| pubmed-article:17854217 | rdf:type | pubmed:Citation | lld:pubmed |
| pubmed-article:17854217 | lifeskim:mentions | umls-concept:C0037003 | lld:lifeskim |
| pubmed-article:17854217 | lifeskim:mentions | umls-concept:C0162808 | lld:lifeskim |
| pubmed-article:17854217 | lifeskim:mentions | umls-concept:C0936012 | lld:lifeskim |
| pubmed-article:17854217 | pubmed:issue | 10 | lld:pubmed |
| pubmed-article:17854217 | pubmed:dateCreated | 2007-10-5 | lld:pubmed |
| pubmed-article:17854217 | pubmed:abstractText | We developed a new approach that employs a novel computer algorithm for the sensitive and high-throughput analysis of tertiary and quaternary interaction sites from chemically cross-linked proteins or multi-protein complexes. First, we directly analyze the digests of the chemically cross-linked proteins using only high-accuracy LC-MS/MS data. We analyze these data using a computer algorithm, we term X!Link, to find cross-links between two peptides. Our algorithm is rapid, taking only a few seconds to analyze approximately 5000 MS/MS spectra. We applied this algorithm to analyze cross-linked sites generated chemically using the amino specific reagent, BS3, in both cytochrome c and the mitochondrial division dynamin mutant, Dnm1G385D, which exists as a stable homodimer. From cytochrome c, a well-established test protein, we identified a total of 31 cross-links, 21 interpeptide and 10 intrapeptide cross-links, in 257 MS/MS spectra from a single LC-MS/MS data set. The high sensitivity of this technique is indicated by the fact that all 19 lysines in cytochrome c were detected as a cross-link product and 33% of all the Lys pairs within 20 A were also observed as a cross-link. Analysis of the cross-linked dimeric form of Dnm1G385D identified a total of 46 cross-links, 38 interpeptide and 8 intrapeptide cross-links, in 98 MS/MS spectra in a single LC-MS/MS data set. These results represent the most abundant cross-links identified in a single protein or protein dimer to date. Statistical analysis suggests a 1% false discovery rate after optimization of filtering parameters. Further analysis of the cross-links identified using our approach indicates that careful manual inspection is important for the correct assignment of cross-linking sites when multiple cross-linkable sites or several similar sequences exist. In summary, we have developed a sensitive MS-based approach to identify peptide-peptide cross-links that does not require isotopic labeling or comparison with non-cross-linked controls, making it faster and simpler than current methodologies. | lld:pubmed |
| pubmed-article:17854217 | pubmed:grant | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:17854217 | pubmed:grant | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:17854217 | pubmed:language | eng | lld:pubmed |
| pubmed-article:17854217 | pubmed:journal | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:17854217 | pubmed:citationSubset | IM | lld:pubmed |
| pubmed-article:17854217 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:17854217 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:17854217 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:17854217 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:17854217 | pubmed:status | MEDLINE | lld:pubmed |
| pubmed-article:17854217 | pubmed:month | Oct | lld:pubmed |
| pubmed-article:17854217 | pubmed:issn | 1535-3893 | lld:pubmed |
| pubmed-article:17854217 | pubmed:author | pubmed-author:LeeYoung... | lld:pubmed |
| pubmed-article:17854217 | pubmed:author | pubmed-author:PhinneyBrett... | lld:pubmed |
| pubmed-article:17854217 | pubmed:author | pubmed-author:LacknerLaura... | lld:pubmed |
| pubmed-article:17854217 | pubmed:author | pubmed-author:NunnariJodi... | lld:pubmed |
| pubmed-article:17854217 | pubmed:issnType | Print | lld:pubmed |
| pubmed-article:17854217 | pubmed:volume | 6 | lld:pubmed |
| pubmed-article:17854217 | pubmed:owner | NLM | lld:pubmed |
| pubmed-article:17854217 | pubmed:authorsComplete | Y | lld:pubmed |
| pubmed-article:17854217 | pubmed:pagination | 3908-17 | lld:pubmed |
| pubmed-article:17854217 | pubmed:meshHeading | pubmed-meshheading:17854217... | lld:pubmed |
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| pubmed-article:17854217 | pubmed:meshHeading | pubmed-meshheading:17854217... | lld:pubmed |
| pubmed-article:17854217 | pubmed:meshHeading | pubmed-meshheading:17854217... | lld:pubmed |
| pubmed-article:17854217 | pubmed:meshHeading | pubmed-meshheading:17854217... | lld:pubmed |
| pubmed-article:17854217 | pubmed:meshHeading | pubmed-meshheading:17854217... | lld:pubmed |
| pubmed-article:17854217 | pubmed:meshHeading | pubmed-meshheading:17854217... | lld:pubmed |
| pubmed-article:17854217 | pubmed:meshHeading | pubmed-meshheading:17854217... | lld:pubmed |
| pubmed-article:17854217 | pubmed:meshHeading | pubmed-meshheading:17854217... | lld:pubmed |
| pubmed-article:17854217 | pubmed:year | 2007 | lld:pubmed |
| pubmed-article:17854217 | pubmed:articleTitle | Shotgun cross-linking analysis for studying quaternary and tertiary protein structures. | lld:pubmed |
| pubmed-article:17854217 | pubmed:affiliation | Proteomics Core Facility, Genome Center, and Molecular and Cellular Biology, University of California, Davis 95616, USA. yojlee@ucdavis.edu | lld:pubmed |
| pubmed-article:17854217 | pubmed:publicationType | Journal Article | lld:pubmed |
| pubmed-article:17854217 | pubmed:publicationType | Research Support, N.I.H., Extramural | lld:pubmed |
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