Cytosol has a small effect on protein backbone dynamics

Biochemistry

Volumn 45, Issue 33, 2006, Pages 10085-10091

  Bryant, Julie E ^a,e   Lecomte, Juliette T J ^d   Lee, Andrew L ^b,c   Young, Gregory B ^b   Pielak, Gary J ^a,b,c  

^a University of North Carolina at Chapel Hill   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

^e MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOLOGY; DATA REDUCTION; DYNAMICS; MACROMOLECULES; MATHEMATICAL MODELS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

CYTOSOLS; DILUTE SOLUTION; OVERHAUSER ENHANCEMENT; PROTEIN BACKBONE DYNAMICS;

PROTEINS;

CYTOCHROME B5;

ARTICLE; CYTOSOL; DILUTION; DYNAMICS; ESCHERICHIA COLI; MACROMOLECULE; MODEL; NITROGEN NUCLEAR MAGNETIC RESONANCE; NONHUMAN; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; QUANTITATIVE ANALYSIS; VISCOSITY;

CELL NUCLEUS; CYTOCHROMES B5; CYTOSOL; ENZYME STABILITY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION; PROTEIN FOLDING; SOLUTIONS; TIME FACTORS; VISCOSITY;

ESCHERICHIA COLI;

EID: 33747462159     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi060547b     Document Type: Article

References (31)

1. Luby-Phelps, K. (2000) Cytoarchitecture and physical properties of cytoplasm: Volume, viscosity, diffusion, intracellular surface area, Int. Rev. Cytol. 192, 189-221.
2. Dedmon, M. M., Patel, C. N., Young, G. B., and Pielak, G. J. (2002) FlgM gains structure in living cells, Proc. Natl. Acad. Sci. U.S.A. 99, 12681-12684.
3. McNulty, B. C., Young, G. B., and Pielak, G. J. (2006) Macromolecular crowding in the Escherichia coli periplasm maintains α-synuclein disorder, J. Mol. Biol. 355, 893-897.
4. Rivas, G., Fernandez, J. A., and Minton, A. P. (2001) Direct observation of the enhancement of noncooperative protein self-assembly by macromolecular crowding: Indefinite linear self-association of bacterial cell division protein FtsZ, Proc. Natl. Acad. Sci. U.S.A. 98, 3150-3155.
5. Sasahara, K., McPhie, P., and Minton, A. P. (2003) Effect of dextran on protein stability and conformation attributed to macromolecular crowding, J. Mol. Biol. 326, 1227-1237.
6. Serber, Z., Corsini, L., Durst, F., and Dötsch, V. (2005) In-cell NMR spectroscopy, Methods Enzymol. 394, 17-41.
7. 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.
8. Bryant, J. E., Lecomte, J. T. J., Lee, A. L., Young, G. B., and Pielak, G. J. (2005) Protein dynamics in living cells, Biochemistry 44, 9275-9279.
9. 5, Biochemistry 35, 6519-6526.
10. 5, Biochemistry 40, 4879-4891.
11. 5 in its native, partially folded state, Biochemistry 38, 2577-2589.
12. Abragam, A. (1961) The Principles of Nuclear Magnetism, Clarendon Press, Oxford, U.K.
13. Palmer, A. G., III (2001) NMR probes of molecular dynamics: Overview and comparison with other techniques, Annu. Rev. Biophys. Biomol. Struct. 30, 129-155.
14. Lipari, G., and Szabo, A. (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity, J. Am. Chem. Soc. 104, 4546-4559.
15. Lipari, G., and Szabo, A. (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results, J. Am. Chem. Soc. 104, 4559-4570.
16. 2 values in proteins, J. Magn. Reson. 97, 359-375.
17. Kay, L. E., Keifer, P., and Saarinen, T. (1992) Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity, J. Am. Chem. Soc. 114, 10663-10665.
18. 15N NMR relaxation, Biochemistry 33, 5984-6003.
19. 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.
20. Taylor, J. R. (1982) An Introduction to Error Analysis, 2nd ed., University Science Books, Sausalito, CA.
21. Lee, A. L., and Wand, A. J. (1999) Assessing potential bias in the determination of rotational correlations times of proteins by NMR, J. Biomol. NMR 13, 101-112.
22. Dellwo, M. J., and Wand, A. J. (1989) Model-independent and model-dependent analysis of the global and internal dynamics of cyclosporin A, J. Am. Chem. Soc. III, 4571-4578.
23. 15N NMR relaxation, J. Am. Chem. Soc. 117, 12562-12566.
24. Jarymowycz, V. A., and Stone, M. J. (2006) Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences, Chem. Rev. 106, 1624-1671.
25. 19F NMR measurements of the rotational mobility of proteins, Biophys. J. 72, 490-498.
26. 15N relaxation of the cold shock protein CspB at various solvent viscosities, J. Biomol. NMR 27, 221-234.
27. Ernst, R. R., Blackledge, M. J., Bremi, T., Brüshweiler, R., Ernst, M., Griesinger, C., Mádi, Z. L., Peng, J. M., Schmid, J. M., and Xu, P. (1996) in NMR as a Structural Tool for Macromolecules: Current Status and Future Directions (Nageswara Rao, B. D. N., and Kempleeds, M. D., Eds.) pp 15-30, Plenum Press, New York.
28. Palmer, A. G., III (2004) NMR characterization of the dynamics of biomacromolecules, Chem. Rev. 104, 3623-3640.
29. Mittermaier, A., and Kay, L. E. (2006) New tools provide new insights in NMR studies of protein dynamics, Science 312, 224-228.
30. Pedersen, S., Bloch, P. L., and Neidhardt, F. C. (1978) Patterns of protein expression in E. coli: A catalog of the amount of 140 individual proteins at different growth rates, Cell 14, 179-190.
31. DeLano, W. L. (2005) MacPyMOL: A PyMOL-based Molecular Graphics Application for MacOS X, DeLano Scientific LLC, South San Francisco, CA (http://www.pymol.org).