Techniques: Oxidative cross-linking as an emergent tool for the analysis of receptor-mediated signalling events

Kodadek, Thomas; Duroux-Richard, Isabelle; Bonnafous, Jean‐Claude

doi:10.1016/j.tips.2005.02.010

Cited by 53 publications

(55 citation statements)

References 36 publications

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“…Recently, oxidative crosslinking techniques have been developed that are mediated by high-valent metal-chelate complexes. The main advantage of that type of reaction is that they are extremely rapid and do not require a chemical modification of the protein (Kodadek, Duroux-Richard, & Bonnafous, 2005). The high-valent metal complexes employed are derived from stable, lower-valent species, such as His6-Ni 2þ , Gly-Gly-His-Ni 2þ , or tris(2,2 0 -bipyridyl)ruthenium (II) dication ([Ru(bipy) 3 ] 2þ ) (Kodadek, Duroux-Richard, & Bonnafous, 2005).…”

Section: Chemical Cross-linking and Mass Spectrometry For Protein Stumentioning

confidence: 99%

“…A number of reviews have been published recently that either focus on chemical cross-linking reagents and application protocols (Brunner, 1993;Kluger & Alagic, 2004;Melcher, 2004;Kodadek, Duroux-Richard, & Bonnafous, 2005) or on the identification of protein-protein interactions, using chemical cross-linking combined with a mass spectrometric analysis of the cross-linked products (Back et al, 2003;Sinz, 2003;Friedhoff, 2005;Trakselis, Alley, & Ishmael, 2005). The issue of using the obtained information as a basis to create structural models of the protein complexes has been addressed as well (Van Dijk, Boelens, & Bonvin, 2005) and cross-linking combined with mass spectrometry has been used to distinguish between the crystallographic and physiological interface in dimeric proteins (Petrotchenko et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

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Chemical cross‐linking and mass spectrometry to map three‐dimensional protein structures and protein–protein interactions

Sinz

2006

Mass Spectrometry Reviews

612

597

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Closely related to studying the function of a protein is the analysis of its three-dimensional structure and the identification of interaction sites with its binding partners. An alternative approach to the high-resolution methods for three-dimensional protein structure analysis, such as X-ray crystallography and NMR spectroscopy, consists of covalently connecting two functional groups of the protein(s) under investigation. The location of the created cross-links imposes a distance constraint on the location of the respective side chains and allows one to draw conclusions on the three-dimensional structure of the protein or a protein complex. Recently, chemical cross-linking of proteins has been combined with a mass spectrometric analysis of the created cross-linked products. This review article describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the different available strategies that employ chemical cross-linking and different mass spectrometric techniques. The challenges for mass spectrometry caused by the enormous complexity of the cross-linking reaction mixtures are emphasized. The various approaches described in the literature to facilitate the mass spectrometric detection of cross-linked products as well as computer software for data analyses are reviewed.

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Section: Chemical Cross-linking and Mass Spectrometry For Protein Stumentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Chemical cross‐linking and mass spectrometry to map three‐dimensional protein structures and protein–protein interactions

Sinz

2006

Mass Spectrometry Reviews

612

597

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“…Different publications indicate that they can be generated from various processes, such as photo-oxidation under UV irradiation [30] or by oxygen photosensitization, [31] or with an Ru II complex, like [RuA C H T U N G T R E N N U N G (bpy) 3 ] 2 + , in the presence of an oxidant, such as oxygen or ammonium persulfate (APS) used for photo-induced crosslinking of unmodified proteins (PICUP). [32] In the present case, the tryptophanyl radicals can of course be produced from the PET reaction (Equation (2) with 1, for example) in which the Trp radical cation [pK a (Trp)C + = 4.7] [33] is deprotonated at pH 7. Thus, in the present mass spectra, the observation of dimerization and oxidation products of peptides, in addition to the bi-adduct detection, can be easily rationalized.…”

Section: Corresponding To [A + Bà2 H]mentioning

confidence: 96%

“…[32,34] Therefore, after optimization of the electrophoresis conditions by using a stacking gel (see the Experimental Section) in order to enhance the resolution of the slowest migrating spot seen in Figure 8 2 + cannot form photo-adducts of the complex. By comparison of the electrophoretic mobilities of the different spots of lanes 2, 4, and 5 ( Figure 9), it is clear that 2 photo-induces a first type of photocrosslinking, which would be a Trp dimerization (b) and a second one, which would correspond to the addition of two Trp residues on the Ru complex (a).…”

