Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments

. 2019 Jul ; 16 (7) : 595-602. [epub] 20190627

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/pmid31249422

Grantová podpora
MC_U105184308 Medical Research Council - United Kingdom
R35 GM118117 NIGMS NIH HHS - United States

Odkazy

PubMed 31249422
PubMed Central PMC6614034
DOI 10.1038/s41592-019-0459-y
PII: 10.1038/s41592-019-0459-y
Knihovny.cz E-zdroje

Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful biophysical technique being increasingly applied to a wide variety of problems. As the HDX-MS community continues to grow, adoption of best practices in data collection, analysis, presentation and interpretation will greatly enhance the accessibility of this technique to nonspecialists. Here we provide recommendations arising from community discussions emerging out of the first International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX; 2017). It is meant to represent both a consensus viewpoint and an opportunity to stimulate further additions and refinements as the field advances.

Bijvoet Center for Biomolecular Research Utrecht University Utrecht the Netherlands

Biogen Idec Cambridge MA USA

Codiak Biosciences Cambridge MA USA

Department of Biochemistry and Biophysics University of Pennsylvania Philadelphia PA USA

Department of Biochemistry and Microbiology University of Victoria Victoria BC Canada

Department of Biochemistry and Molecular Biology University of Calgary Calgary AB Canada

Department of Biochemistry and Molecular Biology University of Southern Denmark Campusvej Odense Denmark

Department of Biochemistry University of Colorado Boulder CO USA

Department of Biological Chemistry The Hebrew University of Jerusalem Jerusalem Israel

Department of Biological Science National University of Singapore Singapore Singapore

Department of Chemistry and Chemical Biology Northeastern University Boston MA USA

Department of Chemistry The University of Western Ontario London ON Canada

Department of Chemistry University of California Berkeley Berkeley CA USA

Department of Chemistry University of Massachusetts Amherst Amherst MA USA

Department of Chemistry Washington University in St Louis St Louis MO USA

Department of Chemistry York University Toronto ON Canada

Department of Early Stage Pharmaceutical Development Genentech Inc South San Francisco CA USA

Department of Integrative Structural and Computational Biology Scripps Florida The Scripps Research Institute Jupiter FL USA

Department of Medicinal Chemistry School of Pharmacy University of Washington Seattle WA USA

Department of Molecular Medicine The Scripps Research Institute Jupiter FL USA

Department of Pharmaceutical Chemistry University of Kansas Lawrence KS USA

Department of Pharmaceutical Sciences University of Maryland School of Pharmacy Baltimore MD USA

Department of Pharmacy University of Copenhagen Copenhagen Denmark

Genome BC Proteomics Centre University of Victoria Victoria BC Canada

Institut Pasteur Chemistry and Structural Biology Department Paris France

Institute of Microbiology Czech Academy of Sciences Prague Czech Republic

Johnson and Johnson Pharmaeutical Research and Development Jersey City NJ USA

MRC Laboratory of Molecular Biology Cambridge UK

Novo Nordisk Måløv Denmark

Process Development Amgen Thousand Oaks CA USA

Roche Innovation Center Penzberg Penzberg Germany

Roy J Carver Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA USA

UCB Celltech Slough UK

Zobrazit více v PubMed

Weis, D. D. Hydrogen Exchange Mass Spectrometry of Proteins (John Wiley & Sons, 2016).

Konermann L, Pan J, Liu Y-H. Hydrogen exchange mass spectrometry for studying protein structure and dynamics. Chem. Soc. Rev. 2011;40:1224–1234. doi: 10.1039/C0CS00113A. PubMed DOI

Hvidt A, Nielsen SO. Hydrogen exchange in proteins. Adv. Protein Chem. 1966;21:287–386. doi: 10.1016/S0065-3233(08)60129-1. PubMed DOI

Englander SW, Kallenbach NR. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 1983;16:521–655. doi: 10.1017/S0033583500005217. PubMed DOI

Trabjerg E, Nazari ZE, Rand KD. Conformational analysis of complex protein states by hydrogen/deuterium exchange mass spectrometry (HDX-MS): challenges and emerging solutions. TrAC Trends Anal. Chem. 2018;106:125–138. doi: 10.1016/j.trac.2018.06.008. DOI

