Skip to main content
Top

2013 | OriginalPaper | Chapter

8. Hydrogen/Deuterium Exchange Mass Spectrometry for Protein Higher-Order Structure Characterization

Authors : Hui Wei, Adrienne A. Tymiak, Guodong Chen

Published in: Characterization of Protein Therapeutics using Mass Spectrometry

Publisher: Springer US

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

Abstract

As some of the most essential molecules of life, proteins fulfill a plethora of biochemical functions within every living organism. They are involved in virtually all cell functions, such as cell division, cell death, immune response, signal transduction, and ligand binding. In contrast to small molecules, proteins are significantly more complicated in structure. In biophysical conditions, proteins fold into unique three-dimensional structures in solution that are flexible and dynamic.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Literature
1.
go back to reference Kuntz ID, Chen K, Sharp KA, Kollman PA (1999) The maximal affinity of ligands. Proc Natl Acad Sci USA 96:9997–10002 Kuntz ID, Chen K, Sharp KA, Kollman PA (1999) The maximal affinity of ligands. Proc Natl Acad Sci USA 96:9997–10002
2.
go back to reference Hvidt A, Linderstrom-Lang K (1954) Exchange of hydrogen atoms in insulin with deuterium atoms in aqueous solutions. Biochim Biophys Acta 14:574–575 Hvidt A, Linderstrom-Lang K (1954) Exchange of hydrogen atoms in insulin with deuterium atoms in aqueous solutions. Biochim Biophys Acta 14:574–575
3.
go back to reference Hvidt A, Linderstrom-Lang K (1955) The kinetics of the deuterium exchange of insulin with D2O; an amendment. Biochim Biophys Acta 16:168–169 Hvidt A, Linderstrom-Lang K (1955) The kinetics of the deuterium exchange of insulin with D2O; an amendment. Biochim Biophys Acta 16:168–169
4.
go back to reference Englander SW (1963) A hydrogen exchange method using tritium and sephadex: its application to ribonuclease. Biochemistry 2:798–807 Englander SW (1963) A hydrogen exchange method using tritium and sephadex: its application to ribonuclease. Biochemistry 2:798–807
5.
go back to reference Haris PI, Chapman D (1995) The conformational analysis of peptides using fourier transform IR spectroscopy. Biopolymers 37:251–263 Haris PI, Chapman D (1995) The conformational analysis of peptides using fourier transform IR spectroscopy. Biopolymers 37:251–263
6.
go back to reference Englander JJ, Calhoun DB, Englander SW (1979) Measurement and calibration of peptide group hydrogen-deuterium exchange by ultraviolet spectrophotometry. Anal Biochem 92:517–524 Englander JJ, Calhoun DB, Englander SW (1979) Measurement and calibration of peptide group hydrogen-deuterium exchange by ultraviolet spectrophotometry. Anal Biochem 92:517–524
7.
go back to reference Bentley GA, Delepierre M, Dobson CM, Wedin RE, Mason SA, Poulsen FM (1983) Exchange of individual hydrogens for a protein in a crystal and in solution. J Mol Biol 170:243–247 Bentley GA, Delepierre M, Dobson CM, Wedin RE, Mason SA, Poulsen FM (1983) Exchange of individual hydrogens for a protein in a crystal and in solution. J Mol Biol 170:243–247
8.
go back to reference Englander SW, Mayne L (1992) Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. Annu Rev Biophys Biomol Struct 21:243–265 Englander SW, Mayne L (1992) Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. Annu Rev Biophys Biomol Struct 21:243–265
9.
go back to reference Jeng MF, Dyson HJ (1995) Comparison of the hydrogen-exchange behavior of reduced and oxidized Escherichia coli thioredoxin. Biochemistry 34:611–619 Jeng MF, Dyson HJ (1995) Comparison of the hydrogen-exchange behavior of reduced and oxidized Escherichia coli thioredoxin. Biochemistry 34:611–619
10.
go back to reference Dempsey CE (2001) Hydrogen exchange in peptides and proteins using NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 39:135–170 Dempsey CE (2001) Hydrogen exchange in peptides and proteins using NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 39:135–170
11.
go back to reference Paterson Y, Englander SW, Roder H (1990) An antibody binding site on cytochrome c defined by hydrogen exchange and two-dimensional NMR. Science 249:755–759 Paterson Y, Englander SW, Roder H (1990) An antibody binding site on cytochrome c defined by hydrogen exchange and two-dimensional NMR. Science 249:755–759
12.
go back to reference Rosa JJ, Richards FM (1979) An experimental procedure for increasing the structural resolution of chemical hydrogen-exchange measurements on proteins: application to ribonuclease S peptide. J Mol Biol 133:399–416 Rosa JJ, Richards FM (1979) An experimental procedure for increasing the structural resolution of chemical hydrogen-exchange measurements on proteins: application to ribonuclease S peptide. J Mol Biol 133:399–416
13.
go back to reference Englander JJ, Rogero JR, Englander SW (1985) Protein hydrogen exchange studied by the fragment separation method. Anal Biochem 147:234–244 Englander JJ, Rogero JR, Englander SW (1985) Protein hydrogen exchange studied by the fragment separation method. Anal Biochem 147:234–244
14.
go back to reference Katta V, Chait BT (1991) Conformational changes in proteins probed by hydrogen-exchange electrospray-ionization mass spectrometry. Rapid Commun Mass Spectrom 5:214–217 Katta V, Chait BT (1991) Conformational changes in proteins probed by hydrogen-exchange electrospray-ionization mass spectrometry. Rapid Commun Mass Spectrom 5:214–217
15.
go back to reference Zhang Z, Smith DL (1993) Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci 2:522–531 Zhang Z, Smith DL (1993) Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci 2:522–531
16.
go back to reference Johnson RS, Walsh KA (1994) Mass spectrometric measurement of protein amide hydrogen exchange rates of apo- and holo-myoglobin. Protein Sci 3:2411–2418 Johnson RS, Walsh KA (1994) Mass spectrometric measurement of protein amide hydrogen exchange rates of apo- and holo-myoglobin. Protein Sci 3:2411–2418
17.
go back to reference Pan J, Rintala-Dempsey AC, Li Y, Shaw GS, Konermann L (2006) Folding kinetics of the S100A11 protein dimer studied by time-resolved electrospray mass spectrometry and pulsed hydrogen-deuterium exchange. Biochemistry 45:3005–3013 Pan J, Rintala-Dempsey AC, Li Y, Shaw GS, Konermann L (2006) Folding kinetics of the S100A11 protein dimer studied by time-resolved electrospray mass spectrometry and pulsed hydrogen-deuterium exchange. Biochemistry 45:3005–3013
18.
go back to reference Eyles SJ, Kaltashov IA (2004) Methods to study protein dynamics and folding by mass spectrometry. Methods 34:88–99 Eyles SJ, Kaltashov IA (2004) Methods to study protein dynamics and folding by mass spectrometry. Methods 34:88–99
19.
go back to reference Miranker A, Robinson CV, Radford SE, Aplin RT, Dobson CM (1993) Detection of transient protein folding populations by mass spectrometry. Science 262:896–900 Miranker A, Robinson CV, Radford SE, Aplin RT, Dobson CM (1993) Detection of transient protein folding populations by mass spectrometry. Science 262:896–900
20.
go back to reference Zhu MM, Rempel DL, Zhao J, Giblin DE, Gross ML (2003) Probing Ca2+-induced conformational changes in porcine calmodulin by H/D exchange and ESI-MS: effect of cations and ionic strength. Biochemistry 42:15388–15397 Zhu MM, Rempel DL, Zhao J, Giblin DE, Gross ML (2003) Probing Ca2+-induced conformational changes in porcine calmodulin by H/D exchange and ESI-MS: effect of cations and ionic strength. Biochemistry 42:15388–15397
21.
go back to reference Lanman J, Lam TT, Barnes S, Sakalian M, Emmett MR, Marshall AG, Prevelige PE Jr (2003) Identification of novel interactions in HIV-1 capsid protein assembly by high-resolution mass spectrometry. J Mol Biol 325:759–772 Lanman J, Lam TT, Barnes S, Sakalian M, Emmett MR, Marshall AG, Prevelige PE Jr (2003) Identification of novel interactions in HIV-1 capsid protein assembly by high-resolution mass spectrometry. J Mol Biol 325:759–772
22.
go back to reference Zhang Z, Post CB, Smith DL (1996) Amide hydrogen exchange determined by mass spectrometry: application to rabbit muscle aldolase. Biochemistry 35:779–791 Zhang Z, Post CB, Smith DL (1996) Amide hydrogen exchange determined by mass spectrometry: application to rabbit muscle aldolase. Biochemistry 35:779–791
23.
go back to reference Hoofnagle AN, Resing KA, Ahn NG (2003) Protein analysis by hydrogen exchange mass spectrometry. Annu Rev Biophys Biomol Struct 32:1–25 Hoofnagle AN, Resing KA, Ahn NG (2003) Protein analysis by hydrogen exchange mass spectrometry. Annu Rev Biophys Biomol Struct 32:1–25
24.
go back to reference Wales TE, Engen JR (2006) Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom Rev 25:158–170 Wales TE, Engen JR (2006) Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom Rev 25:158–170
25.
go back to reference Powell KD, Fitzgerald MC (2001) Measurements of protein stability by H/D exchange and matrix-assisted laser desorption/ionization mass spectrometry using picomoles of material. Anal Chem 73:3300–3304 Powell KD, Fitzgerald MC (2001) Measurements of protein stability by H/D exchange and matrix-assisted laser desorption/ionization mass spectrometry using picomoles of material. Anal Chem 73:3300–3304
26.
go back to reference Englander SW, Kallenbach NR (1983) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys 16:521–655 Englander SW, Kallenbach NR (1983) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys 16:521–655
27.
go back to reference Hamuro Y, Coales SJ, Southern MR, Nemeth-Cawley JF, Stranz DD, Griffin PR (2003) Rapid analysis of protein structure and dynamics by hydrogen/deuterium exchange mass spectrometry. J Biomol Tech 14:171–182 Hamuro Y, Coales SJ, Southern MR, Nemeth-Cawley JF, Stranz DD, Griffin PR (2003) Rapid analysis of protein structure and dynamics by hydrogen/deuterium exchange mass spectrometry. J Biomol Tech 14:171–182
28.
go back to reference Garcia RA, Pantazatos D, Villarreal FJ (2004) Hydrogen/deuterium exchange mass spectrometry for investigating protein-ligand interactions. Assay Drug Dev Technol 2:81–91 Garcia RA, Pantazatos D, Villarreal FJ (2004) Hydrogen/deuterium exchange mass spectrometry for investigating protein-ligand interactions. Assay Drug Dev Technol 2:81–91
29.
go back to reference Busenlehner LS, Armstrong RN (2005) Insights into enzyme structure and dynamics elucidated by amide H/D exchange mass spectrometry. Arch Biochem Biophys 433:34–46 Busenlehner LS, Armstrong RN (2005) Insights into enzyme structure and dynamics elucidated by amide H/D exchange mass spectrometry. Arch Biochem Biophys 433:34–46
30.
go back to reference Goshe MB, Anderson VE (1999) Hydroxyl radical-induced hydrogen/deuterium exchange in amino acid carbon-hydrogen bonds. Radiat Res 151:50–58 Goshe MB, Anderson VE (1999) Hydroxyl radical-induced hydrogen/deuterium exchange in amino acid carbon-hydrogen bonds. Radiat Res 151:50–58
31.
go back to reference Bai Y, Milne JS, Mayne L, Englander SW (1993) Primary structure effects on peptide group hydrogen exchange. Proteins 17:75–86 Bai Y, Milne JS, Mayne L, Englander SW (1993) Primary structure effects on peptide group hydrogen exchange. Proteins 17:75–86
32.
go back to reference Molday RS, Englander SW, Kallen RG (1972) Primary structure effects on peptide group hydrogen exchange. Biochemistry 11:150–158 Molday RS, Englander SW, Kallen RG (1972) Primary structure effects on peptide group hydrogen exchange. Biochemistry 11:150–158
33.
go back to reference Fersht AR (1971) Acyl-transfer reactions of amides and esters with alcohols and thiols. A reference system for the serine and cysteine proteinases. Concerning the N protonation of amides and amide-imidate equilibria. J Am Chem Soc 93:3504–3515 Fersht AR (1971) Acyl-transfer reactions of amides and esters with alcohols and thiols. A reference system for the serine and cysteine proteinases. Concerning the N protonation of amides and amide-imidate equilibria. J Am Chem Soc 93:3504–3515
34.
go back to reference Eriksson MA, Hard T, Nilsson L (1995) On the pH dependence of amide proton exchange rates in proteins. Biophys J 69:329–339 Eriksson MA, Hard T, Nilsson L (1995) On the pH dependence of amide proton exchange rates in proteins. Biophys J 69:329–339
35.
go back to reference Brier S, Engen JR (2008) Hydrogen exchange mass spectrometry: principles and capabilities. In: Chance M (ed) Mass spectrometry analysis for protein–protein interactions and dynamics. Wiley, New Jersey Brier S, Engen JR (2008) Hydrogen exchange mass spectrometry: principles and capabilities. In: Chance M (ed) Mass spectrometry analysis for protein–protein interactions and dynamics. Wiley, New Jersey
36.
go back to reference Berger A, Loewenstein A, Meiboom S (1959) Nuclear magnetic resonance and the proteolysis of N-methylacetamide. J Am Chem Soc 81(1):62–67 Berger A, Loewenstein A, Meiboom S (1959) Nuclear magnetic resonance and the proteolysis of N-methylacetamide. J Am Chem Soc 81(1):62–67
37.
go back to reference Dempsey CE (2001) Hydrogen exchange in peptides and proteins using NMR spectroscopy. Prog Nucl Magn Reson Spectro 39:135–170 Dempsey CE (2001) Hydrogen exchange in peptides and proteins using NMR spectroscopy. Prog Nucl Magn Reson Spectro 39:135–170
38.
go back to reference Connelly GP, Bai Y, Jeng MF, Englander SW (1993) Isotope effects in peptide group hydrogen exchange. Proteins 17:87–92 Connelly GP, Bai Y, Jeng MF, Englander SW (1993) Isotope effects in peptide group hydrogen exchange. Proteins 17:87–92
39.
go back to reference Barksdale AD, Rosenberg A (1982) Acquisition and interpretation of hydrogen exchange data from peptides, polymers, and proteins. Methods Biochem Anal 28:1–113 Barksdale AD, Rosenberg A (1982) Acquisition and interpretation of hydrogen exchange data from peptides, polymers, and proteins. Methods Biochem Anal 28:1–113
40.
go back to reference Hvidt A, Nielsen SO (1966) Hydrogen exchange in proteins. Adv Protein Chem 21:287–386 Hvidt A, Nielsen SO (1966) Hydrogen exchange in proteins. Adv Protein Chem 21:287–386
41.
go back to reference Konermann L, Tong X, Pan Y (2008) Protein structure and dynamics studied by mass spectrometry: H/D exchange, hydroxyl radical labeling, and related approaches. J Mass Spectrom 43:1021–1036 Konermann L, Tong X, Pan Y (2008) Protein structure and dynamics studied by mass spectrometry: H/D exchange, hydroxyl radical labeling, and related approaches. J Mass Spectrom 43:1021–1036
42.
go back to reference Maier CS, Schimerlik MI, Deinzer ML (1999) Thermal denaturation of escherichia coli thioredoxin studied by hydrogen/deuterium exchange and electrospray ionization mass spectrometry: monitoring a two-state protein unfolding transition. Biochemistry 38:1136–1143 Maier CS, Schimerlik MI, Deinzer ML (1999) Thermal denaturation of escherichia coli thioredoxin studied by hydrogen/deuterium exchange and electrospray ionization mass spectrometry: monitoring a two-state protein unfolding transition. Biochemistry 38:1136–1143
43.
