Probing serpin conformational change using mass spectrometry and related methods

Methods in Enzymology

Volumn 501, Issue , 2011, Pages 325-350

  Tsutsui, Yuko ^a   Sarkar, Anindya ^b   Wintrode, Patrick L ^b  

^a California Institute of Technology   (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

HXMS; Hydrogen deuterium exchange; Mass spectrometry; Misfolding disease; Protein dynamics; Protein folding; Serpin

Indexed keywords

SERINE PROTEINASE INHIBITOR;

ARTICLE; CONFORMATIONAL TRANSITION; DEUTERIUM HYDROGEN EXCHANGE; ION MOBILITY SPECTROMETRY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; THERMODYNAMICS;

EID: 80955125281     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385950-1.00015-8     Document Type: Chapter

References (42)

1. J.H. Baek, W.S. Yang, C. Lee, and M.H. Yu Functional unfolding of alpha1-antitrypsin probed by hydrogen-deuterium exchange coupled with mass spectrometry Mol. Cell. Proteomics 8 2009 1072 1081
2. Y. Bai, J.S. Milne, L. Mayne, and S.W. Englander Primary structure effects on peptide group hydrogen exchange Proteins 17 1993 75 86 (Pubitemid 23261059)
3. L.D. Cabrita, J.C. Whisstock, and S.P. Bottomley Probing the role of the F-helix in serpin stability through a single tryptophan substitution Biochemistry 41 2002 4575 4581 (Pubitemid 34275658)
4. W.S.W. Chang, J.C. Whisstock, P.C.R. Hopkins, A.M. Lesk, R.W. Carrell, and M.R. Wardell Importance of the release of strand 1C to the polymerization mechanism of inhibitory serpins Protein Sci. 6 1997 89 98 (Pubitemid 27045247)
5. T.R. Dafforn, R. Mahadeva, P.R. Elliott, P. Sivasothy, and D.A. Lomas A kinetic mechanism for the polymerization of alpha1-antitrypsin J. Biol. Chem. 274 1999 9548 9555
6. Y.Z. Deng, and D.L. Smith Rate and equilibrium constants for protein unfolding and refolding determined by hydrogen exchange-mass spectrometry Anal. Biochem. 276 1999 150 160 (Pubitemid 30013035)
7. G.L. Devlin, M.K. Chow, G.J. Howlett, and S.P. Bottomley Acid Denaturation of alpha1-antitrypsin: Characterization of a novel mechanism of serpin polymerization J. Mol. Biol. 324 2002 859 870 (Pubitemid 36044118)
8. K.A. Dill, and D. Shortle Denatured states of proteins Annu. Rev. Biochem. 60 1991 795 825
9. M.A. Dunstone, W. Dai, J.C. Whisstock, J. Rossjohn, R.N. Pike, S.C. Feil, B.F. Le Bonniec, M.W. Parker, and S.P. Bottomley Cleaved antitrypsin polymers at atomic resolution Protein Sci. 9 2000 417 420 (Pubitemid 30127015)
10. U.I. Ekeowa, J. Freeke, E. Miranda, B. Gooptu, M.F. Bush, J. Perez, J. Teckman, C.V. Robinson, and D.A. Lomas Defining the mechanism of polymerization in the serpinopathies Proc. Natl. Acad. Sci. USA 2010 17146 17151
11. P.R. Elliott, X.Y. Pei, T.R. Dafforn, and D.A. Lomas Topography of a 2.0 A structure of alpha1-antitrypsin reveals targets for rational drug design to prevent conformational disease Protein Sci. 9 2000 1274 1281 (Pubitemid 30602280)
12. P.G. Gettins Serpin structure, mechanism, and function Chem. Rev. 102 2002 4751 4804
13. B. Gooptu, B. Hazes, W.S. Chang, T.R. Dafforn, R.W. Carrell, R.J. Read, and D.A. Lomas Inactive conformation of the serpin alpha(1)-antichymotrypsin indicates two-stage insertion of the reactive loop: Implications for inhibitory function and conformational disease Proc. Natl. Acad. Sci. USA 97 2000 67 72 (Pubitemid 30055785)
14. B. Gooptu, E. Miranda, I. Nobeli, M. Mallya, A. Purkiss, S.C. Brown, C. Summers, R.L. Phillips, D.A. Lomas, and T.E. Barrett Crystallographic and cellular characterisation of two mechanisms stabilising the native fold of alpha1-antitrypsin: Implications for disease and drug design J. Mol. Biol. 387 2009 857 868
15. J.Q. Guan, and M.R. Chance Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry Trends Biochem. Sci. 30 2005 583 592 (Pubitemid 41356497)
16. E.L. James, J.C. Whisstock, M.G. Gore, and S.P. Bottomley Probing the unfolding pathway of alpha1-antitrypsin J. Biol. Chem. 274 1999 9482 9488
17. D. Kim, and M.H. Yu Folding pathway of human alpha 1-antitrypsin: Characterization of an intermediate that is active but prone to aggregation Biochem. Biophys. Res. Commun. 226 1996 378 384 (Pubitemid 26331911)
18. K.S. Kwon, and M.H. Yu Effect of glycosylation on the stability of alpha1-antitrypsin toward urea denaturation and thermal deactivation Biochim. Biophys. Acta Gen. Subj. 1335 1997 265 272