Harrison RA, Engen JR. Conformational insight into multi-protein signaling assemblies by hydrogen-deuterium exchange mass spectrometry. Curr. Opin. Struct. Biol. 2016;41:187–193. doi: 10.1016/j.sbi.2016.08.003. PubMed DOI PMC

Chalmers MJ, Busby SA, Pascal BD, West GM, Griffin PR. Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions. Expert Rev. Proteom. 2011;8:43–59. doi: 10.1586/epr.10.109. PubMed DOI PMC

Englander JJ, et al. Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry. Proc. Natl Acad. Sci. USA. 2003;100:7057–7062. doi: 10.1073/pnas.1232301100. PubMed DOI PMC

Englander SW, Mayne L. The nature of protein folding pathways. Proc. Natl Acad. Sci. USA. 2014;111:15873–15880. doi: 10.1073/pnas.1411798111. PubMed DOI PMC

Balasubramaniam D, Komives EA. Hydrogen-exchange mass spectrometry for the study of intrinsic disorder in proteins. Biochim. Biophys. Acta. 2013;1834:1202–1209. doi: 10.1016/j.bbapap.2012.10.009. PubMed DOI PMC

Vadas O, Jenkins ML, Dornan GL, Burke JE. Using hydrogen-deuterium exchange mass spectrometry to examine protein-membrane interactions. Methods Enzymol. 2017;583:143–172. doi: 10.1016/bs.mie.2016.09.008. PubMed DOI

Deng B, Lento C, Wilson DJ. Hydrogen deuterium exchange mass spectrometry in biopharmaceutical discovery and development—a review. Anal. Chim. Acta. 2016;940:8–20. doi: 10.1016/j.aca.2016.08.006. PubMed DOI

Marciano DP, Dharmarajan V, Griffin PR. HDX-MS guided drug discovery: small molecules and biopharmaceuticals. Curr. Opin. Struct. Biol. 2014;28:105–111. doi: 10.1016/j.sbi.2014.08.007. PubMed DOI PMC

Hvidt A, Linderstrøm-Lang K. Exchange of hydrogen atoms in insulin with deuterium atoms in aqueous solutions. Biochim. Biophys. Acta. 1954;14:574–575. doi: 10.1016/0006-3002(54)90241-3. PubMed DOI

Englander SW, Mayne L, Bai Y, Sosnick TR. Hydrogen exchange: the modern legacy of Linderstrom-Lang. Protein Sci. 1997;6:1101–1109. doi: 10.1002/pro.5560060517. PubMed DOI PMC

Englander SW, Sosnick TR, Englander JJ, Mayne L. Mechanisms and uses of hydrogen exchange. Curr. Opin. Struct. Biol. 1996;6:18–23. doi: 10.1016/S0959-440X(96)80090-X. PubMed DOI PMC

Johnson RS, Walsh KA. Mass spectrometric measurement of protein amide hydrogen exchange rates of apo- and holo-myoglobin. Protein Sci. 1994;3:2411–2418. doi: 10.1002/pro.5560031224. PubMed DOI PMC

Zhang Z, Smith DL. Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci. 1993;2:522–531. doi: 10.1002/pro.5560020404. PubMed DOI PMC

Smith DL, Deng Y, Zhang Z. Probing the non-covalent structure of proteins by amide hydrogen exchange and mass spectrometry. J. Mass Spectrom. 1997;32:135–146. doi: 10.1002/(SICI)1096-9888(199702)32:2<135::AID-JMS486>3.0.CO;2-M. PubMed DOI

Rey M, et al. Mass spec studio for integrative structural biology. Structure. 2014;22:1538–1548. doi: 10.1016/j.str.2014.08.013. PubMed DOI PMC

Wales TE, Eggertson MJ, Engen JR. Considerations in the analysis of hydrogen exchange mass spectrometry data. Methods Mol. Biol. 2013;1007:263–288. doi: 10.1007/978-1-62703-392-3_11. PubMed DOI PMC

Pascal BD, et al. HDX workbench: software for the analysis of H/D exchange MS data. J. Am. Soc. Mass Spectrom. 2012;23:1512–1521. doi: 10.1007/s13361-012-0419-6. PubMed DOI PMC