go back to reference Deng Y, Smith DL (1998) Identification of unfolding domains in large proteins by their unfolding rates. Biochemistry 37:6256–6262 Deng Y, Smith DL (1998) Identification of unfolding domains in large proteins by their unfolding rates. Biochemistry 37:6256–6262
44.
go back to reference Swint-Kruse L, Robertson AD (1996) Temperature and pH dependences of hydrogen exchange and global stability for ovomucoid third domain. Biochemistry 35:171–180 Swint-Kruse L, Robertson AD (1996) Temperature and pH dependences of hydrogen exchange and global stability for ovomucoid third domain. Biochemistry 35:171–180
45.
go back to reference Clarke J, Itzhaki LS (1998) Hydrogen exchange and protein folding. Curr Opin Struct Biol 8:112–118 Clarke J, Itzhaki LS (1998) Hydrogen exchange and protein folding. Curr Opin Struct Biol 8:112–118
46.
go back to reference Chetty PS, Mayne L, Lund-Katz S, Stranz D, Englander SW, Phillips MC (2009) Helical structure and stability in human apolipoprotein A-I by hydrogen exchange and mass spectrometry. Proc Natl Acad Sci USA 106:19005–19010 Chetty PS, Mayne L, Lund-Katz S, Stranz D, Englander SW, Phillips MC (2009) Helical structure and stability in human apolipoprotein A-I by hydrogen exchange and mass spectrometry. Proc Natl Acad Sci USA 106:19005–19010
47.
go back to reference Englander SW, Englander JJ (1972) Hydrogen-tritium exchange. Methods Enzymol, 26 PtC, 406–413 Englander SW, Englander JJ (1972) Hydrogen-tritium exchange. Methods Enzymol, 26 PtC, 406–413
48.
go back to reference Maier CS, Deinzer ML (2005) Protein conformations, interactions, and H/D exchange. Methods Enzymol 402:312–360 Maier CS, Deinzer ML (2005) Protein conformations, interactions, and H/D exchange. Methods Enzymol 402:312–360
49.
go back to reference Woodward CK, Ellis LM, Rosenberg A (1975) The solvent dependence of hydrogen exchange kinetics of folded proteins. J Biol Chem 250:440–444 Woodward CK, Ellis LM, Rosenberg A (1975) The solvent dependence of hydrogen exchange kinetics of folded proteins. J Biol Chem 250:440–444
50.
go back to reference Engen JR, Smithgall TE, Gmeiner WH, Smith DL (1997) Identification and localization of slow, natural, cooperative unfolding in the hematopoietic cell kinase SH3 domain by amide hydrogen exchange and mass spectrometry. Biochemistry 36:14384–14391 Engen JR, Smithgall TE, Gmeiner WH, Smith DL (1997) Identification and localization of slow, natural, cooperative unfolding in the hematopoietic cell kinase SH3 domain by amide hydrogen exchange and mass spectrometry. Biochemistry 36:14384–14391
51.
go back to reference Houde D, Berkowitz SA, Engen JR (2011) The utility of hydrogen/deuterium exchange mass spectrometry in biopharmaceutical comparability studies. J Pharm Sci 100(6):2071–2086 Houde D, Berkowitz SA, Engen JR (2011) The utility of hydrogen/deuterium exchange mass spectrometry in biopharmaceutical comparability studies. J Pharm Sci 100(6):2071–2086
52.
go back to reference Zhou B, Zhang ZY (2007) Application of hydrogen/deuterium exchange mass spectrometry to study protein tyrosine phosphatase dynamics, ligand binding, and substrate specificity. Methods 42:227–233 Zhou B, Zhang ZY (2007) Application of hydrogen/deuterium exchange mass spectrometry to study protein tyrosine phosphatase dynamics, ligand binding, and substrate specificity. Methods 42:227–233
53.
go back to reference Chalmers MJ, Busby SA, Pascal BD, He Y, Hendrickson CL, Marshall AG, Griffin PR (2006) Probing protein ligand interactions by automated hydrogen/deuterium exchange mass spectrometry. Anal Chem 78:1005–1014 Chalmers MJ, Busby SA, Pascal BD, He Y, Hendrickson CL, Marshall AG, Griffin PR (2006) Probing protein ligand interactions by automated hydrogen/deuterium exchange mass spectrometry. Anal Chem 78:1005–1014
54.
go back to reference Keppel TR, Howard BA, Weis DD (2011) Mapping unstructured regions and synergistic folding in intrinsically disordered proteins with amide H/D exchange mass spectrometry. Biochemistry 50:8722–8732 Keppel TR, Howard BA, Weis DD (2011) Mapping unstructured regions and synergistic folding in intrinsically disordered proteins with amide H/D exchange mass spectrometry. Biochemistry 50:8722–8732
55.
go back to reference Coales SJ, Tuske SJ, Tomasso JC, Hamuro Y (2009) Epitope mapping by amide hydrogen/deuterium exchange coupled with immobilization of antibody, on-line proteolysis, liquid chromatography and mass spectrometry. Rapid Commun Mass Spectrom 23:639–647 Coales SJ, Tuske SJ, Tomasso JC, Hamuro Y (2009) Epitope mapping by amide hydrogen/deuterium exchange coupled with immobilization of antibody, on-line proteolysis, liquid chromatography and mass spectrometry. Rapid Commun Mass Spectrom 23:639–647
56.
go back to reference Deng Y, Zhang Z, Smith DL (1999) Comparison of continuous and pulsed labeling amide hydrogen exchange/mass spectrometry for studies of protein dynamics. J Am Soc Mass Spectrom 10:675–684 Deng Y, Zhang Z, Smith DL (1999) Comparison of continuous and pulsed labeling amide hydrogen exchange/mass spectrometry for studies of protein dynamics. J Am Soc Mass Spectrom 10:675–684
57.
go back to reference Konermann L, Simmons DA (2003) Protein-folding kinetics and mechanisms studied by pulse-labeling and mass spectrometry. Mass Spectrom Rev 22:1–26 Konermann L, Simmons DA (2003) Protein-folding kinetics and mechanisms studied by pulse-labeling and mass spectrometry. Mass Spectrom Rev 22:1–26
58.
go back to reference Hossain BM, Konermann L (2006) Pulsed hydrogen/deuterium exchange MS/MS for studying the relationship between noncovalent protein complexes in solution and in the gas phase after electrospray ionization. Anal Chem 78:1613–1619 Hossain BM, Konermann L (2006) Pulsed hydrogen/deuterium exchange MS/MS for studying the relationship between noncovalent protein complexes in solution and in the gas phase after electrospray ionization. Anal Chem 78:1613–1619
59.
go back to reference Yang H, Smith DL (1997) Kinetics of cytochrome c folding examined by hydrogen exchange and mass spectrometry. Biochemistry 36:14992–14999 Yang H, Smith DL (1997) Kinetics of cytochrome c folding examined by hydrogen exchange and mass spectrometry. Biochemistry 36:14992–14999
60.
go back to reference Rogero JR, Englander JJ, Englander SW (1986) Individual breathing reactions measured by functional labeling and hydrogen exchange methods. Methods Enzymol 131:508–517 Rogero JR, Englander JJ, Englander SW (1986) Individual breathing reactions measured by functional labeling and hydrogen exchange methods. Methods Enzymol 131:508–517
61.
go back to reference Baerga-Ortiz A, Hughes CA, Mandell JG, Komives EA (2002) Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Sci 11:1300–1308 Baerga-Ortiz A, Hughes CA, Mandell JG, Komives EA (2002) Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Sci 11:1300–1308
62.
go back to reference Smith DL, Deng Y, Zhang Z (1997) Probing the non-covalent structure of proteins by amide hydrogen exchange and mass spectrometry. J Mass Spectrom 32:135–146 Smith DL, Deng Y, Zhang Z (1997) Probing the non-covalent structure of proteins by amide hydrogen exchange and mass spectrometry. J Mass Spectrom 32:135–146
63.
go back to reference Engen JR (2003) Analysis of protein complexes with hydrogen exchange and mass spectrometry. Analyst 128:623–628 Engen JR (2003) Analysis of protein complexes with hydrogen exchange and mass spectrometry. Analyst 128:623–628
64.
go back to reference Jr Woods VL, Hamuro Y (2001) High resolution, high-throughput amide deuterium exchange-mass spectrometry (DXMS) determination of protein binding site structure and dynamics: utility in pharmaceutical design. J Cell Biochem Suppl 37:89–98 Jr Woods VL, Hamuro Y (2001) High resolution, high-throughput amide deuterium exchange-mass spectrometry (DXMS) determination of protein binding site structure and dynamics: utility in pharmaceutical design. J Cell Biochem Suppl 37:89–98
65.
go back to reference Ghaemmaghami S, Fitzgerald MC, Oas TG (2000) A quantitative, high-throughput screen for protein stability. Proc Natl Acad Sci USA 97:8296–8301 Ghaemmaghami S, Fitzgerald MC, Oas TG (2000) A quantitative, high-throughput screen for protein stability. Proc Natl Acad Sci USA 97:8296–8301
66.
go back to reference Mandell JG, Falick AM, Komives EA (1998) Identification of protein–protein interfaces by decreased amide proton solvent accessibility. Proc Natl Acad Sci USA 95:14705–14710 Mandell JG, Falick AM, Komives EA (1998) Identification of protein–protein interfaces by decreased amide proton solvent accessibility. Proc Natl Acad Sci USA 95:14705–14710
67.
go back to reference Kipping M, Schierhorn A (2003) Improving hydrogen/deuterium exchange mass spectrometry by reduction of the back-exchange effect. J Mass Spectrom 38:271–276 Kipping M, Schierhorn A (2003) Improving hydrogen/deuterium exchange mass spectrometry by reduction of the back-exchange effect. J Mass Spectrom 38:271–276
68.
go back to reference Anderegg RJ, Wagner DS, Stevenson CL (1994) The mass spectrometry of helical unfolding in peptides. J Am Chem Soc 5:425–433 Anderegg RJ, Wagner DS, Stevenson CL (1994) The mass spectrometry of helical unfolding in peptides. J Am Chem Soc 5:425–433
69.
go back to reference Demmers JA, Haverkamp J, Heck AJ, Koeppe RE 2nd, Killian JA (2000) Electrospray ionization mass spectrometry as a tool to analyze hydrogen/deuterium exchange kinetics of transmembrane peptides in lipid bilayers. Proc Natl Acad Sci USA 97:3189–3194 Demmers JA, Haverkamp J, Heck AJ, Koeppe RE 2nd, Killian JA (2000) Electrospray ionization mass spectrometry as a tool to analyze hydrogen/deuterium exchange kinetics of transmembrane peptides in lipid bilayers. Proc Natl Acad Sci USA 97:3189–3194
70.
go back to reference Jorgensen TJ, Gardsvoll H, Ploug M, Roepstorff P (2005) Intramolecular migration of amide hydrogens in protonated peptides upon collisional activation. J Am Chem Soc 127:2785–2793 Jorgensen TJ, Gardsvoll H, Ploug M, Roepstorff P (2005) Intramolecular migration of amide hydrogens in protonated peptides upon collisional activation. J Am Chem Soc 127:2785–2793
71.
go back to reference Kaltashov IA, Eyles SJ (2002) Crossing the phase boundary to study protein dynamics and function: combination of amide hydrogen exchange in solution and ion fragmentation in the gas phase. J Mass Spectrom 37:557–565 Kaltashov IA, Eyles SJ (2002) Crossing the phase boundary to study protein dynamics and function: combination of amide hydrogen exchange in solution and ion fragmentation in the gas phase. J Mass Spectrom 37:557–565
72.
go back to reference Ferguson PL, Pan J, Wilson DJ, Dempsey B, Lajoie G, Shilton B, Konermann L (2007) Hydrogen/deuterium scrambling during quadrupole time-of-flight MS/MS analysis of a zinc-binding protein domain. Anal Chem 79:153–160 Ferguson PL, Pan J, Wilson DJ, Dempsey B, Lajoie G, Shilton B, Konermann L (2007) Hydrogen/deuterium scrambling during quadrupole time-of-flight MS/MS analysis of a zinc-binding protein domain. Anal Chem 79:153–160
73.
go back to reference Rand KD, Adams CM, Zubarev RA, Jorgensen TJ (2008) Electron capture dissociation proceeds with a low degree of intramolecular migration of peptide amide hydrogens. J Am Chem Soc 130:1341–1349 Rand KD, Adams CM, Zubarev RA, Jorgensen TJ (2008) Electron capture dissociation proceeds with a low degree of intramolecular migration of peptide amide hydrogens. J Am Chem Soc 130:1341–1349
74.
go back to reference Zubarev RA (2003) Reactions of polypeptide ions with electrons in the gas phase. Mass Spectrom Rev 22:57–77 Zubarev RA (2003) Reactions of polypeptide ions with electrons in the gas phase. Mass Spectrom Rev 22:57–77
75.
go back to reference Horn DM, Breuker K, Frank AJ, McLafferty FW (2001) Kinetic intermediates in the folding of gaseous protein ions characterized by electron capture dissociation mass spectrometry. J Am Chem Soc 123:9792–9799 Horn DM, Breuker K, Frank AJ, McLafferty FW (2001) Kinetic intermediates in the folding of gaseous protein ions characterized by electron capture dissociation mass spectrometry. J Am Chem Soc 123:9792–9799
76.
go back to reference Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 101:9528–9533 Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 101:9528–9533
77.
go back to reference Xia Y, Thomson BA, McLuckey SA (2007) Bidirectional ion transfer between quadrupole arrays: MSn ion/ion reaction experiments on a quadrupole/time-of-flight tandem mass spectrometer. Anal Chem 79:8199–8206 Xia Y, Thomson BA, McLuckey SA (2007) Bidirectional ion transfer between quadrupole arrays: MSn ion/ion reaction experiments on a quadrupole/time-of-flight tandem mass spectrometer. Anal Chem 79:8199–8206
78.
go back to reference Zehl M, Rand KD, Jensen ON, Jorgensen TJ (2008) Electron transfer dissociation facilitates the measurement of deuterium incorporation into selectively labeled peptides with single residue resolution. J Am Chem Soc 130:17453–17459 Zehl M, Rand KD, Jensen ON, Jorgensen TJ (2008) Electron transfer dissociation facilitates the measurement of deuterium incorporation into selectively labeled peptides with single residue resolution. J Am Chem Soc 130:17453–17459
79.
go back to reference Rand KD, Zehl M, Jensen ON, Jorgensen TJ (2009) Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry. Anal Chem 81:5577–5584 Rand KD, Zehl M, Jensen ON, Jorgensen TJ (2009) Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry. Anal Chem 81:5577–5584
80.
go back to reference Landgraf RR, Chalmers MJ, Griffin PR (2012) Automated hydrogen/deuterium exchange electron transfer dissociation high resolution mass spectrometry measured at single-amide resolution. J Am Soc Mass Spectrom 23:301–309 Landgraf RR, Chalmers MJ, Griffin PR (2012) Automated hydrogen/deuterium exchange electron transfer dissociation high resolution mass spectrometry measured at single-amide resolution. J Am Soc Mass Spectrom 23:301–309
81.
go back to reference Villanueva J, Hoshino M, Katou H, Kardos J, Hasegawa K, Naiki H, Goto Y (2004) Increase in the conformational flexibility of beta 2-microglobulin upon copper binding: a possible role for copper in dialysis-related amyloidosis. Protein Sci 13:797–809 Villanueva J, Hoshino M, Katou H, Kardos J, Hasegawa K, Naiki H, Goto Y (2004) Increase in the conformational flexibility of beta 2-microglobulin upon copper binding: a possible role for copper in dialysis-related amyloidosis. Protein Sci 13:797–809
82.
