A new method for C-terminal sequence analysis in the proteomic era

Samyn, Bart; Sergeant, Kjell; Castanheira, Pedro; Faro, Carlos; van Beeumen, Jozef
March 2005
Nature Methods;Mar2005, Vol. 2 Issue 3, p193
Academic Journal
The overall study of post-translational modifications (PTMs) of proteins is gaining strong interest. Beside phosphorylation and glycosylation, truncations of the nascent polypeptide chain at the amino or carboxy terminus are by far the most common types of PTMs in proteins. In contrast to the analysis of phosphorylation and glycosylation sites, relatively little attention has been paid to the development of approaches for the systematic analysis of proteolytic processing events. Here we present a new mass spectrometry (MS)-based strategy that allows the identification of the C-terminal sequence of proteins. The method can be directly applied to proteins cleaved with cyanogen bromide (CNBr) and purified either by SDS-PAGE, by two-dimensional (2D) PAGE or in solution, and it therefore eliminates the need for specific isolation of the C-terminal peptide. Using Shewanella oneidensis as a model system, we have demonstrated that this approach can be used for C-terminal sequence analysis at a proteomic scale. We also applied the method to study the C-terminal proteolytic processing of procardosin A.


Related Articles

  • AMS 3.0: prediction of post-translational modifications. Basu, Subhadip; Plewczynski, Dariusz // BMC Bioinformatics;2010, Vol. 11, p210 

    Background: We present here the recent update of AMS algorithm for identification of post-translational modification (PTM) sites in proteins based only on sequence information, using artificial neural network (ANN) method. The query protein sequence is dissected into overlapping short sequence...

  • The application of proteomics to plant biology: a review. Rampitsch, Christof; Srinivasan, Murali // Canadian Journal of Botany;Jun2006, Vol. 84 Issue 6, p883 

    The term proteomics, although still less than a decade old, is becoming commonplace in the vocabulary of biologists. Advances made in yeast and humans have been remarkable, sustained by equally remarkable progress in mass spectrometry, bioinformatics, and separation techniques. Progress in...

  • Structural Proteomics: Inferring Function from Protein Structure. Wild, David L.; Saqi, Mansoor A. S. // Current Proteomics;Jan2004, Vol. 1 Issue 1, p59 

    We describe how knowledge of three dimensional protein structure can add to the understanding of as yet functionally unannotated protein sequences. Structure determination may reveal that the new protein shares structural similarity with a previously observed structure or that it is a novel...

  • Amino Acid Sequence Database Suitable for the Protein and Proteome Analysis. Kawakami, Takao; Ozaki, Junko; Kondo, Kazuhiro; Sato, Shinji; Yunokawa, Harunobu // Current Proteomics;Dec2008, Vol. 5 Issue 4, p267 

    Amino acid sequence database is one of the essential components in the current proteomics with mass spectrometry. Protein identification routine as well as posttranslational modification analysis is based on correlation between the mass spectrometry data of peptides obtained from proteome and...

  • Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources. Mizianty, Marcin J.; Stach, Wojciech; Ke Chen; Kedarisetti, Kanaka Durga; Disfani, Fatemeh Miri; Kurgan, Lukasz // Bioinformatics;Sep2010, Vol. 26 Issue 18, pi489 

    Motivation: Intrinsically disordered proteins play a crucial role in numerous regulatory processes. Their abundance and ubiquity combined with a relatively low quantity of their annotations motivate research toward the development of computational models that predict disordered regions from...

  • Statistical Properties of Neutral Evolution. Bastolla, Ugo; Porto, Markus; Eduardo Roman, H.; Vendruscolo, Michele // Journal of Molecular Evolution;Aug2003 Supplement 1, Vol. 57, pS103 

    Neutral evolution is the simplest model of molecular evolution and thus it is most amenable to a comprehensive theoretical investigation. In this paper, we characterize the statistical properties of neutral evolution of proteins under the requirement that the native state remains...

  • Information on the secondary structure improves the quality of protein sequence alignment. Litvinov, I. I.; Lobanov, M. Yu.; Mironov, A. A.; Finkelshtein, A. V.; Roytberg, M. A. // Molecular Biology;May2006, Vol. 40 Issue 3, p474 

    The most popular algorithms employed in the pairwise alignment of protein primary structures (Smith-Watermann (SW) algorithm, FASTA, BLAST, etc.) only analyze the amino acid sequence. The SW algorithm is the most accurate, yielding alignments that agree best with superimpositions of the...

  • Accelerated Buffer System for Amino Acid Analysis. Lolia, AurĂ©lie // LC-GC Europe;Dec2007 Applications Book, Vol. 20, p17 

    The article examines the use of accelerated buffer system for amino acid analysis. The study used the Biochrom 30 amino acid analyzer for the specific analysis of amino acids for the pharmaceutical, proteomics, food and feedstuffs industries. It was concluded that accelerated buffer system is an...

  • Understanding how proteins accessorize. Smith, Caitlin // Nature Methods;Apr2006, Vol. 3 Issue 4, p315 

    The article reports on technologies that have emerged to assist in identification and analysis of post-translational modifications (PTM) of proteins. The results provided understanding on an important layer of proteomic complexity. Commonly used techniques used in PTM include mass spectrometry,...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics