메뉴 건너뛰기




Volumn 53, Issue 12, 2014, Pages 1971-1981

Strategies for protein NMR in Escherichia coli

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CELLS; COMPLEXATION; CYTOLOGY; DEUTERIUM; ESCHERICHIA COLI; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

EID: 84898071694     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi500079u     Document Type: Article
Times cited : (27)

References (58)
  • 1
    • 0026344818 scopus 로고
    • Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli
    • Zimmerman, S. B. and Trach, S. O. (1991) Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli J. Mol. Biol. 222, 599-620
    • (1991) J. Mol. Biol. , vol.222 , pp. 599-620
    • Zimmerman, S.B.1    Trach, S.O.2
  • 2
    • 0033991590 scopus 로고    scopus 로고
    • Cytoarchitecture and physical properties of cytoplasm: Volume, viscosity, diffusion, intracellular surface area
    • Luby-Phelps, K. (1999) Cytoarchitecture and physical properties of cytoplasm: Volume, viscosity, diffusion, intracellular surface area Int. Rev. Cytol. 192, 189-221
    • (1999) Int. Rev. Cytol. , vol.192 , pp. 189-221
    • Luby-Phelps, K.1
  • 3
    • 0037040878 scopus 로고    scopus 로고
    • Macromolecular crowding accelerates amyloid formation by human apolipoprotein C-II
    • Hatters, D. M., Minton, A. P., and Howlett, G. J. (2002) Macromolecular crowding accelerates amyloid formation by human apolipoprotein C-II J. Biol. Chem. 277, 7824-7830
    • (2002) J. Biol. Chem. , vol.277 , pp. 7824-7830
    • Hatters, D.M.1    Minton, A.P.2    Howlett, G.J.3
  • 4
    • 78049249046 scopus 로고    scopus 로고
    • Effects of macromolecular crowding on protein conformational changes
    • Dong, H., Qin, S., and Zhou, H. (2010) Effects of macromolecular crowding on protein conformational changes PLoS Comput. Biol. 6, e1000833-1-e1000833-10
    • (2010) PLoS Comput. Biol. , vol.6
    • Dong, H.1    Qin, S.2    Zhou, H.3
  • 5
    • 77955044557 scopus 로고    scopus 로고
    • Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state
    • Hong, J. and Gierasch, L. M. (2010) Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state J. Am. Chem. Soc. 132, 10445-10452
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 10445-10452
    • Hong, J.1    Gierasch, L.M.2
  • 7
    • 37649016316 scopus 로고    scopus 로고
    • Molecular crowding enhances native structure and stability of α/β protein flavodoxin
    • Stagg, L., Zhang, S., Cheung, M. S., and Wittung-Stafshede, P. (2007) Molecular crowding enhances native structure and stability of α/β protein flavodoxin Proc. Natl. Acad. Sci. U.S.A. 104, 18976-18981
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 18976-18981
    • Stagg, L.1    Zhang, S.2    Cheung, M.S.3    Wittung-Stafshede, P.4
  • 9
    • 34250680620 scopus 로고    scopus 로고
    • In-cell NMR for protein-protein interactions (STINT-NMR)
    • Burz, D. S., Dutta, K., Cowburn, D., and Shekhtman, A. (2006) In-cell NMR for protein-protein interactions (STINT-NMR) Nat. Protoc. 1, 146-152
    • (2006) Nat. Protoc. , vol.1 , pp. 146-152
    • Burz, D.S.1    Dutta, K.2    Cowburn, D.3    Shekhtman, A.4
  • 10
  • 13
    • 43949111008 scopus 로고    scopus 로고
    • Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: Implications for in-cell NMR spectroscopy
    • 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
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 6310-6311
    • Li, C.1    Charlton, L.M.2    Lakkavaram, A.3    Seagle, C.4    Wang, G.5    Young, G.B.6    Macdonald, J.M.7    Pielak, G.J.8
  • 14
  • 19
    • 33747059858 scopus 로고    scopus 로고
    • Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes
