348
Views
48
CrossRef citations to date
0
Altmetric
Review

Mass spectrometry-based approaches to protein–ligand interactions

, &
Pages 475-485 | Published online: 09 Jan 2014

References

  • Kuntz ID, Chen K, Sharp KA, Kollman PA. The maximal affinity of ligands. Proc. Natl Acad. Sci. USA 96, 9997–10002 (1999).
  • Burgess RR, Thompson NE. Advances in gentle immunoaffinity chromatography. Curr. Opin. Biotechnol. 13, 304–308 (2002).
  • McDonnell JM. Surface plasmon resonance: towards an understanding of the mechanisms of biological molecular recognition. Curr. Opin. Chem. Biol. 5, 572–577 (2001).
  • Gradl G, Guenther R, Sterrer S. Fluorescence correlation spectroscopy (FCS): measuring biological interactions in microstructures. BioMethods 10, 331–351 (1999).
  • Hajduk P, Meadows RP, Fesik SW. NMR-based screening in drug discovery. Q. Rev. Biophys. 32, 211–240 (1999).
  • Fenn JB. Electrospray wings for molecular elephants (Nobel lecture). Angew. Chem. Int. Ed. 42, 3871–3894 (2003).
  • Tanaka K. The origin of macromolecule ionization by laser irradiation (Nobel lecture). Angew. Chem. Int. Ed. 42, 3861–3870 (2003).
  • Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60, 2299–2301 (1988).
  • Keller BO, Li L. Detection of 25,000 molecules of substance P by MALDI-TOF mass spectrometry and investigations into the fundamental limits of detection in MALDI. J. Am. Soc. Mass Spectrom. 12, 1055–1063 (2001).
  • Kebarle P, Peschke M. On the mechanisms by which the charged droplets produced by electrospray lead to gas phase ions. Anal. Chim. Acta 406, 11–35 (2000).
  • Kaltashov IA, Eyles SJ. Studies of biomolecular conformations and conformational dynamics by mass spectrometry. Mass Spectrom. Rev. 21, 37–71 (2002).
  • Konermann L, Simmons DA. Protein folding kinetics and mechanisms studied by pulse-labeling and mass spectrometry. Mass Spectrom. Rev. 22, 1–26 (2003).
  • Fabris D. Mass spectrometric approaches for the investigation of dynamic processes in condensed phase. Mass Spectrom. Rev. 24, 30–54 (2005).
  • Wilson DJ, Konermann L. A capillary mixer with adjustable reaction chamber volume for millisecond time resolved studies by electrospray mass spectrometry. Anal. Chem. 75, 6408–6414 (2003).
  • Wilson DJ, Rafferty SP, Konermann L. Kinetic unfolding mechanism of the inducible nitric oxide synthase oxygenase domain determined by time-resolved electrospray mass spectrometry. Biochemistry 44, 2276–2283 (2005).
  • Wilm M, Mann M. Analytical properties of the nanoelectrospray ion source. Anal. Chem. 68, 1–8 (1996).
  • Loo JA. Electrospray ionization mass spectrometry: a technology for studying noncovalent macromolecular complexes. Int. J. Mass Spectrom. 200, 175–186 (2000).
  • Wang W, Kitova EN, Klassen JS. Influence of solution and gas phase processes on protein–carbohydrate binding affinities determined by nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 75, 4945–4955 (2003).
  • Katta V, Chait BT. Observation of the heme–globin complex in native myoglobin by electrospray-ionisation mass spectrometry. J. Am. Chem. Soc. 113, 8534–8535 (1991).
  • Ganem B, Henion JD. Going gently into flight: analyzing noncovalent interactions by mass spectrometry. Bioorg. Med. Chem. 11, 311–314 (2003).
  • Chen W-H, Qin Y, Cai Z, Chan C-L, Luo G-A, Jiang ZH. Spectrometric studies of cytotoxic protoberberine alkaloids binding to double-stranded DNA. Bioorg. Med. Chem. 13, 1859–1866 (2005).
  • Smith JC, Siu MKW, Rafferty SP. Collisional cooling enhances the ability to observe non-covalent interactions within the inducible nitric oxide synthase oxygenase domain: dimerization, complexation and dissociation. J. Am. Soc. Mass Spectrom. 15, 629–638 (2004).
