Hydrogen/deuterium exchange mass spectrometry: Potential for investigating innate immunity proteins

Advances in Experimental Medicine and Biology

Volumn 598, Issue , 2007, Pages 407-417

  Schuster, Michael C ^a   Chen, Hui ^b   Lambris, John D ^b  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTHRAX TOXIN; COMPLEMENT COMPONENT C3; MUTANT PROTEIN; NEF PROTEIN; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; VIRUS PROTEIN;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; CONFERENCE PAPER; DEUTERIUM HYDROGEN EXCHANGE; ELECTROSPRAY MASS SPECTROMETRY; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INNATE IMMUNITY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; VIRUS REPLICATION;

EID: 84934442924     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-0-387-71767-8_28     Document Type: Conference Paper

References (49)

1. Alsenz, J., Becherer, J.D., Nilsson, B. and Lambris, J.D. (1990). Structural and Functional-Analysis of C3 Using Monoclonal-Antibodies. Current Topics in Microbiology and Immunology, 153, 235-248.
2. Arold, S., Franken, P., Strub, M.P., Hoh, F., Benichou, S., Benarous, R. and Dumas, C. (1997). The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling. Structure, 5(10), 1361-1372.
3. Arold, S.T. and Bauer, A.S. (2001). Dynamic Nef and Nef dynamics: how structure could explain the complex activities of this small HIV protein. Trends in Biochemical Sciences, 26(6), 356-363.
4. Becherer, J.D., Alsenz, J. and Lambris, J.D. (1990). Molecular Aspects of C3 Interactions and Structural Functional-Analysis of C3 from Different Species. Current Topics in Microbiology and Immunology, 153, 45-72.
5. Berger, J.P., Petro, A.E., Macnaul, K.L., Kelly, L.J., Zhang, B.B., Richards, K., Elbrecht, A., Johnson, B.A., Zhou, G.C., Doebber, T.W., Biswas, C., Parikh, M., Sharma, N., Tanen, M.R., Thompson, G.M., Ventre, J., Adams, A.D., Mosley, R., Surwit, R.S. and Moller, D.E. (2003). Distinct properties and advantages of a novel peroxisome proliferator-activated protein gamma selective modulator. Molecular Endocrinology, 17(4), 662-676.
6. Bradley, K.A., Mogridge, J., Mourez, M., Collier, R.J. and Young, J.A.T. (2001). Identification of the cellular receptor for anthrax toxin. Nature, 414(6860), 225-229.
7. Brown, K.K., Henke, B.R., Blanchard, S.G., Cobb, J.E., Mook, R., Kaldor, I., Kliewer, S.A., Lehmann, J.M., Lenhard, J.M., Harrington, W.W., Novak, P.J., Faison, W., Binz, J.G., Hashim, M.A., Oliver, W.O., Brown, H.R., Parks, D.J., Plunket, K.D., Tong, W.Q., Menius, J.A., Adkison, K., Noble, S.A. and Willson, T.M. (1999). A novel N-aryl tyrosine activator of peroxisome proliferator-activated receptor-gamma reverses the diabetic phenotype of the Zucker diabetic fatty rat. Diabetes, 48(7), 1415-1424.
8. Busenlehner, L.S. and Armstrong, R.N. (2005). Insights into enzyme structure and dynamics elucidated by amide H/D exchange mass spectrometry. Archives of Biochemistry and Biophysics, 433(1), 34-46.
9. Carroll, M.C. and Holers, V.M. (2005). Innate autoimmunity. Advances in Immunology, 86, 137-157.
10. Cravello, L., Lascoux, D. and Forest, E. (2003). Use of different proteases working in acidic conditions to improve sequence coverage and resolution in hydrogen/deuterium exchange of large proteins. Rapid Communications in Mass Spectrometry, 17(21), 2387-2393.
11. Cunningham, K., Lacy, D.B., Mogridge, J. and Collier, R.J. (2002). Mapping the lethal factor and edema factor binding sites on oligomeric anthrax protective antigen. Proceedings of the National Academy of Sciences of the United States of America, 99(10), 7049-7053.
12. Domon, B. and Aebersold, R. (2006). Review - Mass spectrometry and protein analysis. Science, 312(5771), 212-217.
13. Elliott, J.L., Mogridge, J. and Collier, R.J. (2000). A quantitative study of the interactions of Bacillus anthracis edema factor and lethal factor with activated protective antigen. Biochemistry, 39(22), 6706-6713.