    • 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. U.S.A. 103, 11904-11909
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 11904-11909
    • Selenko, P.1    Serber, Z.2    Gadea, B.3    Ruderman, J.4    Wagner, G.5
  • 22
    • 79955024130 scopus 로고    scopus 로고
    • Protein interactions in the Escherichia coli cytosol: An impediment to in-cell NMR spectroscopy
    • Crowley, P. B., Chow, E., and Papkovskaia, T. (2011) Protein interactions in the Escherichia coli cytosol: An impediment to in-cell NMR spectroscopy ChemBioChem 12, 1043-1048
    • (2011) ChemBioChem , vol.12 , pp. 1043-1048
    • Crowley, P.B.1    Chow, E.2    Papkovskaia, T.3
  • 24
    • 33846809165 scopus 로고    scopus 로고
    • 19F-amino acid into proteins as an NMR probe for characterizing protein structure and reactivity
    • 19F-amino acid into proteins as an NMR probe for characterizing protein structure and reactivity J. Am. Chem. Soc. 129, 1160-1166
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 1160-1166
    • Jackson, J.C.1    Hammill, J.T.2    Mehl, R.A.3
  • 25
    • 0024788406 scopus 로고
    • Monitoring intracellular metabolism by nuclear magnetic resonance
    • Cohen, J. S., Lyon, R. C., and Daly, P. F. (1989) Monitoring intracellular metabolism by nuclear magnetic resonance Methods Enzymol. 177, 435-452
    • (1989) Methods Enzymol. , vol.177 , pp. 435-452
    • Cohen, J.S.1    Lyon, R.C.2    Daly, P.F.3
  • 26
    • 0026578167 scopus 로고
    • NMR spectroscopy of cells
    • Szwergold, B. S. (1992) NMR spectroscopy of cells Annu. Rev. Physiol. 54, 775-798
    • (1992) Annu. Rev. Physiol. , vol.54 , pp. 775-798
    • Szwergold, B.S.1
  • 27
    • 0035807847 scopus 로고    scopus 로고
    • In-cell NMR spectroscopy
    • Serber, Z. and Dötsch, V. (2001) In-cell NMR spectroscopy Biochemistry 40, 14317-14323
    • (2001) Biochemistry , vol.40 , pp. 14317-14323
    • Serber, Z.1    Dotsch, V.2
  • 30
    • 0035913735 scopus 로고    scopus 로고
    • Evaluation of parameters critical to observing proteins inside living Escherichia coli by in-cell NMR spectroscopy
    • Serber, Z., Ledwidge, R., Miller, S. M., and 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
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 8895-8901
    • Serber, Z.1    Ledwidge, R.2    Miller, S.M.3    Dotsch, V.4
  • 32
    • 84877014249 scopus 로고    scopus 로고
    • Soft interactions and crowding
    • Sarkar, M., Li, C., and Pielak, G. J. (2013) Soft interactions and crowding Biophys. Rev. 5, 187-194
    • (2013) Biophys. Rev. , vol.5 , pp. 187-194
    • Sarkar, M.1    Li, C.2    Pielak, G.J.3
  • 33
    • 84888376873 scopus 로고    scopus 로고
    • Impact of reconstituted cytosol on protein stability
    • Sarkar, M., Smith, A. E., and Pielak, G. J. (2013) Impact of reconstituted cytosol on protein stability Proc. Natl. Acad. Sci. U.S.A. 110, 19342-19347
    • (2013) Proc. Natl. Acad. Sci. U.S.A. , vol.110 , pp. 19342-19347
    • Sarkar, M.1    Smith, A.E.2    Pielak, G.J.3
  • 34
    • 63149177937 scopus 로고    scopus 로고
    • Using NMR to distinguish viscosity effects from nonspecific protein binding under crowded conditions
    • Li, C. and Pielak, G. J. (2009) Using NMR to distinguish viscosity effects from nonspecific protein binding under crowded conditions J. Am. Chem. Soc. 131, 1368-1369
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 1368-1369
    • Li, C.1    Pielak, G.J.2
  • 35
    • 80055013471 scopus 로고    scopus 로고
    • Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell nuclear magnetic resonance spectroscopy
    • Wang, Q., Zhuravleva, A., and Gierasch, L. M. (2011) Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell nuclear magnetic resonance spectroscopy Biochemistry 50, 9225-9236
