Chapter 14 Real Time Investigation of Protein Folding, Structure, and Dynamics in Living Cells

Methods in Cell Biology

Volumn 90, Issue C, 2008, Pages 287-325

  Li, Qianqian ^a   Huang, Yuefei ^a   Xiao, Nan ^a   Murray, Victoria ^a   Chen, Jianglei ^a   Wang, Jianjun ^a,b  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b This work was supported by an RO1 grant from NIH (HL074365 to JW)   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN A1; APOLIPOPROTEIN E; CHAPERONE; DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS; GREEN FLUORESCENT PROTEIN; PEPTIDE HYDROLASE;

ANIMAL; ARTICLE; CELL LINE; CELL SURVIVAL; CHEMISTRY; ENZYMOLOGY; FLUORESCENCE; GENETIC TRANSDUCTION; HUMAN; INTRACELLULAR SPACE; METABOLISM; METHODOLOGY; MOUSE; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN FOLDING; PROTEIN PROCESSING; PROTEIN TERTIARY STRUCTURE; STANDARD; THREE DIMENSIONAL IMAGING; TIME;

ANIMALS; APOLIPOPROTEIN A-I; APOLIPOPROTEINS E; CELL LINE; CELL SURVIVAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FLUORESCENCE; GREEN FLUORESCENT PROTEINS; HUMANS; IMAGING, THREE-DIMENSIONAL; INDICATORS AND REAGENTS; INTRACELLULAR SPACE; MICE; MOLECULAR CHAPERONES; PEPTIDE HYDROLASES; PROTEIN FOLDING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY; REFERENCE STANDARDS; TIME FACTORS; TRANSDUCTION, GENETIC;

EID: 59049107963     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0091-679X(08)00814-5     Document Type: Review

References (65)

1. Alberts B., Johnson A., Lewis J., Raff M., Roberts K., and Walter P. Molecular Biology of the Cell. 4th edn (2002), Garland Science, New York, NY 1463
2. Appenzeller-Herzog C., and Hauri H.P. The ER-Golgi intermediate compartment (ERGIC): In search of its identity and function. J. Cell. Sci. 119 (2006) 2173-2183
3. Blobel G., and Sabatini D.D. Ribosome-membrane interaction in eukaryotic cells. In: Manson L.A. (Ed). Biomembranes (1971), Plenum, New York 193-195
4. Breyer B., Jiang W., Cheng H., Zhou L., Paul R., Feng T., and He T.C. Adenoviral vector-mediated gene transfer for human gene therapy. Curr. Gene Ther. 1 (2001) 149-162
5. Bu G., and Schwartz A.L. RAP, a novel type of ER chaperone. Trends Cell Biol. 8 (1998) 272-276
6. Burz D.S., Dutta K., Cowburn D., and Shekhtman A. Mapping structural interactions using in-cell NMR spectroscopy (STINT-NMR). Nat. Methods 3 (2006) 91-93
7. Chen J., Cheng J., Li Q., Bu G., and Wang J. NMR structure and dynamics of the most conserved domain of MESD, a specialized chaperone for the LDL receptor super-family. Biochemistry (2008) Submitted for Publication
8. Chen J., Cheng J., Li Q., Bu G., and Wang J. MESD uses different domains to regulate its chaperone function and escort activity. Mol. Cell (2008) Submitted for Publication
9. Culi J., and Mann R.S. Boca, an endoplasmic reticulum protein required for wingless signaling and trafficking of LDL receptor family members in Drosophila. Cell 112 3 (2003) 343-354
10. Culi J., Springer T.A., and Mann R.S. Boca-dependent maturation of beta-propeller/EGF modules in low-density lipoprotein receptor proteins. EMBO J. 23 6 (2004) 1372-1380
11. D'Arcangelo G. Apoer2: A reelin receptor to remember. Neuron 47 (2005) 471-473
12. Deshayes S., Morris M.C., Divita G., and Heitz F. Cell-penetrating peptides: Tools for intracellular delivery of therapeutics. Cell Mol. Life Sci. 62 (2005) 1839-1849
13. dos Remedios C.G., and Moens P.D. Fluorescence resonance energy transfer spectroscopy is a reliable "ruler" for measuring structural changes in proteins. Dispelling the problem of the unknown orientation factor. J. Struct. Biol. 115 (1995) 175-185
14. Ellis R.J., and Minton A.P. Protein aggregation in crowded environments. Biol. Chem. 387 5 (2006) 485-497
15. Foged C., and Nielsen H.M. Cell-penetrating peptides for drug delivery across membrane barriers. Expert Opin. Drug Deliv. 5 (2008) 105-117
16. Frank J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies (2006), Oxford University Press, New York
17. Futami J., Kitazoe M., Maeda T., Nukui E., Sakaguchi M., Kosaka J., Miyazaki M., Kosaka M., Tada H., Seno M., Sasaki J., Huh N.H., et al. Intracellular delivery of proteins into mammalian living cells by polyethylenimine-cationization. J. Biosci. Bioeng. 99 (2005) 95-103
18. Giepmans B.N., Adams S.R., Ellisman M.H., and Tsien R.Y. The fluorescent toolbox for assessing protein location and function. Science 312 (2006) 217-224
19. Hatters D.M., Peters-Libeu C.A., and Weisgraber K.H. Apolipoprotein E structure: Insights into function. Trends Biochem. Sci. 31 (2006) 445-454
20. He X., Semenov M., Tamai K., and Zeng X. LDL receptor-related proteins 5 and 6 in Wnt/beta-catenin signaling: Arrows point the way. Development 131 (2004) 1663-1677
21. Heikkila J.J., Kaldis A., and Abdulle R. Analysis of molecular chaperones using a Xenopus oocyte protein refolding assay. Methods Mol. Biol. 322 (2006) 213-222
22. Herz J., and Marschang P. Coaxing the LDL receptor family into the fold. Cell 112 (2003) 289-292
23. Hsieh J.C., Lee L., Zhang L., Wefer S., Brown K., DeRossi C., Wines M.E., Rosenquist T., and Holdener B.C. Mesd encodes an LRP5/6 chaperone essential for specification of mouse embryonic polarity. Cell 112 3 (2003) 355-367
24. Hu Y.C. Baculoviral vectors for gene delivery: A review. Curr. Gene Ther. 8 (2008) 54-65
25. Huang Y.C., Riddle K., Rice K.G., and Mooney D.J. Long-term in vivo gene expression via delivery of PEI-DNA condensates from porous polymer scaffolds. Hum. Gene Ther. 16 (2005) 609-617
26. Huang Y.F., Wang J., and Li Q. Using intracellular folding machinery to produce large quantity of properly folded, functional proteins. Nat. Biotechnol. (2008) Submitted for Publication
27. Jeon H., Meng W., Takagi J., Eck M.J., Springer T.A., and Blacklow S.C. Implications for familial hypercholesterolemia from the structure of the LDL receptor YWTD-EGF domain pair. Nat. Struct. Biol. 8 (2001) 499-504
28. Kelly A.E., Ou H.D., Withers R., and Dötsch V. Low-conductivity buffers for high-sensitivity NMR measurements. J. Amer. Chem. Soc. 124 (2002) 12013-12019
29. Korthout H.A., Berecki G., Bruin W., van Duijn B., and Wang M. The presence and subcellular localization of caspase 3-like proteinases in plant cells. FEBS Lett. 475 2 (2000) 139-144
30. Lakowicz J.R. Principles of Fluorescence Spectroscopy. 3rd edn (2006), Springer 954 XXVI
31. Li Y., Cam J., and Bu G. Low-density lipoprotein receptor family: Endocytosis and signal transduction. Mol. Neurobiol. 23 (2001) 53-67
32. Li Q., Huang Y.F., and Wang J. A novel protein transduction method with target capability to specific intracellular compartment. Nat. Method (2008) Submitted for Publication
