H/D Exchange Centroid Monitoring is Insufficient to Show Differences in the Behavior of Protein States

  • Jun Zhang
  • Pradeep Ramachandran
  • Rajiv Kumar
  • Michael L. Gross
Application Note

Abstract

Differential hydrogen/deuterium exchange (H/DX) coupled with mass spectrometry (H/DX-MS) offers a rapid and sensitive characterization of changes in proteins following perturbations induced by changes in folding, ligand binding, oligomerization, and modification. The characterization of H/DX rates by software tools and automated data processing often relies on the centroid mass calculation and, thereby, the deuterium distribution in the mass spectra is neglected. Here we present an example demonstrating the clear limitation of using only a centroid approach to characterize the H/DX rate, in which the change in protein is not reflected as the difference in deuterium uptake based on centroid calculation.

Key words

Hydrogen/deuterium exchange Mass spectrometry Centroid of D distribution DREAM protein EX1 and EX2 kinetics 

Supplementary material

13361_2012_555_MOESM1_ESM.doc (72 kb)
ESM 1(DOC 71 kb)

References

  1. 1.
    Englander, S.W., Kallenbach, N.R.: Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16, 521–655 (1984)CrossRefGoogle Scholar
  2. 2.
    Bai, Y., Milne, J.S., Mayne, L., Englander, S.W.: Primary structure effects on peptide group hydrogen exchange. Proteins 17, 75–86 (1993)CrossRefGoogle Scholar
  3. 3.
    Zhang, Z., Smith, D.L.: Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci. 2, 522–531 (1993)CrossRefGoogle Scholar
  4. 4.
    Engen, J.R., Smith, D.L.: Investigating protein structure and dynamics by hydrogen exchange MS. Anal. Chem. 73, 256A–265A (2001)CrossRefGoogle Scholar
  5. 5.
    Hamuro, Y., Coales, S.J., Morrow, J.A., Molnar, K.S., Tuske, S.J., Southern, M.R., Griffin, P.R.: Hydrogen/deuterium-exchange (H/D-Ex) of PPARγ LBD in the presence of various modulators. Protein Sci. 15, 1883–1892 (2006)CrossRefGoogle Scholar
  6. 6.
    Bruning, J.B., Chalmers, M.J., Prasad, S., Busby, S.A., Kamenecka, T.M., He, Y., Nettles, K.W., Griffin, P.R.: Partial agonists activate PPARγ using a helix 12 independent mechanism. Structure 15, 1258–1271 (2007)CrossRefGoogle Scholar
  7. 7.
    West, G.M., Chien, E.Y., Katritch, V., Gatchalian, J., Chalmers, M.J., Stevens, R.C., Griffin, P.R.: Ligand-dependent perturbation of the conformational ensemble for the GPCR β2 adrenergic receptor revealed by HDX. Structure 19, 1424–1432 (2011)CrossRefGoogle Scholar
  8. 8.
    Chik, J.K., Schriemer, D.C.: Hydrogen/deuterium exchange mass spectrometry of actin in various biochemical contexts. J. Mol. Biol. 334, 373–385 (2003)CrossRefGoogle Scholar
  9. 9.
    Coales, S.J., Tuske, S.J., Tomasso, J.C., Hamuro, Y.: 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 (2009)CrossRefGoogle Scholar
  10. 10.
    Huang, R.Y., Wen, J., Blankenship, R.E., Gross, M.L.: Hydrogen/deuterium exchange mass spectrometry reveals the interaction of Fenna-Matthews-Olson protein and chlorosome CsmA protein. Biochemistry 51, 187–193 (2012)CrossRefGoogle Scholar
  11. 11.
    Iacob, R.E., Zhang, J., Gray, N.S., Engen, J.R.: Allosteric interactions between the myristate- and ATP-site of the Abl kinase. PLoS One 6, e15929 (2011)CrossRefGoogle Scholar
  12. 12.
    Zhang, J., Chalmers, M.J., Stayrook, K.R., Burris, L.L., Wang, Y.J., Busby, S.A., Pascal, B.D., Garcia-Ordonez, R.D., Bruning, J.B., Istrate, M.A., Kojetin, D.J., Dodge, J.A., Burris, T.P., Griffin, P.R.: DNA binding alters coactivator interaction surfaces of the intact VDR–RXR complex. Nat. Struct. Mol. Biol. 18, 556–563 (2011)Google Scholar
  13. 13.
    Rand, K.D., Jorgensen, T.J., Olsen, O.H., Persson, E., Jensen, O.N., Stennicke, H.R., Andersen, M.D.: Allosteric activation of coagulation factor VIIa visualized by hydrogen exchange. J. Biol. Chem. 281, 23018–23024 (2006)CrossRefGoogle Scholar
  14. 14.
    Pascal, B.D., Chalmers, M.J., Busby, S.A., Mader, C.C., Southern, M.R., Tsinoremas, N.F., Griffin, P.R.: The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data. BMC Bioinforma 8, 156–167 (2007)Google Scholar
  15. 15.
    Slysz, G.W., Baker, C.A., Bozsa, B.M., Dang, A., Percy, A.J., Bennett, M., Schriemer, D.C.: Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses. BMC Bioinformatics 10, 162 (2009)CrossRefGoogle Scholar
  16. 16.
