CrossWork: Software-assisted identification of cross-linked peptides

被引:42
作者
Rasmussen, Morten I. [1 ]
Refsgaard, Jan C. [1 ]
Peng, Li [1 ]
Houen, Gunnar [2 ]
Hojrup, Peter [1 ]
机构
[1] Univ So Denmark, DK-5230 Odense M, Denmark
[2] Statens Serum Inst, DK-2300 Copenhagen S, Denmark
关键词
Cross-linking; Bioinformatics; Protein structure; BS2G; BS3; ERp72; Complement C3; PROTEIN DISULFIDE-ISOMERASE; CYTOCHROME-C-OXIDASE; MASS-SPECTROMETRY; STRUCTURAL-ANALYSIS; TANDEM MS; LINKING; SPECTRA; COMPLEX; ERP72; FRAGMENTATION;
D O I
10.1016/j.jprot.2011.04.019
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The increased interest in chemical cross-linking for probing protein structure and interaction has led to a large increase in literature describing new cross-linkers and search programs. However, this has not led to a corresponding increase in the analysis of large and complex proteins. A major obstacle is that the new cross-linkers are either not readily available and/or have a low reactivity. In combination with aging search programs that are slow and have low sensitivity, or new search programs that are described but not released, these efforts do little to advance the field of cross-linking. Here we present a method pipeline for chemical cross-linking, using two standard cross-linkers, BS3 and BS2G, combined with our freely available CrossWork search program. By this approach we generate cross-link data sufficient to derive structural information for large and complex proteins. CrossWork searches batches of tandem mass-spectrometric data, and identifies crosslinked and non-cross-linked peptides using a standard PC. We tested CrossWork by searching mass-spectrometric datasets of cross-linked complement factor C3 against small (1 protein) and large (1000 proteins) search spaces, and show that the resulting distance constraints agree with the established structures. We further investigated the structure of the multi-domain ERp72, and combined the individual domains of ERp72 into a single structure. (C) 2011 Elsevier B.V. All rights reserved.
引用
收藏
页码:1871 / 1883
页数:13
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