14. Englander, S.W. and Kallenbach, N.R. (1983). Hydrogen-Exchange and Structural Dynamics of Proteins and Nucleic-Acids. Quarterly Reviews of Biophysics, 16(4), 521-655.
15. Englander, S.W., Mayne, L., Bai, Y. and Sosnick, T.R. (1997). Hydrogen exchange: The modern legacy of Linderstrom-Lang. Protein Science, 6(5), 1101-1109.
16. Eyles, S.J. and Kaltashov, I.A. (2004). Methods to study protein dynamics and folding by mass spectrometry. Methods, 34(1), 88-99.
17. Fishelson, Z., Pangburn, M.K. and Mullereberhard, H.J. (1984). Characterization of the Initial C-3 Convertase of the Alternative Pathway of Human-Complement. Journal of Immunology, 132(3), 1430-1434.
18. Gampe, R.T., Montana, V.G., Lambert, M.H., Miller, A.B., Bledsoe, R.K., Milburn, M.V., Kliewer, S.A., Willson, T.M. and Xu, H.E. (2000). Asymmetry in the PPAR gamma/RXR alpha crystal structure reveals the molecular basis of heterodimerization among nuclear receptors. Molecular Cell, 5(3), 545-555.
19. Geyer, M., Fackler, O.T. and Peterlin, B.M. (2001). Structure-function relationships in HIV-1 Nef. Embo Reports, 2(7), 580-585.
20. Grzesiek, S., Bax, A., Clore, G.M., Gronenborn, A.M., Hu, J.S., Kaufman, J., Palmer, I., Stahl, S.J. and Wingfield, P.T. (1996). The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase. Nature Structural Biology, 3(4), 340-345.
21. Grzesiek, S., Bax, A., Hu, J.S., Kaufman, J., Palmer, I., Stahl, S.J., Tjandra, N. and Wingfield, P.T. (1997). Refined solution structure and backbone dynamics of HIV-1 Nef. Protein Science, 6(6), 1248-1263.
22. Hamuro, Y., Coales, S.J., Morrow, J.A., Molnar, K.S., Tuske, S.J., Southern, M.R. and Griffin, P.R. (2006). Hydrogen/deuterium-exchange (H/D-Ex) of PPAR gamma LBD in the presence of various modulators. Protein Science, 15(8), 1883-1892.
23. Hochrein, J.M., Wales, T.E., Lerner, E.C., Schiavone, A.P., Smithgall, T.E. and Engen, J.R. (2006). Conformational features of the full-length HIV and SIV Nef proteins determined by mass spectrometry. Biochemistry, 45(25), 7733-7739.
24. Hoofnagle, A.N., Resing, K.A. and Ahn, N.G. (2003). Protein analysis by hydrogen exchange mass spectrometry. Annual Review of Biophysics and Biomolecular Structure, 32, 1-25.
25. Janssen, B.J.C., Huizinga, E.G., Raaijmakers, H.C.A., Roos, A., Daha, M.R., Nilsson-Ekdahl, K., Nilsson, B. and Gros, P. (2005). Structures of complement component C3 provide insights into the function and evolution of immunity. Nature, 437(7058), 505-511.
26. Kallenberger, B.C., Love, J.D., Chatterjee, V.K.K. and Schwabe, J.W.R. (2003). A dynamic mechanism of nuclear receptor activation and its perturbation in a human disease. Nature Structural Biology, 10(2), 136-140.
27. Kenzel, S. and Henneke, P. (2006). The innate immune system and its relevance to neonatal sepsis. Current Opinion in Infectious Diseases, 19(3), 264-270.
28. Lacy, D.B., Mourez, M., Fouassier, A. and Collier, R.J. (2002). Mapping the anthrax protective antigen binding site on the lethal and edema factors. Journal of Biological Chemistry, 277(4), 3006-3010.
29. Lambris, J.D. (1988). The Multifunctional Role of C-3, the 3rd Component of Complement. Immunology Today, 9(12), 387-393.
30. Lanman, J. and Prevelige, P.E. (2004). High-sensitivity mass spectrometry for imaging subunit interactions: hydrogen/deuterium exchange. Current Opinion in Structural Biology, 14(2), 181-188.
31. Lee, C.H., Saksela, K., Mirza, U.A., Chait, B.T. and Kuriyan, J. (1996). Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain. Cell, 85(6), 931-942.
