期刊
JOURNAL OF PROTEOME RESEARCH
卷 9, 期 1, 页码 626-635出版社
AMER CHEMICAL SOC
DOI: 10.1021/pr900771r
关键词
disulfide; tandem mass spectrometry; DBond; persulfide; dehydroalanine; disulfide fragmentation; secretagogin; nucleoside diphosphate kinase; NDPK; methionine sulfoxide reductase
资金
- National Core Research Center (NCRC) [R15-2006-020]
- Korean Ministry of Education, Science Technology [FPR08-A1-020, FPR05-A2-480]
- WCU [R31-2008-000-10010-0]
- University of Seoul 2008 Research Fund
- Brain Korea 21 (BK21) Project
- Seoul Science Fellowship (SSF)
Identifying the sites of disulfide bonds in a protein is essential for thorough understanding of a protein's tertiary and quaternary structures and its biological functions. Disulfide linked peptides are usually identified indirectly by labeling free sulfhydryl groups with alkylating agents, followed by chemical reduction and mass spectral comparison or by detecting the expected masses of disulfide linked peptides on mass scan level. However, these approaches for determination of disulfide bonds become ambiguous when the protein is highly bridged and modified. For accurate identification of disulfide linked peptides, we present here an algorithmic solution for the analysis of tandem mass (MS/MS) spectra of disulfide bonded peptides under nonreducing condition. A new algorithm called DBond analyzes disulfide linked peptides based on specific features of disulfide bonds. To determine disulfide linked sites, DBond takes into account fragmentation patterns of disulfide linked peptides in nucleoside diphosphate kinase (NDPK) as a model protein, considering fragment ions including cysteine, cysteine thioaldehyde (-2 Da, C-T), cysteine persulfide (+32 Da, C-S) and dehydroalanine (-34 Da, C boolean AND). Using this algorithm, we successfully identified about a dozen novel disulfide bonds in a hexa EF-hand calcium binding protein secretagogin and in a methionine sulfoxide reductase. We believe that DBond, taking into account the disulfide bond fragmentation characteristics and post-translational modifications, offers a novel approach for automatic identification of unknown disulfide bonds and their sites in proteins from MS/MS spectra.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据