidimensional NMR of proteins. J. Biomol. NMR 25, 349-354.
27. Schanda, P., Kupce, E., and Brutscher, B. (2005) SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds. J. Biomol. NMR 33, 199-211. (Pubitemid 43118574)
28. Kupce, E., and Freeman, R. (2003) Projectionreconstruction of three-dimensional NMR spectra. J. Am. Chem. Soc. 125, 13958-13959.
29. Coggins, B. E., Venters, R. A., and Zhou, P. (2004) Generalized reconstruction of n-D NMR spectra from multiple projections: application to the 5-D HACACONH spectrum of protein G B1 domain. J. Am. Chem. Soc. 126, 1000-1001. (Pubitemid 38140713)
30. Coggins, B. E., and Zhou, P. (2007) Sampling of the NMR time domain along concentric rings. J. Magn. Reson. 184, 207-221. (Pubitemid 46177664)
31. Barna, J. C. J., Laue, E. D., Mayger, M. R., Skilling, J., and Worrall, S. J. P. (1987) Exponential Sampling, an alternative method for sampling in two-dimensional NMR experiments. J. Magn. Reson. 73, 69-77.
32. Hiller, S., Fiorito, F., Wuthrich, K., and Wider, G. (2005) Automated projection spectroscopy (APSY). Proc. Natl. Acad. Sci. USA 102, 10876-10881. (Pubitemid 41105960)
33. Eghbalnia, H. R., Bahrami, A., Tonelli, M., Hallenga, K., and Markley, J. L. (2005) Highresolution iterative frequency identification for NMR as a general strategy for multidimensional data collection. J. Am. Chem. Soc. 127, 12528-12536. (Pubitemid 41292171)
34. Kupce, E., and Freeman, R. (2004) Projectionreconstruction technique for speeding up multidimensional NMR spectroscopy. J. Am. Chem. Soc. 126, 6429-6440. (Pubitemid 38657067)
35. Venters, R. A., Coggins, B. E., Kojetin, D., Cavanagh, J., and Zhou, P. (2005) (4,2)D Projection-reconstruction experiments for protein backbone assignment: application to human carbonic anhydrase II and calbindin D(28 K). J. Am. Chem. Soc. 127, 8785-8795. (Pubitemid 40868260)
36. Coggins, B. E., Venters, R. A., and Zhou, P. (2005) Filtered backprojection for the reconstruction of a high-resolution (4,2)D CH3-NH NOESY spectrum on a 29 kDa protein. J. Am. Chem. Soc. 127, 11562-11563. (Pubitemid 41208719)
37. Kupce, E., and Freeman, R. (2003) Reconstruction of the three-dimensional NMR spectrum of a protein from a set of plane projections. J. Biomol. NMR 27, 383-387. (Pubitemid 37322109)
38. Coggins, B. E., and Zhou, P. (2006) Polar Fourier transforms of radially sampled NMR data. J. Magn. Reson. 182, 84-95. (Pubitemid 44293437)
39. Selenko, P., Serber, Z., Gadea, B., Ruderman, J., and 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. (Pubitemid 44215784)
40. Inomata, K., Ohno, A., Tochio, H., Isogai, S., Tenno, T., Nakase, I., Takeuchi, T., Futaki, S., Ito, Y., Hiroaki, H., and Shirakawa, M. (2009) High-resolution multi-dimensional NMR spectroscopy of proteins in human cells. Nature 458, 106-109.
41. Beckman, J. S., and Siedow, J. N. (1985) Bactericidal agents generated by the peroxidasecatalyzed oxidation of para-hydroquinones. J. Biol. Chem. 260, 14604-14609. (Pubitemid 16210984)
42. Sambrook, J., and Russell, D. W., (Eds.) (2001) Molecular Cloning: A Laboratory Manual, Vol. 3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor.