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.
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Kuntz ID, Chen K, Sharp KA, Kollman PA (1999) The maximal affinity of ligands. Proc Natl Acad Sci USA 96:9997–10002
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 (1955) The kinetics of the deuterium exchange of insulin with D2O; an amendment. Biochim Biophys Acta 16:168–169
Englander SW (1963) A hydrogen exchange method using tritium and sephadex: its application to ribonuclease. Biochemistry 2:798–807
Haris PI, Chapman D (1995) The conformational analysis of peptides using fourier transform IR spectroscopy. Biopolymers 37:251–263
Englander JJ, Calhoun DB, Englander SW (1979) Measurement and calibration of peptide group hydrogen-deuterium exchange by ultraviolet spectrophotometry. Anal Biochem 92:517–524
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
Englander SW, Mayne L (1992) Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. Annu Rev Biophys Biomol Struct 21:243–265
Jeng MF, Dyson HJ (1995) Comparison of the hydrogen-exchange behavior of reduced and oxidized Escherichia coli thioredoxin. Biochemistry 34:611–619
Dempsey CE (2001) Hydrogen exchange in peptides and proteins using NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 39:135–170
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
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
Englander JJ, Rogero JR, Englander SW (1985) Protein hydrogen exchange studied by the fragment separation method. Anal Biochem 147:234–244
Katta V, Chait BT (1991) Conformational changes in proteins probed by hydrogen-exchange electrospray-ionization mass spectrometry. Rapid Commun Mass Spectrom 5:214–217
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
Johnson RS, Walsh KA (1994) Mass spectrometric measurement of protein amide hydrogen exchange rates of apo- and holo-myoglobin. Protein Sci 3:2411–2418
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
Eyles SJ, Kaltashov IA (2004) Methods to study protein dynamics and folding by mass spectrometry. Methods 34:88–99
Miranker A, Robinson CV, Radford SE, Aplin RT, Dobson CM (1993) Detection of transient protein folding populations by mass spectrometry. Science 262:896–900
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
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
Zhang Z, Post CB, Smith DL (1996) Amide hydrogen exchange determined by mass spectrometry: application to rabbit muscle aldolase. Biochemistry 35:779–791
Hoofnagle AN, Resing KA, Ahn NG (2003) Protein analysis by hydrogen exchange mass spectrometry. Annu Rev Biophys Biomol Struct 32:1–25
Wales TE, Engen JR (2006) Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom Rev 25:158–170
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
Englander SW, Kallenbach NR (1983) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys 16:521–655
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
Garcia RA, Pantazatos D, Villarreal FJ (2004) Hydrogen/deuterium exchange mass spectrometry for investigating protein-ligand interactions. Assay Drug Dev Technol 2:81–91
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
Goshe MB, Anderson VE (1999) Hydroxyl radical-induced hydrogen/deuterium exchange in amino acid carbon-hydrogen bonds. Radiat Res 151:50–58
Bai Y, Milne JS, Mayne L, Englander SW (1993) Primary structure effects on peptide group hydrogen exchange. Proteins 17:75–86
Molday RS, Englander SW, Kallen RG (1972) Primary structure effects on peptide group hydrogen exchange. Biochemistry 11:150–158
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
Eriksson MA, Hard T, Nilsson L (1995) On the pH dependence of amide proton exchange rates in proteins. Biophys J 69:329–339
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
Berger A, Loewenstein A, Meiboom S (1959) Nuclear magnetic resonance and the proteolysis of N-methylacetamide. J Am Chem Soc 81(1):62–67
Dempsey CE (2001) Hydrogen exchange in peptides and proteins using NMR spectroscopy. Prog Nucl Magn Reson Spectro 39:135–170
Connelly GP, Bai Y, Jeng MF, Englander SW (1993) Isotope effects in peptide group hydrogen exchange. Proteins 17:87–92
Barksdale AD, Rosenberg A (1982) Acquisition and interpretation of hydrogen exchange data from peptides, polymers, and proteins. Methods Biochem Anal 28:1–113
Hvidt A, Nielsen SO (1966) Hydrogen exchange in proteins. Adv Protein Chem 21:287–386
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
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
Deng Y, Smith DL (1998) Identification of unfolding domains in large proteins by their unfolding rates. Biochemistry 37:6256–6262
Swint-Kruse L, Robertson AD (1996) Temperature and pH dependences of hydrogen exchange and global stability for ovomucoid third domain. Biochemistry 35:171–180
Clarke J, Itzhaki LS (1998) Hydrogen exchange and protein folding. Curr Opin Struct Biol 8:112–118
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
Englander SW, Englander JJ (1972) Hydrogen-tritium exchange. Methods Enzymol, 26 PtC, 406–413
Maier CS, Deinzer ML (2005) Protein conformations, interactions, and H/D exchange. Methods Enzymol 402:312–360
Woodward CK, Ellis LM, Rosenberg A (1975) The solvent dependence of hydrogen exchange kinetics of folded proteins. J Biol Chem 250:440–444
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
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
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
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
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
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
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
Konermann L, Simmons DA (2003) Protein-folding kinetics and mechanisms studied by pulse-labeling and mass spectrometry. Mass Spectrom Rev 22:1–26
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
Yang H, Smith DL (1997) Kinetics of cytochrome c folding examined by hydrogen exchange and mass spectrometry. Biochemistry 36:14992–14999
Rogero JR, Englander JJ, Englander SW (1986) Individual breathing reactions measured by functional labeling and hydrogen exchange methods. Methods Enzymol 131:508–517
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
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
