Bioinformatický seminár

Tue 15 Jan. 2013, 17:20

Title: Hosein Mohimani et al. (2011) Cycloquest: identification of cyclopeptides via database search of their massspectra against genome databases
Speaker: Eliška Pätoprstá

Hundreds of ribosomally synthesized cyclopeptides have been isolated from all
domains of life, the vast majority having been reported in the last 15 years.
Studies of cyclic peptides have highlighted their exceptional potential both as
stable drug scaffolds and as biomedicines in their own right. Despite this,
computational techniques for cyclopeptide identification are still in their
infancy, with many such peptides remaining uncharacterized. Tandem mass
spectrometry has occupied a niche role in cyclopeptide identification, taking
over from traditional techniques such as nuclear magnetic resonance spectroscopy 
(NMR). MS/MS studies require only picogram quantities of peptide (compared to
milligrams for NMR studies) and are applicable to complex samples, abolishing the
requirement for time-consuming chromatographic purification. While database
search tools such as Sequest and Mascot have become standard tools for the MS/MS 
identification of linear peptides, they are not applicable to cyclopeptides, due 
to the parent mass shift resulting from cyclization and different fragmentation
patterns of cyclic peptides. In this paper, we describe the development of a
novel database search methodology to aid in the identification of cyclopeptides
by mass spectrometry and evaluate its utility in identifying two peptide rings
from Helianthus annuus, a bacterial cannibalism factor from Bacillus subtilis,
and a theta-defensin from Rhesus macaque.