Московский семинар по биоинформатике - 6 мая 2010

Павел Певзнер

Секвенирование антибиотиков

Четверг, 6 мая 2010, 18.00
Институт молекулярной биологии (Вавилова, 32), к. 309.

Pavel Pevzner

University of California, San Diego

Multiplex De Novo Sequencing of Antibiotics

Sequencing antibiotics, once a heroic effort, remains time-consuming and error-prone. Most antibiotics represent cyclic nonribosomal peptides (NRPs) that contain nonstandard amino acids. Moreover, the dominant technique for sequencing antibiotics (NMR) requires large amounts (milligrams) of highly purified materials that, for most compounds, are nearly impossible to obtain. Therefore, there is a need for sequencing NRPs by tandem mass spectrometry from picograms of material. Since nearly all NRPs are produced as related analogs by the same microorganism, we develop a mass spectrometry approach for sequencing all related peptides at once (in difference from the existing approach that analyzes individual peptides). Our results suggest that the current experimental protocol for sequencing antibiotics (and other NRPs) should be changed. Instead of attempting to isolate and NMR-sequence the most abundant compound, one should acquire spectra of many related compounds and sequence all of them at once using mass spec
The talk will mainly focus on biological/technological challenges and applications of the developed algorithms for studies of bacterial cannibalism (collaboration with Pieter Dorrestein) and allelopathy (collaboration with Pedro Leao). If time allows I will also cover the computational aspects of this work.