go back to reference Pan J, Han J, Borchers CH, Konermann L (2008) Electron capture dissociation of electrosprayed protein ions for spatially resolved hydrogen exchange measurements. J Am Chem Soc 130:11574–11575 Pan J, Han J, Borchers CH, Konermann L (2008) Electron capture dissociation of electrosprayed protein ions for spatially resolved hydrogen exchange measurements. J Am Chem Soc 130:11574–11575
83.
go back to reference Abzalimov RR, Kaplan DA, Easterling ML, Kaltashov IA (2009) Protein conformations can be probed in top-down HDX MS experiments utilizing electron transfer dissociation of protein ions without hydrogen scrambling. J Am Soc Mass Spectrom 20:1514–1517 Abzalimov RR, Kaplan DA, Easterling ML, Kaltashov IA (2009) Protein conformations can be probed in top-down HDX MS experiments utilizing electron transfer dissociation of protein ions without hydrogen scrambling. J Am Soc Mass Spectrom 20:1514–1517
84.
go back to reference Kaltashov IA, Bobst CE, Abzalimov RR (2009) H/D exchange and mass spectrometry in the studies of protein conformation and dynamics: is there a need for a top–down approach? Anal Chem 81:7892–7899 Kaltashov IA, Bobst CE, Abzalimov RR (2009) H/D exchange and mass spectrometry in the studies of protein conformation and dynamics: is there a need for a top–down approach? Anal Chem 81:7892–7899
85.
go back to reference Wang L, Pan H, Smith DL (2002) Hydrogen exchange-mass spectrometry: optimization of digestion conditions. Mol Cell Proteomics 1:132–138 Wang L, Pan H, Smith DL (2002) Hydrogen exchange-mass spectrometry: optimization of digestion conditions. Mol Cell Proteomics 1:132–138
86.
go back to reference Resing KA, Hoofnagle AN, Ahn NG (1999) Modeling deuterium exchange behavior of ERK2 using pepsin mapping to probe secondary structure. J Am Soc Mass Spectrom 10:685–702 Resing KA, Hoofnagle AN, Ahn NG (1999) Modeling deuterium exchange behavior of ERK2 using pepsin mapping to probe secondary structure. J Am Soc Mass Spectrom 10:685–702
87.
go back to reference Hoofnagle AN, Resing KA, Ahn NG (2004) Practical methods for deuterium exchange/mass spectrometry. Methods Mol Biol 250:283–298 Hoofnagle AN, Resing KA, Ahn NG (2004) Practical methods for deuterium exchange/mass spectrometry. Methods Mol Biol 250:283–298
88.
go back to reference Feng L, Orlando R, Prestegard JH (2006) Amide proton back-exchange in deuterated peptides: applications to MS and NMR analyses. Anal Chem 78:6885–6892 Feng L, Orlando R, Prestegard JH (2006) Amide proton back-exchange in deuterated peptides: applications to MS and NMR analyses. Anal Chem 78:6885–6892
89.
go back to reference Weis DD, Wales TE, Engen JR, Hotchko M, Ten Eyck LF (2006) Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis. J Am Soc Mass Spectrom 17:1498–1509 Weis DD, Wales TE, Engen JR, Hotchko M, Ten Eyck LF (2006) Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis. J Am Soc Mass Spectrom 17:1498–1509
90.
go back to reference Houde D, Arndt J, Domeier W, Berkowitz S, Engen JR (2009) Characterization of IgG1 conformation and conformational dynamics by hydrogen/deuterium exchange mass spectrometry. Anal Chem 81:5966 Houde D, Arndt J, Domeier W, Berkowitz S, Engen JR (2009) Characterization of IgG1 conformation and conformational dynamics by hydrogen/deuterium exchange mass spectrometry. Anal Chem 81:5966
91.
go back to reference Wei H, Ahn J, Yu YQ, Tymiak A, Engen JR, Chen G (2012) Using hydrogen/deuterium exchange mass spectrometry to study conformational changes in granulocyte colony stimulating factor upon PEGylation. J Am Soc Mass Spectrom 23:498–504 Wei H, Ahn J, Yu YQ, Tymiak A, Engen JR, Chen G (2012) Using hydrogen/deuterium exchange mass spectrometry to study conformational changes in granulocyte colony stimulating factor upon PEGylation. J Am Soc Mass Spectrom 23:498–504
92.
go back to reference Emmett MR, Kazazic S, Marshall AG, Chen W, Shi SD, Bolanos B, Greig MJ (2006) Supercritical fluid chromatography reduction of hydrogen/deuterium back exchange in solution-phase hydrogen/deuterium exchange with mass spectrometric analysis. Anal Chem 78:7058–7060 Emmett MR, Kazazic S, Marshall AG, Chen W, Shi SD, Bolanos B, Greig MJ (2006) Supercritical fluid chromatography reduction of hydrogen/deuterium back exchange in solution-phase hydrogen/deuterium exchange with mass spectrometric analysis. Anal Chem 78:7058–7060
93.
go back to reference Zhang Z (1997) Enhancement of the effective resolution of mass spectra of high-mass biomolecules by maximum entropy-based deconvolution to eliminate the isotopic natural abundance distribution. J Am Chem Soc 8:659–670 Zhang Z (1997) Enhancement of the effective resolution of mass spectra of high-mass biomolecules by maximum entropy-based deconvolution to eliminate the isotopic natural abundance distribution. J Am Chem Soc 8:659–670
94.
go back to reference Hotchko M, Anand GS, Komives EA, Ten Eyck LF (2006) Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments. Protein Sci 15:583–601 Hotchko M, Anand GS, Komives EA, Ten Eyck LF (2006) Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments. Protein Sci 15:583–601
95.
go back to reference Weis DD, Engen JR, Kass IJ (2006) Semi-automated data processing of hydrogen exchange mass spectra using HX-Express. J Am Soc Mass Spectrom 17:1700–1703 Weis DD, Engen JR, Kass IJ (2006) Semi-automated data processing of hydrogen exchange mass spectra using HX-Express. J Am Soc Mass Spectrom 17:1700–1703
96.
go back to reference Buijs J, Hakansson K, Hagman C, Hakansson P, Oscarsson S (2000) A new method for the accurate determination of the isotopic state of single amide hydrogens within peptides using Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom 14:1751–1756 Buijs J, Hakansson K, Hagman C, Hakansson P, Oscarsson S (2000) A new method for the accurate determination of the isotopic state of single amide hydrogens within peptides using Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom 14:1751–1756
97.
go back to reference Pascal BD, Chalmers MJ, Busby SA, Mader CC, Southern MR, Tsinoremas NF, Griffin PR (2007) The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data. BMC Bioinformatics 8:156 Pascal BD, Chalmers MJ, Busby SA, Mader CC, Southern MR, Tsinoremas NF, Griffin PR (2007) The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data. BMC Bioinformatics 8:156
98.
go back to reference Kazazic S, Zhang HM, Schaub TM, Emmett MR, Hendrickson CL, Blakney GT, Marshall AG (2010) Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution Fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 21:550–558 Kazazic S, Zhang HM, Schaub TM, Emmett MR, Hendrickson CL, Blakney GT, Marshall AG (2010) Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution Fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 21:550–558
99.
go back to reference Nikamanon P, Pun E, Chou W, Koter MD, Gershon PD (2008) TOF2H: a precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis. BMC Bioinformatics 9:387 Nikamanon P, Pun E, Chou W, Koter MD, Gershon PD (2008) TOF2H: a precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis. BMC Bioinformatics 9:387
100.
go back to reference Pascal BD, Chalmers MJ, Busby SA, Griffin PR (2009) HD desktop: an integrated platform for the analysis and visualization of H/D exchange data. J Am Soc Mass Spectrom 20:601–610 Pascal BD, Chalmers MJ, Busby SA, Griffin PR (2009) HD desktop: an integrated platform for the analysis and visualization of H/D exchange data. J Am Soc Mass Spectrom 20:601–610
101.
