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Kosi Gramatikoff

Publications and source records attributed to Kosi Gramatikoff.

4 recordsLinked to original sources
PubMed2006

CutDB: a proteolytic event database.

Beyond the well-known role of proteolytic machinery in protein degradation and turnover, many specialized proteases play a key role in various regulatory processes. Thousands of highly specific proteolytic events are associated with normal and pathological conditions, including bacterial and viral infections. However, the information about individual proteolytic events is dispersed over multiple publications and is not easily available for large-scale analysis. CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate and cleavage site. Currently, CutDB integrates 3070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications. CutDB supports various types of data searches and displays, including clickable network diagrams. Most importantly, CutDB is a community annotation resource based on a Wikipedia approach, providing a convenient user interface to input new data online. A recent contribution of 568 proteolytic events by several experts in the field of matrix metallopeptidases suggests that this approach will significantly accelerate the development of CutDB content. CutDB is publicly available at http://cutdb.burnham.org.

Animals↗
PubMed2005

Immunoaffinity separation of plasma proteins by IgY microbeads: meeting the needs of proteomic sample preparation and analysis.

Separation of complex protein mixtures that have a wide dynamic range of concentration, such as plasma or serum, is a challenge for proteomic analysis. Sample preparation to remove high-abundant proteins is essential for proteomics analysis. Immunoglobulin yolk (IgY) antibodies have unique and advantageous features that enable specific protein removal to aid in the detection of low-abundant proteins and biomarker discovery. This report describes the efficiency and effectiveness of IgY microbeads in separating 12 abundant proteins from plasma with an immunoaffinity spin column or LC column. The protein separation and sample preparation process was monitored via SDS-PAGE, 2-DE, LC-MS/MS, or clinical protein assays. The data demonstrate the high specificity of the protein separation, with removal of 95-99.5% of the abundant proteins. IgY microbeads against human proteins can also selectively remove orthologous proteins of other mammals such as mouse, rat, etc. Besides the specificity and reproducibility of the IgY microbeads, the report discusses the factors that may cause potential variations in protein separation such as protein-protein interactions (known as "Interactome"), binding and washing conditions of immunoaffinity reagents, etc. A novel concept of Seppromics is introduced to address methodologies and science of protein separation in a context of proteomics.

Albumins↗
PubMed2003

The SARS-CoV S glycoprotein: expression and functional characterization.

We have cloned, expressed, and characterized the full-length and various soluble fragments of the SARS-CoV (Tor2 isolate) S glycoprotein. Cells expressing S fused with receptor-expressing cells at neutral pH suggesting that the recombinant glycoprotein is functional, its membrane fusogenic activity does not require other viral proteins, and that low pH is not required for triggering membrane fusion; fusion was not observed at low receptor concentrations. S and its soluble ectodomain, S(e), were not cleaved to any significant degree. They ran at about 180-200kDa in SDS gels suggesting post-translational modifications as predicted by previous computer analysis and observed for other coronaviruses. Fragments containing the N-terminal amino acid residues 17-537 and 272-537 but not 17-276 bound specifically to Vero E6 cells and purified soluble receptor, ACE2, recently identified by M. Farzan and co-workers [Nature 426 (2003) 450-454]. Together with data for inhibition of binding by antibodies developed against peptides from S, these findings suggest that the receptor-binding domain is located between amino acid residues 303 and 537. These results also confirm that ACE2 is a functional receptor for the SARS virus and may help in the elucidation of the mechanisms of SARS-CoV entry and in the development of vaccine immunogens and entry inhibitors.

Animals↗