33. Li Q., and Wang J. The QQ-reagent based protein transduction technology and its applications (2008) US patent (Pending)
34. Li Q., and Wang J. A novel fluorescence imaging technique with potential third dimension. Nat. Methods (2008) Submitted for Publication
35. Li Q., Zhang K., Bu G., and Wang J. Exogenous proteins follow Blobal's "signal theory" for the intracellular trafficking and secretion upon transduction inside cells. Nature, Cell Biology (2008) Submitted for Publication
36. Liljas A., Piskur J., Liljas L., Lindblom G., Nissen P., and Kjeldgaard M. Textbook of Structural Biology. 1st edn (2008), World Scientific (ISBN 978-981-277-207-7)
37. Lippincott-Schwartz J., and Patterson G. Development and use of fluorescent protein markers in living cells. Science 300 (2003) 87-91
38. Marcel Y.L., and Kiss R.S. Structure-function relationships of apolipoprotein A-I: A flexible protein with dynamic lipid associations. Curr. Opin. Lipidol. 14 (2003) 151-157
39. Marshall E. Gene therapy on trial. Science 288 (2000) 951-957
40. May P., Herz J., and Bock H.H. Molecular mechanism of lipoprotein receptor signaling. Cell Mol. Life Sci. 62 (2005) 2325-2338
41. 13C for assignment and interpretation of nuclear magnetic resonance spectra of proteins. Q Rev. Biophys. 23 (1990) 1-38
42. Melikov K., and Chernomordik L.V. Arginine-rich cell penetrating peptides: From endosomal uptake to nuclear delivery. Cell Mol. Life Sci. 62 (2005) 2739-2749
43. Nichols B.J., Kenworthy A.K., Polishchuk R.S., Lodge R., Roberts T.H., Hirschberg K., Phair R.D., and Lippincott-Schwartz J. Rapid cycling of lipid raft markers between the cell surface and Golgi complex. J. Cell Biol. 153 (2001) 529-541
44. Nykjaer A., and Willnow T.E. The low-density lipoprotein receptor gene family: A cellular Swiss army knife?. Trends Cell Biol. 12 (2002) 273-280
45. Okuyama M., Laman H., Kingsbury S.R., Visintin C., Leo E., Eward K.L., Stoeber K., Boshoff C., Williams G.H., and Selwood D.L. Small-molecule mimics of an alpha-helix for efficient transport of proteins into cells. Nat. Methods 4 (2007) 153-159
46. Park K., Kim W.J., Cho Y.H., Lee Y.I., Lee H., Jeong S., Cho E.S., Chang S.I., Moon S.K., Kang B.S., Kim Y.J., and Cho S.H. Cancer gene therapy using adeno-associated virus vectors. Front Biosci. 13 (2008) 2653-2659
47. Piston D.W., and Kremers G.J. Fluorescent protein FRET: The good, the bad and the ugly. Trends Biochem. Sci. 32 (2007) 407-414
48. Schwarze S.R., Ho A., Vocero-Akbani A., and Dowdy S.F. In vivo protein transduction: Delivery of a biologically active protein into the mouse. Science 285 (1999) 1569-1572
49. Schwendener R.A. Liposomes in biology and medicine. Adv. Exp. Med. Biol. 620 (2007) 117-128
50. Selenko P., Frueh D.P., Elsaesser S.J., Haas W., Gygi S.P., and Wagner G. In situ observation of protein phosphorylation by high-resolution NMR spectroscopy. Nat. Struct. Mol. Biol. 15 (2008) 321-329
51. Selenko P., Serber Z., Gadea B., Ruderman J., and Wagner G. Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes. Proc. Natl. Acad. Sci. USA 103 (2006) 11904-11909
52. Selenko P., and Wagner G. Looking into live cells with in-cell NMR spectroscopy. J. Struct. Biol. 158 (2007) 244-253
53. Serber Z., Selenko P., Hänsel R., Reckel S., Löhr F., Ferrell Jr. J.E., Wagner G., and Dötsch V. Investigating micromolecules inside cultured and injected cells by in-cell NMR spectroscopy. Nat. Protoc. 1 (2006) 2701-2709
54. Shaikh S.A., Jain T., Sandhu G., Latha N., and Jayaram B. From drug target to leads--sketching a physicochemical pathway for lead molecule design in silico. Curr. Pharm. Des. 13 (2007) 3454-3470
55. Shaner N.C., Patterson G.H., and Davidson M.W. Advances in fluorescent protein technology. J. Cell Sci. 120 Pt 24 (2007) 4247-4260
56. Sivashanmugam A., Victoria Meiners., Chunxian Cui., Yunhuang Yang., Jianjun Wang., and Qianqian L.i. Practical protocols for production of very high-yield of recombinant proteins in Eschericia coli. Protein Sci. (2008) Submitted for Publication
57. Spiro R.G. Protein glycosylation: Nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology 12 (2002) 43R-56R
58. Strickland D.K., Gonias S.L., and Argraves W.S. Diverse roles for the LDL receptor family. Trends Endocrinol. Metab. 13 (2002) 66-74
59. Tréhin R., and Merkle H.P. Chances and pitfalls of cell penetrating peptides for cellular drug delivery. Eur. J. Pharm. Biopharm. 58 (2004) 209-223
60. Tugarinov V., Kanelis V., and Kay L.E. Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy. Nat. Protoc. 1 (2006) 749-754
61. Usón I., and Sheldrick G.M. Advances in direct methods for protein crystallography. Curr. Opin. Struct. Biol 9 5 (1999) 643-648
62. Wadia J.S., and Dowdy S.F. Protein transduction technology. Curr. Opin. Biotechnol. 13 (2002) 52-56
63. Wadia J.S., and Dowdy S.F. Transmembrane delivery of protein and peptide drugs by TAT-mediated transduction in the treatment of cancer. Adv. Drug. Deliv. Rev. 57 (2005) 579-596
64. Wu G.Y., and Wu C.H. Delivery systems for gene therapy. Biotherapy 3 (1991) 87-95
65. Zhang Z., Shen X., Wu J., Sakaki K., Saunders T., Rutkowski D., Back S., and Kaufman R. Endoplasmic reticulum stress activates cleavage of CREBH to induce a systemic inflammatory response. Cell 124 (2006) 587-599