go back to reference Slysz GW, Baker CA, Bozsa BM, Dang A, Percy AJ, Bennett M, Schriemer DC (2009) Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses. BMC Bioinformatics 10:162 Slysz GW, Baker CA, Bozsa BM, Dang A, Percy AJ, Bennett M, Schriemer DC (2009) Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses. BMC Bioinformatics 10:162
102.
go back to reference Kan ZY, Mayne L, Chetty PS, Englander SW (2011) ExMS: data analysis for HX-MS experiments. J Am Soc Mass Spectrom 22:1906–1915 Kan ZY, Mayne L, Chetty PS, Englander SW (2011) ExMS: data analysis for HX-MS experiments. J Am Soc Mass Spectrom 22:1906–1915
103.
go back to reference Tsui V, Garcia C, Cavagnero S, Siuzdak G, Dyson HJ, Wright PE (1999) Quench-flow experiments combined with mass spectrometry show apomyoglobin folds through and obligatory intermediate. Protein Sci 8:45–49 Tsui V, Garcia C, Cavagnero S, Siuzdak G, Dyson HJ, Wright PE (1999) Quench-flow experiments combined with mass spectrometry show apomyoglobin folds through and obligatory intermediate. Protein Sci 8:45–49
104.
go back to reference Wales TE, Fadgen KE, Gerhardt GC, Engen JR (2008) High-speed and high-resolution UPLC separation at zero degrees Celsius. Anal Chem 80:6815–6820 Wales TE, Fadgen KE, Gerhardt GC, Engen JR (2008) High-speed and high-resolution UPLC separation at zero degrees Celsius. Anal Chem 80:6815–6820
105.
go back to reference Hoofnagle AN, Resing KA, Goldsmith EJ, Ahn NG (2001) Changes in protein conformational mobility upon activation of extracellular regulated protein kinase-2 as detected by hydrogen exchange. Proc Natl Acad Sci USA 98:956–961 Hoofnagle AN, Resing KA, Goldsmith EJ, Ahn NG (2001) Changes in protein conformational mobility upon activation of extracellular regulated protein kinase-2 as detected by hydrogen exchange. Proc Natl Acad Sci USA 98:956–961
106.
go back to reference Robbins DJ, Zhen E, Owaki H, Vanderbilt CA, Ebert D, Geppert TD, Cobb MH (1993) Regulation and properties of extracellular signal-regulated protein kinases 1 and 2 in vitro. J Biol Chem 268:5097–5106 Robbins DJ, Zhen E, Owaki H, Vanderbilt CA, Ebert D, Geppert TD, Cobb MH (1993) Regulation and properties of extracellular signal-regulated protein kinases 1 and 2 in vitro. J Biol Chem 268:5097–5106
107.
go back to reference Canagarajah BJ, Khokhlatchev A, Cobb MH, Goldsmith EJ (1997) Activation mechanism of the MAP kinase ERK2 by dual phosphorylation. Cell 90:859–869 Canagarajah BJ, Khokhlatchev A, Cobb MH, Goldsmith EJ (1997) Activation mechanism of the MAP kinase ERK2 by dual phosphorylation. Cell 90:859–869
108.
go back to reference Zhang F, Strand A, Robbins D, Cobb MH, Goldsmith EJ (1994) Atomic structure of the MAP kinase ERK2 at 2.3 a resolution. Nature 367:704–711 Zhang F, Strand A, Robbins D, Cobb MH, Goldsmith EJ (1994) Atomic structure of the MAP kinase ERK2 at 2.3 a resolution. Nature 367:704–711
109.
go back to reference Pan H, Raza AS, Smith DL (2004) Equilibrium and kinetic folding of rabbit muscle triosephosphate isomerase by hydrogen exchange mass spectrometry. J Mol Biol 336:1251–1263 Pan H, Raza AS, Smith DL (2004) Equilibrium and kinetic folding of rabbit muscle triosephosphate isomerase by hydrogen exchange mass spectrometry. J Mol Biol 336:1251–1263
110.
go back to reference Dong A, Matsuura J, Allison SD, Chrisman E, Manning MC, Carpenter JF (1996) Infrared and circular dichroism spectroscopic characterization of structural differences between beta-lactoglobulin A and B. Biochemistry 35:1450–1457 Dong A, Matsuura J, Allison SD, Chrisman E, Manning MC, Carpenter JF (1996) Infrared and circular dichroism spectroscopic characterization of structural differences between beta-lactoglobulin A and B. Biochemistry 35:1450–1457
111.
go back to reference Sugeta H (1991) Study on conformation of biomolecules by infrared circular dichroism. Tanpakushitsu Kakusan Koso 36:1849–1858 Sugeta H (1991) Study on conformation of biomolecules by infrared circular dichroism. Tanpakushitsu Kakusan Koso 36:1849–1858
112.
go back to reference Susi H, Byler DM (1986) Resolution-enhanced Fourier transform infrared spectroscopy of enzymes. Methods Enzymol 130:290–311 Susi H, Byler DM (1986) Resolution-enhanced Fourier transform infrared spectroscopy of enzymes. Methods Enzymol 130:290–311
113.
go back to reference Nguyen LT, Wiencek JM, Kirsch LE (2003) Characterization methods for the physical stability of biopharmaceuticals. PDA J Pharm Sci Technol 57:429–445 Nguyen LT, Wiencek JM, Kirsch LE (2003) Characterization methods for the physical stability of biopharmaceuticals. PDA J Pharm Sci Technol 57:429–445
114.
go back to reference Martin SR, Schilstra MJ (2008) Circular dichroism and its application to the study of biomolecules. Methods Cell Biol 84:263–293 Martin SR, Schilstra MJ (2008) Circular dichroism and its application to the study of biomolecules. Methods Cell Biol 84:263–293
115.
go back to reference Kaltashov IA, Bobst CE, Abzalimov RR, Berkowitz SA, Houde D (2010) Conformation and dynamics of biopharmaceuticals: transition of mass spectrometry-based tools from academe to industry. J Am Soc Mass Spectrom 21:323–337 Kaltashov IA, Bobst CE, Abzalimov RR, Berkowitz SA, Houde D (2010) Conformation and dynamics of biopharmaceuticals: transition of mass spectrometry-based tools from academe to industry. J Am Soc Mass Spectrom 21:323–337
116.
go back to reference Abuchowski A, McCoy JR, Palczuk NC, van Es T, Davis FF (1977) Effect of covalent attachment of polyethylene glycol on immunogenicity and circulating life of bovine liver catalase. J Biol Chem 252:3582–3586 Abuchowski A, McCoy JR, Palczuk NC, van Es T, Davis FF (1977) Effect of covalent attachment of polyethylene glycol on immunogenicity and circulating life of bovine liver catalase. J Biol Chem 252:3582–3586
117.
go back to reference Greenwald RB, Choe YH, McGuire J, Conover CD (2003) Effective drug delivery by PEGylated drug conjugates. Adv Drug Deliv Rev 55:217–250 Greenwald RB, Choe YH, McGuire J, Conover CD (2003) Effective drug delivery by PEGylated drug conjugates. Adv Drug Deliv Rev 55:217–250
118.
go back to reference Chapman AP (2002) PEGylated antibodies and antibody fragments for improved therapy: a review. Adv Drug Deliv Rev 54:531–545 Chapman AP (2002) PEGylated antibodies and antibody fragments for improved therapy: a review. Adv Drug Deliv Rev 54:531–545
119.
go back to reference Reddy KR (2000) Controlled-release, PEGylation, liposomal formulations: new mechanisms in the delivery of injectable drugs. Ann Pharmacother 34:915–923 Reddy KR (2000) Controlled-release, PEGylation, liposomal formulations: new mechanisms in the delivery of injectable drugs. Ann Pharmacother 34:915–923
120.