    • (2011) Biochemistry , vol.50 , pp. 9225-9236
    • Wang, Q.1    Zhuravleva, A.2    Gierasch, L.M.3
  • 36
    • 77955686807 scopus 로고    scopus 로고
    • Effects of proteins on protein diffusion
    • Wang, Y., Li, C., and Pielak, G. J. (2010) Effects of proteins on protein diffusion J. Am. Chem. Soc. 132, 9392-9397
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 9392-9397
    • Wang, Y.1    Li, C.2    Pielak, G.J.3
  • 37
    • 84868122319 scopus 로고    scopus 로고
    • Is buffer a good proxy for a crowded cell-like environment? A comparative NMR study of calmodulin side-chain dynamics in buffer and E coli lysate
    • Latham, M. P. and Kay, L. E. (2012) Is buffer a good proxy for a crowded cell-like environment? A comparative NMR study of calmodulin side-chain dynamics in buffer and E. coli lysate PLoS One 7, e48226-1-e48226-13
    • (2012) PLoS One , vol.7
    • Latham, M.P.1    Kay, L.E.2
  • 39
    • 63649113699 scopus 로고    scopus 로고
    • Origin and function of ubiquitin-like proteins
    • Hochstrasser, M. (2009) Origin and function of ubiquitin-like proteins Nature 458, 422-429
    • (2009) Nature , vol.458 , pp. 422-429
    • Hochstrasser, M.1
  • 40
    • 78650522132 scopus 로고    scopus 로고
    • NMR investigation of calmodulin
    • (Webb, G. A. Ed.), Springer, Dordrecht, The Netherlands
    • Mal, T. K. and Ikura, M. (2006) NMR investigation of calmodulin, In Modern Magnetic Resonance (Webb, G. A., Ed.) pp 503-516, Springer, Dordrecht, The Netherlands.
    • (2006) Modern Magnetic Resonance , pp. 503-516
    • Mal, T.K.1    Ikura, M.2
  • 41
  • 43
    • 33644644556 scopus 로고    scopus 로고
    • 13C labeling of aromatic side chains in proteins for NMR relaxation measurements
    • 13C labeling of aromatic side chains in proteins for NMR relaxation measurements J. Am. Chem. Soc. 128, 2506-2507
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 2506-2507
    • Teilum, K.1    Brath, U.2    Lundstrom, P.3    Akke, M.4
  • 45
    • 0024836418 scopus 로고
    • Expression and nitrogen-15 labeling of proteins for proton and nitrogen-15 nuclear magnetic resonance
    • Muchmore, D. C., McIntosh, L. P., Russell, C. B., Anderson, D. E., and Dahlquist, F. W. (1989) Expression and nitrogen-15 labeling of proteins for proton and nitrogen-15 nuclear magnetic resonance Methods Enzymol. 177, 44-73
    • (1989) Methods Enzymol. , vol.177 , pp. 44-73
    • Muchmore, D.C.1    McIntosh, L.P.2    Russell, C.B.3    Anderson, D.E.4    Dahlquist, F.W.5
  • 46
    • 58149463865 scopus 로고    scopus 로고
    • An efficient protocol for the complete incorporation of methyl-protonated alanine in perdeuterated protein
    • Ayala, I., Sounier, R., Usé, N., Gans, P., and Boisbouvier, J. (2009) An efficient protocol for the complete incorporation of methyl-protonated alanine in perdeuterated protein J. Biomol. NMR 43, 111-119
    • (2009) J. Biomol. NMR , vol.43 , pp. 111-119
    • Ayala, I.1    Sounier, R.2    Usé, N.3    Gans, P.4    Boisbouvier, J.5
  • 47
    • 78650588910 scopus 로고    scopus 로고
    • Alanine methyl groups as NMR probes of molecular structure and dynamics in high-molecular-weight proteins
    • Godoy-Ruiz, R., Guo, C., and Tugarinov, V. (2010) Alanine methyl groups as NMR probes of molecular structure and dynamics in high-molecular-weight proteins J. Am. Chem. Soc. 132, 18340-18350
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 18340-18350
    • Godoy-Ruiz, R.1    Guo, C.2    Tugarinov, V.3
  • 48
    • 78650768713 scopus 로고    scopus 로고
    • In-cell protein NMR and protein leakage