    Weis, D.D., Engen, J.R., Kass, I.J.: Semi-automated data processing of hydrogen exchange mass spectra using HX-Express. J. Am. Soc. Mass Spectrom. 17, 1700–1703 (2006)CrossRefGoogle Scholar
  17. 17.
    Pascal, B.D., Chalmers, M.J., Busby, S.A., Griffin, P.R.: HD desktop: an integrated platform for the analysis and visualization of H/D exchange data. J. Am. Soc. Mass Spectrom. 20, 601–610 (2009)CrossRefGoogle Scholar
  18. 18.
    Pascal, B.D., Willis, S., Lauer, J.L., Landgraf, R.R., West, G.M., Marciano, D., Novick, S., Goswami, D., Chalmers, M.J., Griffin, P.R.: HDX Workbench: software for the analysis of H/D exchange MS data. J. Am. Soc. Mass Spectrom. 23, 1512–1521 (2012)CrossRefGoogle Scholar
  19. 19.
    Nikamanon, P., Pun, E., Chou, W., Koter, M.D., Gershon, P.D.: "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 (2008)CrossRefGoogle Scholar
  20. 20.
    Hotchko, M., Anand, G.S., Komives, E.A., Ten Eyck, L.F.: Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments. Protein Sci. 15, 583–601 (2006)CrossRefGoogle Scholar
  21. 21.
    Kreshuk, A., Stankiewicz, M., Lou, X.H., Kirchner, M., Hamprecht, F.A., Mayer, M.P.: Automated detection and analysis of bimodal isotope peak distributions in H/D exchange mass spectrometry using HeXicon. Int. J. Mass Spectrom. 302, 125–131 (2011)CrossRefGoogle Scholar
  22. 22.
    Craig, T.A., Benson, L.M., Venyaminov, S.Y., Klimtchuk, E.S., Bajzer, Z., Prendergast, F.G., Naylor, S., Kumar, R.: The metal-binding properties of DREAM—evidence for calcium-mediated changes in DREAM structure. J. Biol. Chem. 277, 10955–10966 (2002)CrossRefGoogle Scholar
  23. 23.
    Zhang, J., Chalmers, M.J., Stayrook, K.R., Burris, L.L., Garcia-Ordonez, R.D., Pascal, B.D., Burris, T.P., Dodge, J.A., Griffin, P.R.: Hydrogen/deuterium exchange reveals distinct agonist/partial agonist receptor dynamics within vitamin D receptor/retinoid X receptor heterodimer. Structure 18, 1332–1341 (2010)CrossRefGoogle Scholar
  24. 24.
    Wales, T.E., Engen, J.R.: Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom. Rev. 25, 158–170 (2006)CrossRefGoogle Scholar
  25. 25.
    Carrion, A.M., Link, W.A., Ledo, F., Mellstrom, B., Naranjo, J.R.: DREAM is a Ca2 + -regulated transcriptional repressor. Nature 398, 80–84 (1999)CrossRefGoogle Scholar
  26. 26.
    Lusin, J.D., Vanarotti, M., Li, C., Valiveti, A., Ames, J.B.: NMR structure of DREAM: implications for Ca(2+)-dependent DNA binding and protein dimerization. Biochemistry 47, 2252–2264 (2008)CrossRefGoogle Scholar
  27. 27.
    Osawa, M., Dace, A., Tong, K.I., Valiveti, A., Ikura, M., Ames, J.B.: Mg2+ and Ca2+ differentially regulate DNA binding and dimerization of DREAM. J. Biol. Chem. 280, 18008–18014 (2005)CrossRefGoogle Scholar
  28. 28.
    Weis, D.D., Wales, T.E., Engen, J.R., Hotchko, M., Ten Eyck, L.F.: Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis. J. Am. Soc. Mass Spectrom. 17, 1498–1509 (2006)CrossRefGoogle Scholar
  29. 29.
    Chik, J.K., Vande Graaf, J.L., Schriemer, D.C.: Quantitating the statistical distribution of deuterium incorporation to extend the utility of H/D exchange MS data. Anal. Chem. 78, 207–214 (2006)CrossRefGoogle Scholar
  30. 30.
    Percy, A.J., Rey, M., Burns, K.M., Schriemer, D.C.: Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry—a review. Anal. Chim. Acta 721, 7–21 (2012)Google Scholar
  31. 31.
    Fang, J., Engen, J.R., Beuning, P.J.: Escherichia coli processivity clamp β from DNA polymerase III is dynamic in solution. Biochemistry 50, 5958–5968 (2011)CrossRefGoogle Scholar
  32. 32.
    Morgan, C.R., Hebling, C.M., Rand, K.D., Stafford, D.W., Jorgenson, J.W., Engen, J.R.: Conformational transitions in the membrane scaffold protein of phospholipid bilayer nanodiscs. Mol. Cell. Proteomics 10, 1–11 (2011)Google Scholar
  33. 33.
    Kan, Z.Y., Mayne, L., Chetty, P.S., Englander, S.W.: ExMS: data analysis for HX-MS experiments. J. Am. Soc. Mass Spectrom. 22, 1906–1915 (2011)CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2013

Authors and Affiliations

  • Jun Zhang
    • 1
  • Pradeep Ramachandran
    • 2
    • 3
  • Rajiv Kumar
    • 2
    • 3
  • Michael L. Gross
    • 1
  1. 1.Department of ChemistryWashington University in St. LouisSt. LouisUSA
  2. 2.Division of Nephrology and Hypertension, Department of MedicineMayo ClinicRochesterUSA
  3. 3.Department of Biochemistry and Molecular BiologyMayo ClinicRochesterUSA

Personalised recommendations