go back to reference Tamada T, Honjo E, Maeda Y, Okamoto T, Ishibashi M, Tokunaga M, Kuroki R (2006) Homodimeric cross-over structure of the human granulocyte colony-stimulating factor (GCSF) receptor signaling complex. Proc Natl Acad Sci USA 103:3135–3140 Tamada T, Honjo E, Maeda Y, Okamoto T, Ishibashi M, Tokunaga M, Kuroki R (2006) Homodimeric cross-over structure of the human granulocyte colony-stimulating factor (GCSF) receptor signaling complex. Proc Natl Acad Sci USA 103:3135–3140
121.
go back to reference Morgan CR, Miglionico BV, Engen JR (2011) Effects of HIV-1 Nef on human N-myristoyltransferase 1. Biochemistry 50:3394–3403 Morgan CR, Miglionico BV, Engen JR (2011) Effects of HIV-1 Nef on human N-myristoyltransferase 1. Biochemistry 50:3394–3403
122.
go back to reference Piedmonte DM, Treuheit MJ (2008) Formulation of Neulasta (pegfilgrastim). Adv Drug Deliv Rev 60:50–58 Piedmonte DM, Treuheit MJ (2008) Formulation of Neulasta (pegfilgrastim). Adv Drug Deliv Rev 60:50–58
123.
go back to reference Bobst CE, Abzalimov RR, Houde D, Kloczewiak M, Mhatre R, Berkowitz SA, Kaltashov IA (2008) Detection and characterization of altered conformations of protein pharmaceuticals using complementary mass spectrometry-based approaches. Anal Chem 80:7473–7481 Bobst CE, Abzalimov RR, Houde D, Kloczewiak M, Mhatre R, Berkowitz SA, Kaltashov IA (2008) Detection and characterization of altered conformations of protein pharmaceuticals using complementary mass spectrometry-based approaches. Anal Chem 80:7473–7481
124.
go back to reference Bissantz C, Kuhn B, Stahl M (2010) A medicinal chemist’s guide to molecular interactions. J Med Chem 53:5061–5084 Bissantz C, Kuhn B, Stahl M (2010) A medicinal chemist’s guide to molecular interactions. J Med Chem 53:5061–5084
125.
go back to reference Konermann L, Pan J, Liu YH (2011) Hydrogen exchange mass spectrometry for studying protein structure and dynamics. Chem Soc Rev 40:1224–1234 Konermann L, Pan J, Liu YH (2011) Hydrogen exchange mass spectrometry for studying protein structure and dynamics. Chem Soc Rev 40:1224–1234
126.
go back to reference Yamada N, Suzuki E, Hirayama K (2002) Identification of the interface of a large protein–protein complex using H/D exchange and Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom 16:293–299 Yamada N, Suzuki E, Hirayama K (2002) Identification of the interface of a large protein–protein complex using H/D exchange and Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom 16:293–299
127.
go back to reference Lisal J, Kainov DE, Lam TT, Emmett MR, Wei H, Gottlieb P, Marshall AG, Tuma R (2006) Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage. Virology 351:73–79 Lisal J, Kainov DE, Lam TT, Emmett MR, Wei H, Gottlieb P, Marshall AG, Tuma R (2006) Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage. Virology 351:73–79
128.
go back to reference Derunes C, Burgess R, Iraheta E, Kellerer R, Becherer K, Gessner CR, Li S, Hewitt K, Vuori K, Pasquale EB, Woods VL Jr, Ely KR (2006) Molecular determinants for interaction of SHEP1 with Cas localize to a highly solvent-protected region in the complex. FEBS Lett 580:175–178 Derunes C, Burgess R, Iraheta E, Kellerer R, Becherer K, Gessner CR, Li S, Hewitt K, Vuori K, Pasquale EB, Woods VL Jr, Ely KR (2006) Molecular determinants for interaction of SHEP1 with Cas localize to a highly solvent-protected region in the complex. FEBS Lett 580:175–178
129.
go back to reference Zhang J, Adrian FJ, Jahnke W, Cowan-Jacob SW, Li AG, Iacob RE, Sim T, Powers J, Dierks C, Sun F, Guo GR, Ding Q, Okram B, Choi Y, Wojciechowski A, Deng X, Liu G, Fendrich G, Strauss A, Vajpai N, Grzesiek S, Tuntland T, Liu Y, Bursulaya B, Azam M, Manley PW, Engen JR, Daley GQ, Warmuth M, Gray NS (2010) Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors. Nature 463:501–506 Zhang J, Adrian FJ, Jahnke W, Cowan-Jacob SW, Li AG, Iacob RE, Sim T, Powers J, Dierks C, Sun F, Guo GR, Ding Q, Okram B, Choi Y, Wojciechowski A, Deng X, Liu G, Fendrich G, Strauss A, Vajpai N, Grzesiek S, Tuntland T, Liu Y, Bursulaya B, Azam M, Manley PW, Engen JR, Daley GQ, Warmuth M, Gray NS (2010) Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors. Nature 463:501–506
130.
go back to reference Zhang Q, Willison LN, Tripathi P, Sathe SK, Roux KH, Emmett MR, Blakney GT, Zhang HM, Marshall AG (2011) Epitope mapping of a 95 kDa antigen in complex with antibody by solution-phase amide backbone hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 83:7129–7136 Zhang Q, Willison LN, Tripathi P, Sathe SK, Roux KH, Emmett MR, Blakney GT, Zhang HM, Marshall AG (2011) Epitope mapping of a 95 kDa antigen in complex with antibody by solution-phase amide backbone hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 83:7129–7136
131.
go back to reference Garcia RA, Pantazatos DP, Gessner CR, Go KV, Woods VL Jr, Villarreal FJ (2005) Molecular interactions between matrilysin and the matrix metalloproteinase inhibitor doxycycline investigated by deuterium exchange mass spectrometry. Mol Pharmacol 67:1128–1136 Garcia RA, Pantazatos DP, Gessner CR, Go KV, Woods VL Jr, Villarreal FJ (2005) Molecular interactions between matrilysin and the matrix metalloproteinase inhibitor doxycycline investigated by deuterium exchange mass spectrometry. Mol Pharmacol 67:1128–1136
132.
go back to reference Ehring H (1999) Hydrogen exchange/electrospray ionization mass spectrometry studies of structural features of proteins and protein/protein interactions. Anal Biochem 267:252–259 Ehring H (1999) Hydrogen exchange/electrospray ionization mass spectrometry studies of structural features of proteins and protein/protein interactions. Anal Biochem 267:252–259
133.
go back to reference Zhu MM, Rempel DL, Du Z, Gross ML (2003) Quantification of protein-ligand interactions by mass spectrometry, titration, and H/D exchange: PLIMSTEX. J Am Chem Soc 125:5252–5253 Zhu MM, Rempel DL, Du Z, Gross ML (2003) Quantification of protein-ligand interactions by mass spectrometry, titration, and H/D exchange: PLIMSTEX. J Am Chem Soc 125:5252–5253
134.
go back to reference Zhu MM, Rempel DL, Gross ML (2004) Modeling data from titration, amide H/D exchange, and mass spectrometry to obtain protein-ligand binding constants. J Am Soc Mass Spectrom 15:388–397 Zhu MM, Rempel DL, Gross ML (2004) Modeling data from titration, amide H/D exchange, and mass spectrometry to obtain protein-ligand binding constants. J Am Soc Mass Spectrom 15:388–397
135.
go back to reference Sperry JB, Shi X, Rempel DL, Nishimura Y, Akashi S, Gross ML (2008) A mass spectrometric approach to the study of DNA-binding proteins: interaction of human TRF2 with telomeric DNA. Biochemistry 47:1797–1807 Sperry JB, Shi X, Rempel DL, Nishimura Y, Akashi S, Gross ML (2008) A mass spectrometric approach to the study of DNA-binding proteins: interaction of human TRF2 with telomeric DNA. Biochemistry 47:1797–1807
136.