  • Hernandez H, Robinson CV. Dynamic protein complexes: insights from mass spectrometry. J. Biol. Chem. 276, 46685–46688 (2001).
  • McCammon MG, Robinson CV. Structural change in response to ligand binding. Curr. Opin. Chem. Biol. 8, 60–65 (2004).
  • Rostom AA, Fucini P, Benjamin DR et al. Detection and selective dissociation of intact ribosomes in a mass spectrometer. Proc. Natl Acad. Sci. USA 97, 5185–5190 (2000).
  • Bothner B, Siuzdak G. Electrospray ionization of a whole virus: analyzing mass, structure, and viability. Chembiochem 5, 258–260 (2004).
  • Heck AJR, Van den Heuvel RHH. Investigation of intact protein complexes by mass spectrometry. Mass Spectrom. Rev. 23, 368–389 (2004).
  • Zehl M, Allmaier G. Instrumental parameters in the MALDI-TOF mass spectrometric analysis of quaternary protein structures. Anal. Chem. 77, 103–110 (2005).
  • Zehl M, Allmaier G. Ultraviolet matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of intact hemoglobin complex from whole human blood. Rapid Commun. Mass Spectrom. 18, 1932–1938 (2004).
  • Luo S-Z, Li Y-M, Qiang W et al. Detection of specific noncovalent interaction of peptide with DNA by MALDI-TOF. J. Am. Soc. Mass Spectrom. 15, 28–31 (2004).
  • Clark SM, Konermann L. Screening for noncovalent ligand–receptor interactions by electrospray ionization mass spectrometry-based diffusion measurements. Anal. Chem. 76, 1257–1263 (2004).
  • Wigger M, Eyler JR, Benner SA, Li W, Marshall AG. Fourier transform-ion cyclotron resonance mass spectrometric resolution, identification, and screening of non-covalent complexes of Hck Src homology 2 domain receptor and ligands from a 324-member peptide combinatorial library. J. Am. Soc. Mass Spectrom. 13, 1162–1169 (2002).
  • Daniel JM, Friess SD, Rajagopalan S, Wendt S, Zenobi R. Quantitative determination of noncovalent binding interactions using soft ionization mass spectrometry. Int. J. Mass Spectrom. 216, 1–27 (2002).
  • Hagan N, Fabris D. Direct mass spectrometric determination of the stoichiometry and binding affinity of the complexes between nuclecapsid protein and RNA stem–loop hairpins of the HIV-1 PSI-recognition element. Biochemistry 42, 10736–10745 (2003).
  • Clark SM, Konermann L. Determination of ligand–protein dissociation constants by electrospray mass spectrometry-based diffusion measurements. Anal. Chem. 76, 7077–7083 (2004).
  • Konermann L, Silva EA, Sogbein OF. Electrochemically induced pH changes resulting in protein unfolding in the ion source of an electrospray mass spectrometer. Anal. Chem. 73, 4836–4844 (2001).
  • Robinson CV, Chung EW, Kragelund BB et al. Probing the nature of noncovalent interactions by mass spectrometry. A study of protein–CoA ligand binding and assembly. J. Am. Chem. Soc. 118, 8646–8653 (1996).
  • Xiao H, Kaltashov IA, Eyles SJ. Indirect assessment of small hydrophobic ligand binding to a model protein using a combination of ESI MS and HDX/ESI MS. J. Am. Soc. Mass Spectrom. 14, 506–515 (2003).
  • Mauk MR, Mauk AG, Chen Y-L, Douglas DJ. Tandem mass spectrometry of protein–protein complexes: cytochrome c–cytochrome b5. J. Am. Soc. Mass Spectrom. 13, 59–71 (2002).
  • Li Y, Heitz F, Le Grimellec C, Cole RB. Hydrophobic component in noncovalent binding of fusion peptides to lipids as observed by electrospray mass spectrometry. Rapid Commun. Mass Spectrom. 18, 135–137 (2003).
  • Gupta R, Hamdan SM, Dixon NE, Sheil MM, Beck JL. Application of electrospray ionization mass spectrometry to study the hydrophobic interaction between the ε and θ subunits of DNA polymerase III. Protein Sci. 13, 2878–2887 (2004).
  • Zechel DL, Konermann L, Withers SG, Douglas DJ. Pre-steady-state kinetic analysis of an enzymatic reaction monitored by time-resolved electrospray ionization mass spectrometry. Biochemistry 37, 7664–7669 (1998).
