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PMID: 16901199 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Review

Photoaffinity labeling combined with mass spectrometric approaches as a tool for structural proteomics.

Expert review of proteomics ·Vol. 3 ·No. 4 ·2006-08-00 ·Pages 399-408

Robinette D, Neamati N, Tomer KB, Borchers CH

Abstract

Protein chemistry, such as crosslinking and photoaffinity labeling, in combination with modern mass spectrometric techniques, can provide information regarding protein-protein interactions beyond that normally obtained from protein identification and characterization studies. While protein crosslinking can make tertiary and quaternary protein structure information available, photoaffinity labeling can be used to obtain structural data about ligand-protein interaction sites, such as oligonucleotide-protein, drug-protein and protein-protein interaction. In this article, we describe mass spectrometry-based photoaffinity labeling methodologies currently used and discuss their current limitations. We also discuss their potential as a common approach to structural proteomics for providing 3D information regarding the binding region, which ultimately will be used for molecular modeling and structure-based drug design.

MeSH Terms
Azides/chemistry Benzophenones/chemistry Diazomethane/analogs & derivatives,chemistry Ligands Mass Spectrometry/methods Models, Molecular Photoaffinity Labels Protein Interaction Mapping Proteomics/methods Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Ultraviolet Rays
Chemicals
Azides Benzophenones Ligands Photoaffinity Labels Diazomethane
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Robinette David
University of North Carolina at Chapel Hill, UNC-Duke Proteomics Core Facility, Department of Biochemistry and Biophysics, CB7028, Chapel Hill, NC 27599, USA. robinett@med.unc.edu
Neamati Nouri
Tomer Kenneth B
Borchers Christoph H
References (41)
41 references, click to expand
  1. Fluorescent photoaffinity labeling of cytochrome P450 3A4 by lapachenole: identification of modification sites by mass spectrometry.
    Biochemistry. 2005 Feb 15;44(6):1833-45 PMID: 15697209
  2. Interactome: gateway into systems biology.
    Hum Mol Genet. 2005 Oct 15;14 Spec No. 2:R171-81 PMID: 16162640
  3. Discovery of a small-molecule HIV-1 integrase inhibitor-binding site.
    Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):10080-5 PMID: 16785440
  4. Mass spectral characterization of a protein-nucleic acid photocrosslink.
    Protein Sci. 1999 Dec;8(12):2806-12 PMID: 10631998
  5. Using photolabile ligands in drug discovery and development.
    Trends Biotechnol. 2000 Feb;18(2):64-77 PMID: 10652511
  6. Subfemtomole MS and MS/MS peptide sequence analysis using nano-HPLC micro-ESI fourier transform ion cyclotron resonance mass spectrometry.
    Anal Chem. 2000 Sep 15;72(18):4266-74 PMID: 11008759
  7. The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR.
    EMBO J. 2001 Apr 17;20(8):2041-50 PMID: 11296236
  8. Identification of the bile acid-binding site of the ileal lipid-binding protein by photoaffinity labeling, matrix-assisted laser desorption ionization-mass spectrometry, and NMR structure.
    J Biol Chem. 2001 Mar 9;276(10):7291-301 PMID: 11069906
  9. Binding site elucidation of hydantoin-based antagonists of LFA-1 using multidisciplinary technologies: evidence for the allosteric inhibition of a protein--protein interaction.
    J Am Chem Soc. 2001 Jun 20;123(24):5643-50 PMID: 11403595
  10. Expression, purification, and characterization of a soluble form of the first extracellular domain of the human type 1 corticotropin releasing factor receptor.
    J Biol Chem. 2001 Aug 24;276(34):31528-34 PMID: 11425856
  11. Mass spectrometric analysis of a UV-cross-linked protein-DNA complex: tryptophans 54 and 88 of E. coli SSB cross-link to DNA.
    Protein Sci. 2001 Oct;10(10):1989-2001 PMID: 11567090
  12. Identification of ligand-binding regions of P-glycoprotein by activated-pharmacophore photoaffinity labeling and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry.
    Mol Pharmacol. 2002 Mar;61(3):637-48 PMID: 11854445
  13. Photoaffinity labeling in drug discovery and developments: chemical gateway for entering proteomic frontier.
    Curr Top Med Chem. 2002 Mar;2(3):271-88 PMID: 11944820
  14. Characterization of the dexniguldipine binding site in the multidrug resistance-related transport protein P-glycoprotein by photoaffinity labeling and mass spectrometry.
    Mol Pharmacol. 2002 Jun;61(6):1366-76 PMID: 12021398
  15. The binding protein of corticotropin-releasing factor: ligand-binding site and subunit structure.
    Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12055-60 PMID: 12215497
  16. Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry.
    Mass Spectrom Rev. 2002 May-Jun;21(3):163-82 PMID: 12476441
