Prediction of post‐translational glycosylation and phosphorylation of proteins from the amino acid sequence

Abstract

Post-translational modifications (PTMs) occur on almost all proteins analyzed to date. The function of a modified protein is often strongly affected by these modifications and therefore increased knowledge about the potential PTMs of a target protein may increase our understanding of the molecular processes in which it takes part. High-throughput methods for the identification of PTMs are being developed, in particular within the fields of proteomics and mass spectrometry. However, these methods are still in their early stages, and it is indeed advantageous to cut down on the number of experimental steps by integrating computational approaches into the validation procedures. Many advanced methods for the prediction of PTMs exist and many are made publicly available. We describe our experiences with the development of prediction methods for phosphorylation and glycosylation sites and the development of PTM-specific databases. In addition, we discuss novel ideas for PTM visualization (exemplified by kinase landscapes) and improvements for prediction specificity (by using ESS--evolutionary stable sites). As an example, we present a new method for kinase-specific prediction of phosphorylation sites, NetPhosK, which extends our earlier and more general tool, NetPhos. The new server, NetPhosK, is made publicly available at the URL http://www.cbs.dtu.dk/services/NetPhosK/. The issues of underestimation, over-prediction and strategies for improving prediction specificity are also discussed.

Toll-like receptor 3 regulates Mx expression in rare minnow Gobiocypris rarus after viral infection

“…One face of the horseshoe-shaped structure was completely devoid of any glycosylation (NetNGlyc 1.0 Server; Blom et al 2004). When the surface electrostatic potential of GrTLR3 was calculated with Deepview (Schwede et al 2003), the concave surface of the horseshoe-shaped structure and the glycosylation-free face were largely positively charged, which was consistent with its predicted interaction with dsRNA.…”

Identification of Siah-interacting protein as a potential regulator of apoptosis and curcumin resistance

“…In our study, both curcumin and PKC activator (PMA) cause SIP phosphorylation in MOLT-4 but not MOLT-4/AraG cells. Furthermore, NetPhosK (Blom et al, 2004) and KinasePhos (Huang et al, 2005) programs predict the Ser141 residue of SIP as the phosphorylation site of Figure 6 The Ser141Ala mutation attenuates the nuclear accumulation and the apoptosis-promoting effect of SIP in different cells treated with diverse apoptosis stimuli. The indicated cells were transfected with plasmids expressing EGFP-fused wild-type or mutant SIP for 24 h, incubated for 12 h with 25 mg/ml etoposide (ETO), 500 ng/ml doxorubicin (DOXO), 25 mM nitro mustard (NM), 100 J/m 2 ultraviolet irradiation (UV) or 35 mM curcumin (CUR), then applied to analyses for SIP localization and cell apoptosis.…”

A non‐canonical photopigment, melanopsin, is expressed in the differentiating ganglion, horizontal, and bipolar cells of the chicken retina

“…It has been postulated that in Xenopus melanopsin's conspicuously long cytoplasmic tail contains potential phosphorylation sites, suggesting that its activation state may be regulated by kinases (Provencio et al, 1998). By using an algorithm of NetPhos (Blom et al, 2004), we found that chicken cOpn4-a has 33 predicted phosphorylation sites in the cytoplasmic tail, while a truncated melanopsin, cOpn4-b, has 19 sites in the cytoplasmic region. Thus, it is likely that cOtn4-b may have a lower activity than cOpn4-a, or that these two forms of melanopsin may be differentially regulated by certain kinases.…”