Engen JR (2003) Analysis of protein complexes with hydrogen exchange and mass spectrometry. Analyst 128:623–628
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
Ghaemmaghami S, Fitzgerald MC, Oas TG (2000) A quantitative, high-throughput screen for protein stability. Proc Natl Acad Sci USA 97:8296–8301
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
Kipping M, Schierhorn A (2003) Improving hydrogen/deuterium exchange mass spectrometry by reduction of the back-exchange effect. J Mass Spectrom 38:271–276
Anderegg RJ, Wagner DS, Stevenson CL (1994) The mass spectrometry of helical unfolding in peptides. J Am Chem Soc 5:425–433
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
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
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
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
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
Zubarev RA (2003) Reactions of polypeptide ions with electrons in the gas phase. Mass Spectrom Rev 22:57–77
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
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
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
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
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
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
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
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
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
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
Wang L, Pan H, Smith DL (2002) Hydrogen exchange-mass spectrometry: optimization of digestion conditions. Mol Cell Proteomics 1:132–138
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
Hoofnagle AN, Resing KA, Ahn NG (2004) Practical methods for deuterium exchange/mass spectrometry. Methods Mol Biol 250:283–298
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Kan ZY, Mayne L, Chetty PS, Englander SW (2011) ExMS: data analysis for HX-MS experiments. J Am Soc Mass Spectrom 22:1906–1915
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
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
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
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
Canagarajah BJ, Khokhlatchev A, Cobb MH, Goldsmith EJ (1997) Activation mechanism of the MAP kinase ERK2 by dual phosphorylation. Cell 90:859–869
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
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
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
Sugeta H (1991) Study on conformation of biomolecules by infrared circular dichroism. Tanpakushitsu Kakusan Koso 36:1849–1858
Susi H, Byler DM (1986) Resolution-enhanced Fourier transform infrared spectroscopy of enzymes. Methods Enzymol 130:290–311
Nguyen LT, Wiencek JM, Kirsch LE (2003) Characterization methods for the physical stability of biopharmaceuticals. PDA J Pharm Sci Technol 57:429–445
Martin SR, Schilstra MJ (2008) Circular dichroism and its application to the study of biomolecules. Methods Cell Biol 84:263–293
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
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
Greenwald RB, Choe YH, McGuire J, Conover CD (2003) Effective drug delivery by PEGylated drug conjugates. Adv Drug Deliv Rev 55:217–250
Chapman AP (2002) PEGylated antibodies and antibody fragments for improved therapy: a review. Adv Drug Deliv Rev 54:531–545
Reddy KR (2000) Controlled-release, PEGylation, liposomal formulations: new mechanisms in the delivery of injectable drugs. Ann Pharmacother 34:915–923
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
Morgan CR, Miglionico BV, Engen JR (2011) Effects of HIV-1 Nef on human N-myristoyltransferase 1. Biochemistry 50:3394–3403
Piedmonte DM, Treuheit MJ (2008) Formulation of Neulasta (pegfilgrastim). Adv Drug Deliv Rev 60:50–58
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
Bissantz C, Kuhn B, Stahl M (2010) A medicinal chemist’s guide to molecular interactions. J Med Chem 53:5061–5084
Konermann L, Pan J, Liu YH (2011) Hydrogen exchange mass spectrometry for studying protein structure and dynamics. Chem Soc Rev 40:1224–1234
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
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
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
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 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
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
Ehring H (1999) Hydrogen exchange/electrospray ionization mass spectrometry studies of structural features of proteins and protein/protein interactions. Anal Biochem 267:252–259
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, 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
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
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
Huang YJ, Montelione GT (2005) Structural biology: proteins flex to function. Nature 438:36–37
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
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
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
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
Powell KD, Fitzgerald MC (2004) High-throughput screening assay for the tunable selection of protein ligands. J Comb Chem 6:262–269
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
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
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
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
Chik JK, Schriemer DC (2003) Hydrogen/deuterium exchange mass spectrometry of actin in various biochemical contexts. J Mol Biol 334:373–385
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
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
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
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
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
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Wei, H., Tymiak, A.A., Chen, G. (2013). Hydrogen/Deuterium Exchange Mass Spectrometry for Protein Higher-Order Structure Characterization. In: Chen, G. (eds) Characterization of Protein Therapeutics using Mass Spectrometry. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-7862-2_8
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