  17. Stable isotope-coded proteomic mass spectrometry.
    Curr Opin Biotechnol. 2003 Feb;14(1):101-9 PMID: 12566009
  18. Methods for the study of protein-protein interactions in cancer cell biology.
    Methods Mol Biol. 2003;218:255-67 PMID: 12616725
  19. Met174 side chain is the site of photoinsertion of a substance P competitive peptide antagonist photoreactive in position 8.
    FEBS Lett. 2003 Jun 5;544(1-3):45-9 PMID: 12782288
  20. Isotope and affinity tags in photoreactive substance P analogues to identify the covalent linkage within the NK-1 receptor by MALDI-TOF analysis.
    Anal Chem. 2003 Dec 1;75(23):6536-43 PMID: 14640725
  21. Characterization of peptide-protein interactions using photoaffinity labeling and LC/MS.
    Anal Bioanal Chem. 2004 Feb;378(4):1031-6 PMID: 14668969
  22. Characterization of the binding site for inhibitors of the HPV11 E1-E2 protein interaction on the E2 transactivation domain by photoaffinity labeling and mass spectrometry.
    Anal Chem. 2004 Apr 1;76(7):2095-102 PMID: 15053675
  23. Identification of CRALBP ligand interactions by photoaffinity labeling, hydrogen/deuterium exchange, and structural modeling.
    J Biol Chem. 2004 Jun 25;279(26):27357-64 PMID: 15100222
  24. C-terminus loop 13 of Na+ glucose cotransporter SGLT1 contains a binding site for alkyl glucosides.
    Biochemistry. 2004 Aug 31;43(34):10944-51 PMID: 15323554
  25. A novel strategy for the identification of protein-DNA contacts by photocrosslinking and mass spectrometry.
    Nucleic Acids Res. 2004;32(16):e132 PMID: 15383647
  26. Identification of cytoskeletal [14C]carboplatin-binding proteins reveals reduced expression and disorganization of actin and filamin in cisplatin-resistant cell lines.
    Mol Pharmacol. 2004 Oct;66(4):789-93 PMID: 15385639
  27. A three-dimensional model for the substrate binding domain of the multidrug ATP binding cassette transporter LmrA.
    Mol Pharmacol. 2004 Nov;66(5):1169-79 PMID: 15304548
  28. New photolabeling and crosslinking methods.
    Annu Rev Biochem. 1993;62:483-514 PMID: 8352595
  29. Benzophenone photophores in biochemistry.
    Biochemistry. 1994 May 17;33(19):5661-73 PMID: 8180191
  30. The use of photolabelled peptides to localize the substance-P-binding site in the human neurokinin-1 tachykinin receptor.
    Eur J Biochem. 1996 Aug 15;240(1):215-22 PMID: 8797856
  31. Photocross-linking of nucleic acids to associated proteins.
    Crit Rev Biochem Mol Biol. 1997;32(2):101-40 PMID: 9145285
  32. Comparison of the photochemical behavior of four different photoactivatable probes.
    J Pept Res. 1997 May;49(5):375-83 PMID: 9211218
  33. Crystal structure of the nucleosome core particle at 2.8 A resolution.
    Nature. 1997 Sep 18;389(6648):251-60 PMID: 9305837
  34. Identification of a ligand binding site in the human neutrophil formyl peptide receptor using a site-specific fluorescent photoaffinity label and mass spectrometry.
    J Biol Chem. 1998 Apr 24;273(17):10428-35 PMID: 9553101
  35. RNA-binding site in T7 RNA polymerase.
    Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9111-6 PMID: 9689042
  36. Localization and characterization of two nucleotide-binding sites on the anaerobic ribonucleotide reductase from bacteriophage T4.
    J Biol Chem. 1998 Sep 18;273(38):24853-60 PMID: 9733790
  37. Identification of specific sites involved in ligand binding by photoaffinity labeling of the receptor for the urokinase-type plasminogen activator. Residues located at equivalent positions in uPAR domains I and III participate in the assembly of a composite ligand-binding site.
    Biochemistry. 1998 Nov 24;37(47):16494-505 PMID: 9843416
  38. Photoaffinity labeling and mass spectrometry identify ribosomal protein S3 as a potential target for hybrid polar cytodifferentiation agents.
    J Biol Chem. 1999 May 14;274(20):14280-7 PMID: 10318849
  39. The photolysis of diazoacetylchymotrypsin.
    J Biol Chem. 1962 Sep;237:3006-8 PMID: 13913310
  40. P-glycoprotein substrate binding domains are located at the transmembrane domain/transmembrane domain interfaces: a combined photoaffinity labeling-protein homology modeling approach.
    Mol Pharmacol. 2005 Feb;67(2):365-74 PMID: 15509712
  41. Proteomics by FTICR mass spectrometry: top down and bottom up.
    Mass Spectrom Rev. 2005 Mar-Apr;24(2):168-200 PMID: 15389855
Article Info
Journal
Expert review of proteomics
Abbr.
Expert Rev Proteomics
ISSN
1744-8387
DOI
10.1586/14789450.3.4.399
Email
robinett@med.unc.edu
Published
2006-08-00
Pages
399-408
Language
English
Region
England
NLM ID
101223548
PMCID
PMC2266983
Subset
IM
Grants
NIAID NIH HHS · P30 AI050410 · United States
Intramural NIH HHS · Z01 ES050150-12 · United States
NIAID NIH HHS · 9P30 AI050410 · United States
External Links
PubMed source DOI: 10.1586/14789450.3.4.399 PMC Full Text View journal details
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