Section: A C H T U N G T R E N N U N G (Bpy) 3 ]mentioning

confidence: 99%

Photocrosslinking between Peptide–Peptide or Peptide–Oligonucleotide by Ru^II–TAP Complexes

Ghesquière

Gauthier

Winter

et al. 2011

Chemistry A European J

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Ru(II)-TAP complexes have been shown to be very attractive compounds in the frame of developments of new anticancer drugs targeting the genetic material. This increasing interest originates from observations of covalent bond formations, triggered by photo-induced electron transfer (PET) between Ru(II)-TAP complexes and guanine bases of DNA. This photoreaction has recently been extended to the tryptophan (Trp) amino acid for future applications involving peptides. Thus, a double photo-addition of Trp residues of peptides on Ru(II) complexes is demonstrated by mass spectrometry with some structural issues. Such bi-adduct formations offer the possibility of photocrosslinking two Trp-containing biomolecules, which is investigated in this study. Thus, photocrosslinking between two complementary oligonucleotides (ODNs) derivatized by Trp-containing tripeptides is demonstrated by polyacrylamide gel electrophoresis (PAGE) in the presence of Ru(II)-TAP complexes. Both PAGE and MS indicate that such photocrosslinkings arise from two reaction pathways: either via the double addition of Trp residues on the Ru complex or from dimerization of Trp radicals. The competition between these two pathways depends on the experimental conditions. Heterobridgings between guanine bases and tryptophan residues mediated by Ru(II)-TAP complexes is also examined, opening the way to ODN-peptide photocrosslinkings.

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“…10,11 (3) Metal-chelate complexes which crosslink quickly by oxidation under visible light 12 which rarely effects proteins. 13,14 (4) Benzophenone:…”

Section: Introductionmentioning

confidence: 99%

Development of bifunctional photoactivatable benzophenone probes and their application to glycoside substrates

Qvit¹,

Monderer-Rothkoff²,

Ido³

et al. 2008

Biopolymers

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Photoaffinity labeling is used to covalently attach ligands to macromolecules to determine their spatial arrangement and structure. Benzophenone (BP) groups are widely used for covalent photoaffinity labeling and for probing protein interactions. We developed bifunctional BP photoactivatable derivatives using three different general chemical approaches. In addition to the photoaffinity reactivity of the BP, these derivatives contain an additional group: A radioactive tracer for biological studies, or an N-ethylmaleimide group as an additional crosslinker, or a biotin group to be used during purification and characterization of probe-protein complexes using the high-affinity biotin-avidin interaction. A model series of photoaffinity labeling probes was synthesized based on the arbutin ligand. These compounds can be used as probes to study the arbutin binding site of microbial beta-glucoside transporters by photolabeling residues in its vicinity. The second functionality provides additional options for studying proteins and binding sites. The probes were developed using different methodologies: (i) a diazotation reaction; (ii) protecting group methodology; and (iii) solid-phase synthesis. These procedures are general and provide a simple and versatile approach for synthesizing bifunctional BP ligands, as demonstrated here on arbutin.

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Techniques: Oxidative cross-linking as an emergent tool for the analysis of receptor-mediated signalling events

Cited by 53 publications

References 36 publications

Chemical cross‐linking and mass spectrometry to map three‐dimensional protein structures and protein–protein interactions

Chemical cross‐linking and mass spectrometry to map three‐dimensional protein structures and protein–protein interactions

Photocrosslinking between Peptide–Peptide or Peptide–Oligonucleotide by Ru^II–TAP Complexes

Development of bifunctional photoactivatable benzophenone probes and their application to glycoside substrates

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Techniques: Oxidative cross-linking as an emergent tool for the analysis of receptor-mediated signalling events

Cited by 53 publications

References 36 publications

Chemical cross‐linking and mass spectrometry to map three‐dimensional protein structures and protein–protein interactions

Chemical cross‐linking and mass spectrometry to map three‐dimensional protein structures and protein–protein interactions

Photocrosslinking between Peptide–Peptide or Peptide–Oligonucleotide by RuII–TAP Complexes

Development of bifunctional photoactivatable benzophenone probes and their application to glycoside substrates

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Photocrosslinking between Peptide–Peptide or Peptide–Oligonucleotide by Ru^II–TAP Complexes