Pirrone GF, Iacob RE, Engen JR. Applications of hydrogen/deuterium exchange MS from 2012 to 2014. Anal. Chem. 2015;87:99–118. doi: 10.1021/ac5040242. PubMed DOI PMC

Hamdi K, et al. Structural disorder and induced folding within two cereal, ABA stress and ripening (ASR) proteins. Sci. Rep. 2017;7:15544. doi: 10.1038/s41598-017-15299-4. PubMed DOI PMC

Baños-Mateos S, et al. High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center. Nat. Commun. 2017;8:855. doi: 10.1038/s41467-017-00886-w. PubMed DOI PMC

Lim X-X, et al. Epitope and paratope mapping reveals temperature-dependent alterations in the dengue-antibody interface. Structure. 2017;25:1391–1402. doi: 10.1016/j.str.2017.07.007. PubMed DOI

Masson GR, Maslen SL, Williams RL. Analysis of phosphoinositide 3-kinase inhibitors by bottom-up electron-transfer dissociation hydrogen/deuterium exchange mass spectrometry. Biochem. J. 2017;474:1867–1877. doi: 10.1042/BCJ20170127. PubMed DOI PMC

Merkle PS, et al. Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT. Sci. Adv. 2018;4:eaar6179. doi: 10.1126/sciadv.aar6179. PubMed DOI PMC

Lee S, et al. Allosteric inhibition of antiapoptotic MCL-1. Nat. Struct. Mol. Biol. 2016;23:600–607. doi: 10.1038/nsmb.3223. PubMed DOI PMC

Shukla AK, et al. Visualization of arrestin recruitment by a G-protein-coupled receptor. Nature. 2014;512:21–222. doi: 10.1038/nature13430. PubMed DOI PMC

Adams R, et al. Discovery of a junctional epitope antibody that stabilizes IL-6 and gp80 protein:protein interaction and modulates its downstream signaling. Sci. Rep. 2017;7:37716. doi: 10.1038/srep37716. PubMed DOI PMC

Rostislavleva K, et al. Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes. Science. 2015;350:aac7365. doi: 10.1126/science.aac7365. PubMed DOI PMC

de Vera IMS, et al. Synergistic regulation of coregulator/nuclear receptor interaction by ligand and DNA. Structure. 2017;25:1506–1518. doi: 10.1016/j.str.2017.07.019. PubMed DOI PMC

Moroco JA, Engen JR. Replication in bioanalytical studies with HDX MS: aim as high as possible. Bioanalysis. 2015;7:1065–1067. doi: 10.4155/bio.15.46. PubMed DOI PMC

Iacob RE, Engen JR. Hydrogen exchange mass spectrometry: are we out of the quicksand? J. Am. Soc. Mass Spectrom. 2012;23:1003–1010. doi: 10.1007/s13361-012-0377-z. PubMed DOI PMC

Bennett MJ, Barakat K, Huzil JT, Tuszynski J, Schriemer DC. Discovery and characterization of the laulimalide-microtubule binding mode by mass shift perturbation mapping. Chem. Biol. 2010;17:725–734. doi: 10.1016/j.chembiol.2010.05.019. PubMed DOI

Engen JR, Wales TE. Analytical aspects of hydrogen exchange mass spectrometry. Annu. Rev. Anal. Chem. 2015;8:127–148. doi: 10.1146/annurev-anchem-062011-143113. PubMed DOI PMC

Svensson LA, et al. Crystal structure of a prolactin receptor antagonist bound to the extracellular domain of the prolactin receptor. J. Biol. Chem. 2008;283:19085–19094. doi: 10.1074/jbc.M801202200. PubMed DOI

Lim X-X, et al. Conformational changes in intact dengue virus reveal serotype-specific expansion. Nat. Commun. 2017;8:14339. doi: 10.1038/ncomms14339. PubMed DOI PMC

Pacholarz KJ, et al. Hybrid mass spectrometry approaches to determine how L-histidine feedback regulates the enzyzme mtatp-phosphoribosyltransferase. Structure. 2017;25:730–738.e4. doi: 10.1016/j.str.2017.03.005. PubMed DOI PMC

van de Waterbeemd M, et al. Structural analysis of a temperature-induced transition in a viral capsid probed by HDX-MS. Biophys. J. 2017;112:1157–1165. doi: 10.1016/j.bpj.2017.02.003. PubMed DOI PMC

