Phosphorylation is ubiquitous in control of protein activity, yet its effects on protein structure are poorly understood. Here we investigate the effect of serine phosphorylation in the interior of an α-helix when a salt bridge is present between the phosphate group and a positively charged side chain (in this case lysine) at i,i + 4 spacing. The stabilization of the helix is considerable and can overcome the intrinsically low preference of phosphoserine for the interior of the helix. The effect is pH dependent, as both the lysine and phosphate groups are titratable, and so calculations are given for several charge combinations. These results, with our previous work, highlight the different, context-dependent effects of phosphorylation in the α-helix. The interaction between the phosphate 2− group and the lysine side chain is the strongest yet recorded in helix-coil studies. The results are of interest both in de novo design of peptides and in understanding the structural modes of control by phosphorylation.Phosphorylation and dephosphorylation have long been known as control mechanisms for various processes in biochemistry, and roughly one-third of all proteins in eukaryotes are estimated to undergo reversible phosphorylation (1). Since the middle of the last century it has been known that protein activity can be controlled by the addition or removal of a phosphate group (2-5). The control of gene expression, macromolecule production, and cellular proliferation have since been shown to be orchestrated through multiple intracellular signal transduction pathways. These pathways, or protein kinase cascades, propagate signals received at the plasma membrane to the interior of the cell through a series of phosphorylation-controlled events.The mechanisms of action of phosphorylation are, however, still relatively poorly understood at the structural level, though many studies of individual systems now show some conformational differences between proteins and synthetic peptides before and after phosphorylation (see, e.g., refs 6-13). Previous work from our own group (14) and others (15-17) has shown that phosphorylation at the N-terminus stabilizes α-helices but also that the effect is position dependent. When interior serine residues are phosphorylated, the effect is greatly destabilizing, but at the three N-terminal positions it is greatly stabilizing (phosphoserine at the N2 position in a helix is the most stabilizing interaction yet found at this position). More recent work has suggested that protein phosphorylation sites, especially those for serine and threonine, are predominantly disordered prior to phosphorylation and that phosphorylation sites resemble natively unstructured proteins in terms of their charge, hydrophobicity, and amino acid composition. Some of the exceptions to these sites may be crystallization artifacts, and in others it may be that the substrate undergoes an order- † This work was funded by The Wellcome Trust (award reference 065106).
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