Selective enrichment and identification of cross-linked peptides to study 3-D structures of protein complexes by mass spectrometry

Buncherd, Hansuk; Nessen, Merel A.; Yang, Xiao; Lewis, Peter J.; de Koning, Leo J.; de Koster, Chris G.; de Jong, Luitzen; Nouse, Niels; Stelder, Sacha K.; Roseboom, Winfried; Dekker, Henk L.; Arents, Jos C.; Smeenk, Linde E.; Wanner, Martin J.; van Maarseveen, Jan H.

Title: Selective enrichment and identification of cross-linked peptides to study 3-D structures of protein complexes by mass spectrometry
Creator: Buncherd, Hansuk; Nessen, Merel A.; Yang, Xiao; Lewis, Peter J.; de Koning, Leo J.; de Koster, Chris G.; de Jong, Luitzen; Nouse, Niels; Stelder, Sacha K.; Roseboom, Winfried; Dekker, Henk L.; Arents, Jos C.; Smeenk, Linde E.; Wanner, Martin J.; van Maarseveen, Jan H.
Relation: Journal of Proteomics Vol. 75, Issue 7, p. 2205-2215
Publisher Link: http://dx.doi.org/10.1016/j.jprot.2012.01.025
Publisher: Elsevier BV
Resource Type: journal article
Date: 2012
Description: Chemical cross-linking of protein complexes combined with mass spectrometry is a powerful approach to obtain 3-D structural information by revealing amino residues that are in close spatial proximity. To increase the efficiency of mass spectrometric analysis, we have demonstrated the selective enrichment of cross-linked peptides from the 350 kDa protein complex RNA polymerase (RNAP) from Bacillus subtilis. Bis(succinimidyl)-3-azidomethyl glutarate was used as a cross-linker along with an azide-reactive cyclooctyne-conjugated resin to capture target peptides. Subsequently released peptides were fractionated by strong cation exchange chromatography and subjected to LC-MS/MS. We mapped 10 different intersubunit and 24 intrasubunit cross-links by xComb database searching supplied with stringent criteria for confirmation of the proposed structure of candidate cross-linked peptides. The cross-links fit into a homology model of RNAP. Cross-links between β lobe 1 and the β′ downstream jaw, and cross-links involving the N-terminal and C-terminal parts of the α subunits suggest conformational flexibility. The analytical strategy presented here can be applied to map protein–protein interactions at the amino acid level in biological assemblies of similar complexity. Our approach enables the exploration of alternative peptide fragmentation techniques that may further facilitate cross-link analysis.
Subject: protein cross-linking; click chemistry; mass spectrometry; RNA polymerase
Identifier: http://hdl.handle.net/1959.13/1325445
Identifier: uon:25274
Identifier: ISSN:1874-3919
Language: eng
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