go back to reference Powell KD, Wales TE, Fitzgerald MC (2002) Thermodynamic stability measurements on multimeric proteins using a new H/D exchange- and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-based method. Protein Sci 11:841–851 Powell KD, Wales TE, Fitzgerald MC (2002) Thermodynamic stability measurements on multimeric proteins using a new H/D exchange- and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-based method. Protein Sci 11:841–851
137.
go back to reference Huang YJ, Montelione GT (2005) Structural biology: proteins flex to function. Nature 438:36–37 Huang YJ, Montelione GT (2005) Structural biology: proteins flex to function. Nature 438:36–37
138.
go back to reference Tang L, Hopper ED, Tong Y, Sadowsky JD, Peterson KJ, Gellman SH, Fitzgerald MC (2007) H/D exchange- and mass spectrometry-based strategy for the thermodynamic analysis of protein-ligand binding. Anal Chem 79:5869–5877 Tang L, Hopper ED, Tong Y, Sadowsky JD, Peterson KJ, Gellman SH, Fitzgerald MC (2007) H/D exchange- and mass spectrometry-based strategy for the thermodynamic analysis of protein-ligand binding. Anal Chem 79:5869–5877
139.
go back to reference Roulhac PL, Weaver KD, Adhikari P, Anderson DS, DeArmond PD, Mietzner TA, Crumbliss AL, Fitzgerald MC (2008) Ex vivo analysis of synergistic anion binding to FbpA in gram-negative bacteria. Biochemistry 47:4298–4305 Roulhac PL, Weaver KD, Adhikari P, Anderson DS, DeArmond PD, Mietzner TA, Crumbliss AL, Fitzgerald MC (2008) Ex vivo analysis of synergistic anion binding to FbpA in gram-negative bacteria. Biochemistry 47:4298–4305
140.
go back to reference Hopper ED, Roulhac PL, Campa MJ, Patz EF Jr, Fitzgerald MC (2008) Throughput and efficiency of a mass spectrometry-based screening assay for protein-ligand binding detection. J Am Soc Mass Spectrom 19:1303–1311 Hopper ED, Roulhac PL, Campa MJ, Patz EF Jr, Fitzgerald MC (2008) Throughput and efficiency of a mass spectrometry-based screening assay for protein-ligand binding detection. J Am Soc Mass Spectrom 19:1303–1311
141.
go back to reference Dearmond PD, West GM, Anbalagan V, Campa MJ, Patz EF Jr, Fitzgerald MC (2010) Discovery of novel cyclophilin A ligands using an H/D exchange- and mass spectrometry-based strategy. J Biomol Screen 15:1051–1062 Dearmond PD, West GM, Anbalagan V, Campa MJ, Patz EF Jr, Fitzgerald MC (2010) Discovery of novel cyclophilin A ligands using an H/D exchange- and mass spectrometry-based strategy. J Biomol Screen 15:1051–1062
142.
go back to reference Powell KD, Fitzgerald MC (2004) High-throughput screening assay for the tunable selection of protein ligands. J Comb Chem 6:262–269 Powell KD, Fitzgerald MC (2004) High-throughput screening assay for the tunable selection of protein ligands. J Comb Chem 6:262–269
143.
go back to reference Hopper ED, Pittman AM, Tucker CL, Campa MJ, Patz EF Jr, Fitzgerald MC (2009) Hydrogen/deuterium exchange- and protease digestion-based screening assay for protein-ligand binding detection. Anal Chem 81:6860–6867 Hopper ED, Pittman AM, Tucker CL, Campa MJ, Patz EF Jr, Fitzgerald MC (2009) Hydrogen/deuterium exchange- and protease digestion-based screening assay for protein-ligand binding detection. Anal Chem 81:6860–6867
144.
go back to reference Anand GS, Hughes CA, Jones JM, Taylor SS, Komives EA (2002) Amide H/2H exchange reveals communication between the cAMP and catalytic subunit-binding sites in the R(I)alpha subunit of protein kinase A. J Mol Biol 323:377–386 Anand GS, Hughes CA, Jones JM, Taylor SS, Komives EA (2002) Amide H/2H exchange reveals communication between the cAMP and catalytic subunit-binding sites in the R(I)alpha subunit of protein kinase A. J Mol Biol 323:377–386
145.
go back to reference Akashi S, Takio K (2000) Characterization of the interface structure of enzyme-inhibitor complex by using hydrogen-deuterium exchange and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Protein Sci 9:2497–2505 Akashi S, Takio K (2000) Characterization of the interface structure of enzyme-inhibitor complex by using hydrogen-deuterium exchange and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Protein Sci 9:2497–2505
146.
go back to reference Lee T, Hoofnagle AN, Kabuyama Y, Stroud J, Min X, Goldsmith EJ, Chen L, Resing KA, Ahn NG (2004) Docking motif interactions in MAP kinases revealed by hydrogen exchange mass spectrometry. Mol Cell 14:43–55 Lee T, Hoofnagle AN, Kabuyama Y, Stroud J, Min X, Goldsmith EJ, Chen L, Resing KA, Ahn NG (2004) Docking motif interactions in MAP kinases revealed by hydrogen exchange mass spectrometry. Mol Cell 14:43–55
147.
go back to reference Chik JK, Schriemer DC (2003) Hydrogen/deuterium exchange mass spectrometry of actin in various biochemical contexts. J Mol Biol 334:373–385 Chik JK, Schriemer DC (2003) Hydrogen/deuterium exchange mass spectrometry of actin in various biochemical contexts. J Mol Biol 334:373–385
148.
go back to reference Brier S, Lemaire D, DeBonis S, Kozielski F, Forest E (2006) Use of hydrogen/deuterium exchange mass spectrometry and mutagenesis as a tool to identify the binding region of inhibitors targeting the human mitotic kinesin Eg5. Rapid Commun Mass Spectrom 20:456–462 Brier S, Lemaire D, DeBonis S, Kozielski F, Forest E (2006) Use of hydrogen/deuterium exchange mass spectrometry and mutagenesis as a tool to identify the binding region of inhibitors targeting the human mitotic kinesin Eg5. Rapid Commun Mass Spectrom 20:456–462
149.
go back to reference Mandell JG, Baerga-Ortiz A, Akashi S, Takio K, Komives EA (2001) Solvent accessibility of the thrombin-thrombomodulin interface. J Mol Biol 306:575–589 Mandell JG, Baerga-Ortiz A, Akashi S, Takio K, Komives EA (2001) Solvent accessibility of the thrombin-thrombomodulin interface. J Mol Biol 306:575–589
150.
go back to reference Bailey-Kellogg C, Kelley JJ 3rd, Stein C, Donald BR (2001) Reducing mass degeneracy in SAR by MS by stable isotopic labeling. J Comput Biol 8:19–36 Bailey-Kellogg C, Kelley JJ 3rd, Stein C, Donald BR (2001) Reducing mass degeneracy in SAR by MS by stable isotopic labeling. J Comput Biol 8:19–36
151.
go back to reference Bennett MJ, Barakat K, Huzil JT, Tuszynski J, Schriemer DC (2010) Discovery and characterization of the laulimalide-microtubule binding mode by mass shift perturbation mapping. Chem Biol 17:725–734 Bennett MJ, Barakat K, Huzil JT, Tuszynski J, Schriemer DC (2010) Discovery and characterization of the laulimalide-microtubule binding mode by mass shift perturbation mapping. Chem Biol 17:725–734
152.
go back to reference Demarest SJ, Martinez-Yamout M, Chung J, Chen H, Xu W, Dyson HJ, Evans RM, Wright PE (2002) Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators. Nature 415:549–553 Demarest SJ, Martinez-Yamout M, Chung J, Chen H, Xu W, Dyson HJ, Evans RM, Wright PE (2002) Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators. Nature 415:549–553
Metadata
Title
Hydrogen/Deuterium Exchange Mass Spectrometry for Protein Higher-Order Structure Characterization
Authors
Hui Wei
Adrienne A. Tymiak
Guodong Chen
Copyright Year
2013
Publisher
Springer US
DOI
https://doi.org/10.1007/978-1-4419-7862-2_8

Premium Partners