19. C. Lee, S.H. Park, M.Y. Lee, and M.H. Yu Regulation of protein function by native metastability Proc. Natl. Acad. Sci. USA 97 2000 7727 7731 (Pubitemid 30460715)
20. C. Lee, J.S. Maeng, J.P. Kocher, B. Lee, and M.H. Yu Cavities of alpha(1)-antitrypsin that play structural and functional roles Protein Sci. 10 2001 1446 1453 (Pubitemid 32568111)
21. D.A. Lomas, and R.W. Carrell Serpinopathies and the conformational dementias Nat. Rev. Genet. 3 2002 759 768
22. D.A. Lomas, P.R. Elliott, S.K. Sidhar, R.C. Foreman, J.T. Finch, D.W. Cox, J.C. Whisstock, and R.W. Carrell alpha 1-Antitrypsin Mmalton (Phe52-deleted) forms loop-sheet polymers in vivo. Evidence for the C sheet mechanism of polymerization J. Biol. Chem. 270 1995 16864 16870
23. J.L. Meagher, S.T. Olson, and P.G. Gettins Critical role of the linker region between helix D and strand 2A in heparin activation of antithrombin J. Biol. Chem. 275 2000 2698 2704 (Pubitemid 30082039)
24. K. Mills, P.B. Mills, P.T. Clayton, A.W. Johnson, D.B. Whitehouse, and B.G. Winchester Identification of alpha(1)-antitrypsin variants in plasma with the use of proteomic technology Clin. Chem. 47 2001 2012 2022 (Pubitemid 33010718)
25. A. Sarkar, and P.L. Wintrode Effects of glycosylation on the stability and flexibility of a metastable protein: The human serpin alpha-1 antitrypsin Int. J. Mass Spectrom. 302 2011 69 75
26. T. Sengupta, Y. Tsutsui, and P.L. Wintrode Local and global effects of a cavity filling mutation in a metastable serpin Biochemistry 48 2009 8233 8240
27. E.J. Seo, H. Im, J.S. Maeng, K.E. Kim, and M.H. Yu Distribution of the native strain in human alpha 1-antitrypsin and its association with protease inhibitor function J. Biol. Chem. 275 2000 16904 16909 (Pubitemid 30398928)
28. E.J. Seo, C. Lee, and M.H. Yu Concerted regulation of inhibitory activity of alpha 1-antitrypsin by the native strain distributed throughout the molecule J. Biol. Chem. 277 2002 14216 14220 (Pubitemid 34968035)
29. D. Shental-Bechor, and Y. Levy Effect of glycosylation on protein folding: A close look at thermodynamic stabilization Proc. Natl. Acad. Sci. USA 105 2008 8256 8261 (Pubitemid 351904743)
30. D. Shental-Bechor, and Y. Levy Folding of glycoproteins: Toward understanding the biophysics of the glycosylation code Curr. Opin. Struct. Biol. 19 2009 524 533
31. D. Shortle, H.S. Chan, and K.A. Dill Modeling the effects of mutations on the denatured states of proteins Protein Sci. 1 1992 201 215 (Pubitemid 23007287)
32. P. Sivasothy, T.R. Dafforn, P.G.W. Gettins, and D.A. Lomas Pathogenic a1-antitrypsin polymers are formed by reactive loop-b-sheet A linkage J. Biol. Chem. 275 2000 33663 33668
33. K. Takamoto, and M.R. Chance Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes Annu. Rev. Biophys. Biomol. Struct. 35 2006 251 276 (Pubitemid 43877378)
34. Y. Tsutsui, and P.L. Wintrode Cooperative unfolding of a metastable serpin to a molten globule suggests a link between functional and folding energy landscapes J. Mol. Biol. 371 2007 245 255 (Pubitemid 47030465)
35. Y. Tsutsui, L. Liu, A. Gershenson, and P.L. Wintrode The conformational dynamics of a metastable serpin studied by hydrogen exchange and mass spectrometry Biochemistry 45 2006 6561 6569 (Pubitemid 43825356)
36. Y. Tsutsui, B. Kuri, T. Sengupta, and P.L. Wintrode The structural basis of serpin polymerization studied by hydrogen/deuterium exchange and mass spectrometry J. Biol. Chem. 283 2008 30804 30811
37. A. Varki Biological roles of oligosaccharides: All of the theories are correct Glycobiology 3 1993 97 130 (Pubitemid 23132602)
38. T.E. Wales, and J.R. Engen Hydrogen exchange mass spectrometry for the analysis of protein dynamics Mass Spectrom. Rev. 25 2006 158 170
39. G.H. Xu, and M.R. Chance Hydroxyl radical-mediated modification of proteins as probes for structural proteomics Chem. Rev. 107 2007 3514 3543 (Pubitemid 47333548)
40. M. Yamasaki, W. Li, D.J. Johnson, and J.A. Huntington Crystal structure of a stable dimer reveals the molecular basis of serpin polymerization Nature 455 2008 1255 1258
41. D.P. Yee, H.S. Chan, T.F. Havel, and K.A. Dill Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry J. Mol. Biol. 241 1994 557 573 (Pubitemid 24269329)
42. X.J. Zheng, P.L. Wintrode, and M.R. Chance Complementary structural mass spectrometry techniques reveal local dynamics in functionally important regions of a metastable serpin Structure 16 2008 38 51