Adhikary S, et al. Conformational dynamics of a neurotransmitter:sodium symporter in a lipid bilayer. Proc. Natl Acad. Sci. USA. 2017;114:E1786–E1795. doi: 10.1073/pnas.1613293114. PubMed DOI PMC

Burke JE, et al. Structures of PI4KIIIβ complexes show simultaneous recruitment of Rab11 and its effectors. Science. 2014;344:1035–1038. doi: 10.1126/science.1253397. PubMed DOI PMC

Pantazatos D, et al. Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS. Proc. Natl Acad. Sci. USA. 2004;101:751–756. doi: 10.1073/pnas.0307204101. PubMed DOI PMC

Wales TE, Engen JR. Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom. Rev. 2006;25:158–170. doi: 10.1002/mas.20064. PubMed DOI

Pan J, Han J, Borchers CH, Konermann L. Hydrogen/deuterium exchange mass spectrometry with top-down electron capture dissociation for characterizing structural transitions of a 17 kDa protein. J. Am. Chem. Soc. 2009;131:12801–12808. doi: 10.1021/ja904379w. PubMed DOI

Rand KD, Adams CM, Zubarev RA, Jørgensen TJD. Electron capture dissociation proceeds with a low degree of intramolecular migration of peptide amide hydrogens. J. Am. Chem. Soc. 2008;130:1341–1349. doi: 10.1021/ja076448i. PubMed DOI

Rand KD, Zehl M, Jensen ON, Jørgensen TJD. Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry. Anal. Chem. 2009;81:5577–5584. doi: 10.1021/ac9008447. PubMed DOI

Abzalimov RR, Kaplan DA, Easterling ML, Kaltashov IA. 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. 2009;20:1514–1517. doi: 10.1016/j.jasms.2009.04.006. PubMed DOI PMC

Mistarz UH, Brown JM, Haselmann KF, Rand KD. Simple setup for gas-phase H/D exchange mass spectrometry coupled to electron transfer dissociation and ion mobility for analysis of polypeptide structure on a liquid chromatographic time scale. Anal. Chem. 2014;86:11868–11876. doi: 10.1021/ac5035456. PubMed DOI

Slysz GW, Percy AJ, Schriemer DC. Restraining expansion of the peak envelope in H/D exchange-MS and its application in detecting perturbations of protein structure/dynamics. Anal. Chem. 2008;80:7004–7011. doi: 10.1021/ac800897q. PubMed DOI

Harrison RA, et al. Structural dynamics in Ras and related proteins upon nucleotide switching. J. Mol. Biol. 2016;428:4723–4735. doi: 10.1016/j.jmb.2016.10.017. PubMed DOI PMC

Hoofnagle AN, Resing KA, Ahn NG. Practical methods for deuterium exchange/mass spectrometry. Methods Mol. Biol. 2004;250:283–298. PubMed

Miyagi M, Nakazawa T. Determination of pKa values of individual histidine residues in proteins using mass spectrometry. Anal. Chem. 2008;80:6481–6487. doi: 10.1021/ac8009643. PubMed DOI

Wlodawer A, Minor W, Dauter Z, Jaskolski M. Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J. 2008;275:1–21. doi: 10.1111/j.1742-4658.2007.06178.x. PubMed DOI PMC

Sarpe, V. & Schriemer, D. C. Data processing in bottom‐up hydrogen exchange mass spectrometry. In Hydrogen Exchange Mass Spectrometry of Proteins: Fundamentals, Methods, and Applications (ed. Weis, D. D.) 37–53 (John Wiley & Sons, 2016).

Guttman M, Weis DD, Engen JR, Lee KK. Analysis of overlapped and noisy hydrogen/deuterium exchange mass spectra. J. Am. Soc. Mass Spectrom. 2013;24:1906–1912. doi: 10.1007/s13361-013-0727-5. PubMed DOI PMC

Lee J, et al. Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association. Cell. 1999;99:323–334. doi: 10.1016/S0092-8674(00)81663-3. PubMed DOI

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