Substrate specificity of protein kinases and computational prediction of substrates

Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid

“…The most common and well-known example is the involvement of protein phosphorylation in signal transduction. Analysis of phosphorylation sites has led to a better understanding of kinase substrate specificity (Brinkworth et al 2002;Kobe et al 2005), methods for site prediction (Koenig and Grabe 2004;Huang et al 2005;Plewczynski et al 2005;Xue et al 2005), and a combined experimental/computational approach that has led to a better understanding of the yeast phosphoproteome (Brinkworth et al 2006;Molina et al 2007).…”

“…The most common and well-known example is the involvement of protein phosphorylation in signal transduction. Analysis of phosphorylation sites has led to a better understanding of kinase substrate specificity (Brinkworth et al 2002;Kobe et al 2005), methods for site prediction (Koenig and Grabe 2004;Huang et al 2005;Plewczynski et al 2005;Xue et al 2005), and a combined experimental/computational approach that has led to a better understanding of the yeast phosphoproteome (Brinkworth et al 2006;Molina et al 2007).The reversible oxidation of cysteine side chains to cysteine sulfenic acid (Cys-SOH) has been recognized as Reprint requests to: Jacquelyn S. Fetrow, 100 Olin Physical Laboratory, 7507 Reynolda Station, Wake Forest University, Winston-Salem, NC 27019-7507, USA; e-mail: fetrowjs@wfu.edu; fax: (336) 758-6142.Abbreviations: Prx, peroxiredoxin; Msr, methionine sulfoxide reductase; Cys-SOH, cysteine sulfenic acid; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; PTP, protein tyrosine phosphatase.Article and publication are at …”

Phosphorylation-Regulated Cell Surface Expression of Membrane Proteins

“…Thus, Mode III would be better defined as RXXpS/pTX-COOH. For all three modes of 14-3-3 binding, phosphorylation is a prerequisite and arginine residues located upstream of the phospho-serine/threonine are also important for recognition by a number of kinases (Kobe et al, 2005). Thus, the absence of an arginine residue in the C-terminal 14-3-3 binding sequence in plant H + -ATPase (QQXYpTV-COOH) suggests the possibility that plant and animal differ significantly in kinase recognition.…”

Identifying Atg1 Substrates: Four Means to an End

“…However, it is important to point out that not all occurrences of a given consensus site are necessarily recognized by the relevant protein kinase. 41 For example, many proteins that contain a good match to the PKA consensus are not phosphorylated by this enzyme either in vivo or in vitro. 14 This failure could be due to a variety of factors including the possibility that other domains in substrates may be important for recognition by protein kinases.…”