32. Leesnitzer, L.M., Parks, D.J., Bledsoe, R.K., Cobb, J.E., Collins, J.L., Consler, T.G., Davis, R.G., Hull-Ryde, E.A., Lenhard, J.M., Patel, L., Plunket, K.D., Shenk, J.L., Stimmel, J.B., Therapontos, C., Willson, T.M. and Blanchard, S.G. (2002). Functional consequences of cysteine modification in the ligand binding sites of peroxisome proliferator activated receptors by GW9662. Biochemistry, 41(21), 6640-6650.
33. Melnyk, R.A., Hewitt, K.M., Lacy, D.B., Lin, H.C., Gessner, C.R., Li, S., Woods, V.L. and Collier, R.J. (2006). Structural determinants for the binding of anthrax lethal factor to oligomeric protective antigen. Journal of Biological Chemistry, 281(3), 1630-1635.
34. Molloy, S.S., Bresnahan, P.A., Leppla, S.H., Klimpel, K.R. and Thomas, G. (1992). Human Furin Is a Calcium-Dependent Serine Endoprotease That Recognizes the Sequence Arg-X-X-Arg and Efficiently Cleaves Anthrax Toxin Protective Antigen. Journal of Biological Chemistry, 267(23), 16396-16402.
35. Nagar, B., Jones, R.G., Diefenbach, R.J., Isenman, D.E. and Rini, J.M. (1998). X-ray crystal structure of C3d: A C3 fragment and ligand for complement receptor 2. Science, 280(5367), 1277-1281.
36. Oberfield, J.L., Collins, J.L., Holmes, C.P., Goreham, D.M., Cooper, J.P., Cobb, J.E., Lenhard, J.M., Hull-Ryde, E.A., Mohr, C.P., Blanchard, S.G., Parks, D.J., Moore, L.B., Lehmann, J.M., Plunket, K., Miller, A.B., Milburn, M.V., Kliewer, S.A. and Willson, T.M. (1999). A peroxisome proliferatoractivated receptor gamma ligand inhibits adipocyte differentiation. Proceedings of the National Academy of Sciences of the United States of America, 96(11), 6102-6106.
37. Olefsky, J.M. and Saltiel, A.R. (2000). PPAR gamma and the treatment of insulin resistance. Trends in Endocrinology and Metabolism, 11(9), 362-368.
38. Renkema, G.H. and Saksela, K. (2000). Interactions of HIV-1 Nef with cellular signal transducing proteins. Frontiers in Bioscience, 5, D268-D283.
39. Sahu, A. and Lambris, J.D. (2001). Structure and biology of complement protein C3, a connecting link between innate and acquired immunity. Immunological Reviews, 180, 35-48.
40. Scobie, H.M., Rainey, G.J.A., Bradley, K.A. and Young, J.A.T. (2003). Human capillary morphogenesis protein 2 functions as an anthrax toxin receptor. Proceedings of the National Academy of Sciences of the United States of America, 100(9), 5170-5174.
41. Thurman, J.M. and Holers, V.M. (2006). The central role of the alternative complement pathway in human disease. Journal of Immunology, 176(3), 1305-1310.
42. Wales, T.E. and Engen, J.R. (2006). Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrometry Reviews, 25(1), 158-170.
43. Walport, M.J. (2001a). Advances in immunology: Complement (First of two parts). New England Journal of Medicine, 344(14), 1058-1066.
44. Walport, M.J. (2001b). Advances in immunology: Complement (Second of two parts). New England Journal of Medicine, 344(15), 1140-1144.
45. Winters, M.S., Spellman, D.S. and Lambris, J.D. (2005). Solvent accessibility of native and hydrolyzed human complement protein 3 analyzed by hydrogen/deuterium exchange and mass spectrometry. Journal of Immunology, 174(6), 3469-3474.
46. Xu, Y., Narayana, S.V. and Volanakis, J.E. (2001). Structural biology of the alternative pathway convertase. Immunological Reviews, 180, 123-135.
47. Yang, W., Rachez, C. and Freedman, L.P. (2000). Discrete roles for peroxisome proliferator-activated receptor gamma and retinoid X receptor in recruiting nuclear receptor coactivators. Molecular and Cellular Biology, 20(21), 8008-8017.
48. Zhang, S., Finkelstein, A. and Collier, R.J. (2004). Evidence that translocation of anthrax toxin's lethal factor is initiated by entry of its N terminus into the protective antigen channel. Proceedings of the National Academy of Sciences of the United States of America, 101(48), 16756-16761.
49. Zhang, Z.Q. and Smith, D.L. (1993). Determination of Amide Hydrogen-Exchange by Mass-Spectrometry-a New Tool for Protein-Structure Elucidation. Protein Science, 2(4), 522-531.