Dueling Post-Translational Modifications Trigger Folding and Unfolding of a β-Hairpin Peptide

Abstract

Protein post-translational modifications (PTMs) are used in nature as a means of turning on or off a myriad of biological events. Methylation of lysine and phosphorylation of serine are important PTMs in the histone code found to modulate chromatin packing, which in turn affects gene expression. The design of peptides that fold into secondary structures can help to further our understanding of complex protein interactions. Here we report the design of the Trpswitch peptide sequence that folds into a moderately stable beta-hairpin structure in aqueous solution and show that the stability of the structure can be tuned by incorporation of dimethyllysine or phosphoserine. Dimethylated Trpswitch results in an increase in beta-hairpin stability, while phosphorylated Trpswitch is unstructured at neutral pH. When both modifications are incorporated into Trpswitch, a less stable beta-hairpin structure is observed. This system provides a model to demonstrate how multiple PTMs may work in concert or against each other to influence structure.

Structural Role of RKS Motifs in Chromatin Interactions: A Molecular Dynamics Study of HP1 Bound to a Variably Modified Histone Tail

“…Several recent reports have provided evidence for the ability of lysine residues to interact strongly with phosphoserine in the context of isolated oligopeptides (35,52,55). However, on the timescale of 1 ms used in our MD simulations (the longest reported for these systems, to our knowledge) and in the context of the H3/HP1 model complex studied, we find no indication of a direct interaction between methylated K9 and phosphorylated S10 that is sufficiently strong to destabilize the complex and drive the dissociation of HP1 from chromatin.…”

“…We also explored the possibility of repulsive interactions between the phosphorylated S10 and the aromatic residues of the HP1 binding pocket. Such interactions between a phosphorylated side chain and an aromatic residue have been reported to disrupt the structure and control the folding/unfolding of short b-hairpin peptides mimicking the H3/HP1 complex (51)(52)(53). The distances d4, d5, and d6 between the hydroxyl oxygen of S10 and the centroids in the aromatic rings of Y24, W45, and Y48, respectively, were monitored during the simulation of the complex (Fig.…”

Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein

“…In order to reduce complexity, a large amount of works have been concentrated on protein secondary structure conformational dynamics, such as b-hairpin (Munoz et al 2006;Hughes and Waters 2006;Riemen and Waters 2010;Klimov et al 2002;Zhou and Berne 2002;Guo et al 2000;Du et al 2004). Schulten et al perform flow simulations on the 16-residue b-switch region of platelet glycoprotein Iba (Chen et al 2008).…”

Towards the computational design of protein post-translational regulation

“…For example, Riemen and Waters analysed a 12 residue peptide designed to fold into a β-hairpin structure where the properties that determine the structure are well understood. 72 , 73 In one of the studies the second position of the hairpin was exchanged between a serine and different phosphosites ( Fig. 2 d).…”

“… 72 A similar peptide system was also used to test the combination of phosphorylation and methylation on the stability of the β-hairpin structure. 73 Another elegant example of controlled conformational switches was achieved by Balakrishnan and Zondlo making use of the EF-hand domain. 74 The EF hand domain contains a calcium-binding motif that binds a metal atom, for example calcium in Calmodulin.…”