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Japanese Mushroom Key to Protein Sequencing

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Researchers in the Netherlands used an enzyme found in a Japanese mushroom to develop a method they say can make it significantly easier to identify peptides whose genome is unknown, and help decipher post-translational modifications.

The method, described in a proof-of-principle study in the May issue of Nature Methods, was developed by proteomics researchers at Utrecht University and employs an enzyme called metalloendopeptidase found in the Japanese mushroom Grifola frondosa. The mushroom, also called Maitake or dancing mushroom, cleaves proteins on the amino side of lysine.

Using electron transfer dissociation, the researchers found that peptides containing a single lysine residue that were digested by Lys-N produced spectra dominated by c-type fragment ions, "provid[e] simple ladders for sequence determination," they write in the article. They add that the method can be "a valuable strategy for de novo sequencing and the analysis of post-translation modifications."

For proteomics, such a strategy, if replicated, could become a valuable tool because the genomes of most species remain to be sequenced and de novo protein sequencing can be a painstaking and imperfect task.

Lys-N was originally isolated by Japanese researchers whose work on a model protein predicted that the protease would cleave at the Lys-N terminus of peptides. Picking up on that, the Dutch team decided to test Lys-N and its applicability for proteomics work, says Albert Heck, the corresponding author on the article, and a professor at Utrecht University in the department of biomolecular mass spectrometry.

Normally when a peptide is fragmented, an amino acid sequence of the peptide is generated and the protein is partially sequenced. When done in a mass spectrometer, the sequencing is performed from both the N- and C-termini of the peptide, however. This makes the spectra complicated because a researcher does not know beforehand which are C-terminus fragments and which are N-terminus fragments.

Tony Fong

Proteomics  Notes

GWC Technologies' label-free array systems will be distributed in India by Biotron Healthcare. Tim Burland, president and CEO of GWC, said Biotron has a broad reach across India.

German firms Crelux and ProQinase are expanding their off-the-shelf crystal-grade protein kinase portfolio and will supply customers with crystal-grade protein kinases and kinase complex structures.

Syngene's first Dyversity 6 2D gel imaging system is now installed at the Singapore-based Massachusetts Institute of Technology Alliance for Research and Technology Center. SMART's system includes a 16-bit, six-megapixel CCD-based camera and can generate 2D protein gel images up to 10 times faster than a conventional laser-based scanner.

Datapoint

$1 Billion
Amount the Human Proteome Organization plans to spend to map the human
proteome.

Funded Grants

$371,250/FY2007
High-Throughput assays for imaging human intracellular pathogen infections
Grantee: Hervé Agaisse, Yale University
Began: Jun. 1, 2007; Ends: May 31, 2010

Agaisse will be putting this grant toward developing high-throughput screening assays to image and quantify intracellular pathogens in mammalian cells. In particular, they will be modeling Listeria monocytogenes infections in HeLa cells. Ultimately, they plan to identify bioactive molecules and their gene targets.

$451,425/FY2007
Arsenic Exposure and Birth Outcomes in Bangladesh
Grantee: David Christiani, Harvard University
Began: Sep. 24, 2007; Ends: May 31, 2012

Christiani and his colleagues are studying the effect of inorganic arsenic on expectant mothers and newborns. As part of this grant, they will be evaluating the role of methylated arsenic in urine as a biomarker of exposure and risk as well as determining if proteomic profiles can be used to predict adverse outcome.

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