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.
References
Englander, S.W., Kallenbach, N.R.: Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16, 521–655 (1984)
Bai, Y., Milne, J.S., Mayne, L., Englander, S.W.: Primary structure effects on peptide group hydrogen exchange. Proteins 17, 75–86 (1993)
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)
Engen, J.R., Smith, D.L.: Investigating protein structure and dynamics by hydrogen exchange MS. Anal. Chem. 73, 256A–265A (2001)
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)
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)
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)
Chik, J.K., Schriemer, D.C.: Hydrogen/deuterium exchange mass spectrometry of actin in various biochemical contexts. J. Mol. Biol. 334, 373–385 (2003)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Wales, T.E., Engen, J.R.: Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom. Rev. 25, 158–170 (2006)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Acknowledgment
The authors thank Bruce Pascal from Professor Patrick R. Griffin’s lab at Scripps Florida for help with HDX data analysis and helpful discussion. The work was supported by grants from the National Institute of General Medical Sciences (8 P41 GM103422-35) of the NIH.
Author information
Authors and Affiliations
Corresponding author
Electronic Supplementary Material
Below is the link to the electronic supplementary material.
ESM 1
(DOC 71 kb)
Rights and permissions
About this article
Cite this article
Zhang, J., Ramachandran, P., Kumar, R. et al. H/D Exchange Centroid Monitoring is Insufficient to Show Differences in the Behavior of Protein States. J. Am. Soc. Mass Spectrom. 24, 450–453 (2013). https://doi.org/10.1007/s13361-012-0555-z
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13361-012-0555-z