Formation of non-amidine products in the reaction of primary amines with imido esters

Browne, Douglas T.; Kent, Stephen B. H.

doi:10.1016/0006-291x(75)90292-2

Cited by 110 publications

(36 citation statements)

References 8 publications

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“…Therefore, the proteinprotein cross-links generated by these agents presumably join lysine residues. Two cross-linking mechanisms have been proposed (64,67), both of which may be correct. Browne and Kent (67) have shown that imido esters can form both N-alkyl amidines and N-alkyl imidates when reacted with primary amines (Fig.…”

Section: Monofunctional Irnidatesmentioning

confidence: 96%

Contact-site cross-linking agents

1981

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Contact-site cross-linking agents comprise a heterogeneous grouping of cross-linkers which share the common property of being able to cross-link only very closely juxtaposed residues in macromolecular complexes. We have defined contact-site cross-linking arbitrarily as the covalent joining of residues such that they are constrained to a distance which is equivalent to or less than their closest possible steric approach prior to becoming linked (1). We recognize two classes of contact-site cross-linkers, bridge type and zero-length type. The former, such as formaldehyde, become incorporated during cross-linking as one-atom bridges. The latter, such as the carbodiimides, operate as condensing agents with the result that the cross-linked residues become interjoined directly. Contact-site cross-linkers have been used in several ways as specific probes of both the static and dynamic aspects of macromolecular structure. They can yield precise structural information about macromolecular contacts when actual sites of cross-linking are determined by peptide or nucleotide mapping techniques. In this way exact contacts between histones in the nucleosome, between protein and RNA in the ribosome, and between RNA polymerase and DNA have been determined. Contact-site cross-linkers have also been used to probe the perturbation of contacts following macromolecular conformational changes. Certain histone-histone 'cross-linkable' sites are rendered unreactive after induction of chromatin conformational changes thus serving to localize sites of perturbation.

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Section: Monofunctional Irnidatesmentioning

confidence: 96%

Contact-site cross-linking agents

1981

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“…The N-terminus of the protein as well as the e-amino groups in lysine side chains react best at a pH between 8 and 9. Imidoesters are highly watersoluble, but undergo continuous degradation due to hydrolysis, which reduces the half-life of the imidate group to less than 30 min (Hunter & Ludwig, 1962;Browne & Kent, 1975). The reaction product of the imidoester, an amidine, is protonated and carries a positive charge at physiological pH (Liu, Fairbanks, & Palek, 1977;Kiehm & Ji, 1977;Wilbur, 1992).…”

Section: A Reactivitiesmentioning

confidence: 98%

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

Sinz

2006

Mass Spectrometry Reviews

611

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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“…Imido esters are highly water-soluble, but undergo continuous degradation due to hydrolysis, which causes the half-life of the imidate group to be less than 30 min. 18,19 The reaction product of the imido ester, an amidine, is protonated and thus carries a positive charge at physiological pH. 20 -22 This presents one of the major advantages of imido esters, because one of the greatest problems in retaining the three-dimensional structure of proteins arises from removing the positive charge at the lysine residues when amino groups are targeted in crosslinking reactions.…”

Section: Amine-reactive Cross-linkersmentioning

confidence: 99%

Chemical cross‐linking and mass spectrometry for mapping three‐dimensional structures of proteins and protein complexes

2003

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Chemical cross-linking of proteins, an established method in protein chemistry, has gained renewed interest in combination with mass spectrometric analysis of the reaction products for elucidating low-resolution three-dimensional protein structures and interacting sequences in protein complexes. The identification of the large number of cross-linking sites from the complex mixtures generated by chemical cross-linking, however, remains a challenging task. This review describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the strategies employing intra- or intermolecular chemical cross-linking and mass spectrometry. The various approaches described in the literature to facilitate detection of cross-linking products and also computer software for data analysis are reviewed. Cross-linking techniques combined with mass spectrometry and bioinformatic methods have the potential to provide the basis for an efficient structural characterization of proteins and protein complexes.

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Formation of non-amidine products in the reaction of primary amines with imido esters

Cited by 110 publications

References 8 publications

Contact-site cross-linking agents

Contact-site cross-linking agents

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

Chemical cross‐linking and mass spectrometry for mapping three‐dimensional structures of proteins and protein complexes

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