    • Barnes, C. O. and Pielak, G. J. (2011) In-cell protein NMR and protein leakage Proteins 79, 347-351
    • (2011) Proteins , vol.79 , pp. 347-351
    • Barnes, C.O.1    Pielak, G.J.2
  • 49
    • 2942755921 scopus 로고    scopus 로고
    • A captured folding intermediate involved in dimerization and domain-swapping of GB1
    • Byeon, I. J., Louis, J. M., and Gronenborn, A. M. (2004) A captured folding intermediate involved in dimerization and domain-swapping of GB1 J. Mol. Biol. 340, 615-625
    • (2004) J. Mol. Biol. , vol.340 , pp. 615-625
    • Byeon, I.J.1    Louis, J.M.2    Gronenborn, A.M.3
  • 50
    • 0021886339 scopus 로고
    • Bacterial expression and characterization of proteins derived from the chicken calmodulin cDNA and a calmodulin processed gene
    • Putkey, J., Slaughter, G., and Means, A. (1985) Bacterial expression and characterization of proteins derived from the chicken calmodulin cDNA and a calmodulin processed gene J. Biol. Chem. 260, 4704-4712
    • (1985) J. Biol. Chem. , vol.260 , pp. 4704-4712
    • Putkey, J.1    Slaughter, G.2    Means, A.3
  • 51
    • 0030992890 scopus 로고    scopus 로고
    • De novo design of the hydrophobic core of ubiquitin
    • Lazar, G. A., Desjarlais, J. R., and Handel, T. M. (1997) De novo design of the hydrophobic core of ubiquitin Protein Sci. 6, 1167-1178
    • (1997) Protein Sci. , vol.6 , pp. 1167-1178
    • Lazar, G.A.1    Desjarlais, J.R.2    Handel, T.M.3
  • 52
    • 0029400480 scopus 로고
    • NMRPipe: A multidimensional spectral processing system based on UNIX pipes
    • Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes J. Biomol. NMR 6, 277-293
    • (1995) J. Biomol. NMR , vol.6 , pp. 277-293
    • Delaglio, F.1    Grzesiek, S.2    Vuister, G.W.3    Zhu, G.4    Pfeifer, J.5    Bax, A.6
  • 54
    • 77956458408 scopus 로고    scopus 로고
    • The STINT-NMR method for studying in-cell protein-protein interactions
    • Burz, D. S. and Shekhtman, A. (2010) The STINT-NMR method for studying in-cell protein-protein interactions Curr. Protoc. Protein Sci. 17.11-1-17.11-20
    • (2010) Curr. Protoc. Protein Sci. , pp. 17111-17127
    • Burz, D.S.1    Shekhtman, A.2
  • 55
    • 31744435251 scopus 로고    scopus 로고
    • Mapping structural interactions using in-cell NMR spectroscopy (STINT-NMR)
    • 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
    • (2006) Nat. Methods , vol.3 , pp. 91-93
    • Burz, D.S.1    Dutta, K.2    Cowburn, D.3    Shekhtman, A.4
  • 56
    • 0141928674 scopus 로고    scopus 로고
    • TROSY in NMR studies of the structure and function of large biological macromolecules
    • Fernández, C. and Wider, G. (2003) TROSY in NMR studies of the structure and function of large biological macromolecules Curr. Opin. Struct. Biol. 13, 570-580
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 570-580
    • Fernández, C.1    Wider, G.2
  • 57
    • 84865179944 scopus 로고    scopus 로고
    • 13C relaxation experiments for aromatic side chains employing longitudinal- and transverse-relaxation optimized NMR spectroscopy
    • 13C relaxation experiments for aromatic side chains employing longitudinal- and transverse-relaxation optimized NMR spectroscopy J. Biomol. NMR 53, 181-190
    • (2012) J. Biomol. NMR , vol.53 , pp. 181-190
    • Weininger, U.1    Diehl, C.2    Akke, M.3
  • 58
    • 33846928691 scopus 로고    scopus 로고
    • Quantitative dynamics and binding studies of the 20S proteasome by NMR
    • Sprangers, R. and Kay, L. E. (2007) Quantitative dynamics and binding studies of the 20S proteasome by NMR Nature 445, 618-622
    • (2007) Nature , vol.445 , pp. 618-622
    • Sprangers, R.1    Kay, L.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.