Consensus Prediction of Charged Single Alpha-Helices with CSAHserver
- 2.2k Downloads
Charged single alpha-helices (CSAHs) constitute a rare structural motif. CSAH is characterized by a high density of regularly alternating residues with positively and negatively charged side chains. Such segments exhibit unique structural properties; however, there are only a handful of proteins where its existence is experimentally verified. Therefore, establishing a pipeline that is capable of predicting the presence of CSAH segments with a low false positive rate is of considerable importance. Here we describe a consensus-based approach that relies on two conceptually different CSAH detection methods and a final filter based on the estimated helix-forming capabilities of the segments. This pipeline was shown to be capable of identifying previously uncharacterized CSAH segments that could be verified experimentally. The method is available as a web server at http://csahserver.itk.ppke.hu and also a downloadable standalone program suitable to scan larger sequence collections.
Key wordsCharged single alpha-helix Charged residues Consensus prediction Ion pairs Fourier transform Helicity Coiled coil
This work was supported by a grant from the Hungarian Scientific Research Fund (OTKA/NKFIH NF104198). Z.G. was also supported by a János Bolyai Research Fellowship from the Hungarian Academy of Sciences.
- 6.Samejima K, Platani M, Wolny M, Ogawa H, Vargiu G, Knight PJ, Peckham M, Earnshaw WC (2015) The inner centromere protein (INCENP) coil is a single -helix (SAH) domain that binds directly to microtubules and is important from chromosome passenger complex (CPC) localization and function in mitosis. J Biol Chem 290:21460–21472CrossRefPubMedPubMedCentralGoogle Scholar