  • Wang W, Kitova EN, Klassen JS. Bioactive recognition sites may not be energetically preferred in protein–carbohydrate complexes in the gas phase. J. Am. Chem. Soc. 125, 13630–13631 (2003).
  • Peschke M, Verkerk UH, Kebarle P. Features of the ESI mechanism that affect the observation of multiply charged noncovalent protein complexes and the determination of the association constant by the titration method. J. Am. Soc. Mass Spectrom. 15, 1424–1434 (2004).
  • Clark SM, Leaist DG, Konermann L. Taylor dispersion monitored by electrospray mass spectrometry: a novel approach for studying diffusion in solution. Rapid Commun. Mass Spectrom. 16, 1454–1462 (2002).
  • Clark SM, Konermann L. Diffusion measurements by electrospray mass spectrometry for studying solution-phase noncovalent interactions. J. Am. Soc. Mass Spectrom. 14, 430–441 (2003).
  • Maity H, Maity M, Englander SW. How cytochrome c folds, and why: submolecular foldon units and their stepwise sequential stabilization. J. Mol. Biol. 343, 223–233 (2004).
  • Baker D, Eaton WA. Folding and binding. Curr. Opin. Struct. Biol. 14, 67–69 (2004).
  • Engen JR, Smith DL. Investigating protein structure and dynamics by hydrogen exchange MS. Anal. Chem. 73, 256A–265A (2001).
  • Mandell JG, Baerga-Ortiz A, Akashi S, Takio K, Komives EA. Solvent accessibility of the thrombin–thrombomodulin interface. J. Mol. Biol. 306, 575–589 (2001).
  • Akashi S, Takio K. 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 (2000).
  • Hoerner JK, Xiao H, Dobo A, Kaltashov IA. Is there hydrogen scrambling in the gas phase? Energetic and structural determinants of proton mobility within protein ions. J. Am. Chem. Soc. 126, 7709–7717 (2004).
  • Eyles SJ, Speir JP, Kruppa GH, Gierasch LM, Kaltashov IA. Protein conformational stability probed by fourier transform ion cyclotron resonance mass spectrometry. J. Am. Chem. Soc. 122, 495–500 (2000).
  • Powell KD, Ghaemmaghami S, Wang MZ, Ma L, Oas TG, Fitzgerald MC. A general mass spectrometry-based assay for the quantitation of protein–ligand binding interactions in solution. J. Am. Chem. Soc. 124, 10256–10257 (2002).
  • Powell KD, Fitzgerald MC. Accuracy and precision of a new H/D exchange- and mass spectrometry-based technique for measuring the thermodynamic properties of protein–peptide complexes. Biochemistry 42, 4962–4970 (2003).
  • Powell KD, Fitzgerald MC. High-throughput screening assay for the tunable selection of protein ligands. J. Comb. Chem. 6, 262–269 (2004).
  • Zhu MM, Rempel DL, Du Z, Gross ML. Quantification of protein–ligand interactions by mass spectrometry, titration, and H/D exchange: Plimstex. J. Am. Chem. Soc. 125, 5252–5253 (2003).
  • Zhu MM, Rempel DL, Gross ML. Modeling data from titration, amide H/D exchange, and mass spectrometry to obtain protein–ligand binding constants. J. Am. Soc. Mass Spec. 15, 388–397 (2004).
  • Breuker K. New mass spectrometric methods for the quantification of protein–ligand binding in solution. Angew. Chem. Int. Ed. 43, 22–25 (2004).
  • Schriemer DC. Biosensor alternative: frontal affinity chromatography. Anal. Chem. 76, 441A–448A (2004).
  • Schriemer DC, Bundle DR, Li L, Hindsgaul O. Micro-scale frontal affinity chromatography with mass spectrometric detection: a new method for the screening of compound libraries. Angew. Chem. Int. Ed. 37, 3383–3387 (1998).
  • Hodgson RJ, Chen Y, Zhang Z et al. Protein-doped monolithic silica columns for capillary liquid chromatography prepared by the sol-gel method: applications to frontal affinity chromatography. Anal. Chem. 76, 2780–2790 (2004).
  • Gavin A-C, Bosche M, Krause R et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002).
  • Ho Y, Gruhler A, Heilbut A et al. Systematic identification of protein complexes from Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183 (2002).
  • Titz B, Schlesner M, Uetz P. What do we learn from high-throughput protein interaction data? Expert Rev. Proteomics 1, 111–121 (2004).
  • Zhu H, Bilgin M, Bangham R et al. Global analysis of protein activities using proteome chips. Science 293, 2101 (2001).
  • Viani MB et al. Probing protein–protein interactions in real time. Nature Struct. Biol. 7, 644–647 (2000).
  • Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotech. 17, 1030–1032 (1999).
  • Sinz A. Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes. J. Mass Spectrom. 38, 1225–1237 (2003).
  • Back JW, de Long L, Muijsers AO, de Koster CG. Chemical cross-linking and mass spectrometry for protein structural modeling. J. Mol. Biol. 331, 303–313 (2003).
  • Young MM, Tang N, Hempel JC et al. High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry. Proc. Natl Acad. Sci. USA 97, 5802–5806 (2000).
  • Doneanu CE, Gafken PR, Bennett SE, Barofsky DF. Mass spectrometry of UV-cross-linked protein–nucleic acid complexes: Identification of amino acid residues in the single-stranded DNA-binding domain of human replication protein A. Anal. Chem. 76, 5667–5676 (2004).
  • Kellersberger KA, Yu E, Kruppa GH, Young MM, Fabris D. Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation. Anal. Chem. 76, 2438–2445 (2004).
  • Schulz DM, Ihling C, Clore GM, Sinz A. Mapping the topology and determination of a low-resolution three-dimensional structure of the calmodulin–melittin complex by chemical cross-linking and high-resolution FTICRMS: direct demonstration of multiple binding modes. Biochemistry 43, 4703–4715 (2004).
  • Wine RN, Dial JM, Tomer KB, Borchers CH. Identification of components of protein complexes using a fluorescent photo-cross-linker and mass spectrometry. Anal. Chem. 74, 1939–1945 (2002).
  • Vasilescu J, Guo X, Kast J. Identification of protein–protein interactions using in vivo cross-linking and mass spectrometry. Proteomics 4, 3845–3854 (2004).
  • Maleknia SD, Downard K. Radical approaches to probe protein structure, folding, and interactions by mass spectrometry. Mass Spectrom. Rev. 20, 388–401 (2001).
  • Wong JWH, Maleknia SD, Downard KM. Study of the ribunuclease-s-protein– peptide complex using a radical probe and electrospray ionization mass spectrometry. Anal. Chem. 75, 1557–1563 (2003).
  • Xu G, Chance MR. Radiolytic modification of acidic amino acid residues in peptides: probes for examining protein–protein interactions. Anal. Chem. 76, 1213–1221 (2004).
  • Wabnitz PA, Loo JA. Drug screening of pharmaceutical discovery compounds by micro-size exclusion chromatography/mass spectrometry. Rapid Commun. Mass Spectrom. 16, 85–91 (2002).
  • Hofner G, Wanner KT. Competitive binding assays made easy with a native marker and mass spectrometric quantification. Angew. Chem. Int. Ed. 42, 5235–5237 (2003).
  • Johnson BM, Nikolic D, van Breemen RB. Applications of pulsed ultrafiltration-mass spectrometry. Mass Spectrom. Rev. 21, 76–86 (2002).
  • Lengquist J, Svensson R, Evergreen E, Morgenstern R, Griffiths WJ. Observation of an intact noncovalent homotrimer of detergent-solubilized rat microsomal glutathione transferase-1 by electrospray mass spectrometry. J. Biol. Chem. 279, 13311–13316 (2004).
  • Griffith WP, Kaltashov IA. Highly asymmetric interactions between globin chains during hemoglobin assembly revealed by electrospray ionization mass spectrometry. Biochemistry 42, 10024–10033 (2003).
  • Simmons DA, Wilson DJ, Lajoie GA, Doherty-Kirby A, Konermann L. Subunit disassembly and unfolding kinetics of hemoglobin studied by time-resolved electrospray mass spectrometry. Biochemistry 43, 14792–14801 (2004).
  • Simmons DA, Dunn SD, Konermann L. Conformational dynamics of partially denatured myoglobin studied by time-resolved electrospray mass spectrometry with online hydrogen–deuterium exchange. Biochemistry 42, 5896–5905 (2003).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.