A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw

Abstract

Phosphorylation of proteins by kinases is the most commonly studied class of posttranslational modification, yet its structural consequences are not well understood. The human SR (serine-arginine) protein ASF/SF2 relies on the processive phosphorylation of the serine residues of eight consecutive arginine-serine (RS) dipeptide repeats at the C terminus by SRPK1 before it can be transported into the nucleus. This SR protein plays critical roles in spliceosome assembly, pre-mRNA splicing, and mRNA export, and the phosphorylation process of the RS repeats has been extensively studied experimentally. However, knowledge of the conformational changes associated with the phosphorylation of this simple sequence and how it triggers the importation of the SR protein is lacking. Here, we have carried out extensive molecular dynamics simulations to show that phosphorylation of the eight RS repeats significantly alters the peptide's conformation and leads to the formation of very stable structures that are likely to be involved in the recognition, binding, and transport of the SR protein. Specifically, we found an unusual symmetry-broken phase of conformations of the repetitive and quasi-symmetric phosphorylated peptide sequence. One of the main characteristics of these conformations is the exposed phosphate groups on the periphery, which possibly could serve as the recognition platform for the transport protein transportin-SR2.

Fig. 1.

A cartoon view of the sequence of ASF/SF2 with the RS domain shown in detail.

Fig. 2.

The structure of the unphosphorylated (RS)₈. (a) Two views of the helical structures formed. (b) The secondary structures are coded by colors for a time series of the simulation. The x axis is time, and the y axis is the residue index. For each point (x, y), a blue color indicates a helical structure is present for the residue y at time x, and red or gray indicates a strand or disordered secondary structure, respectively. Only the last one-fifth of the entire simulation is shown.

Fig. 3.

The structure of the phosphorylated (RpS)₈. (a) The “rod” structure formed by the phosphorylated (RpS)₈. (b) The time series of the structure color-coded at the residue resolution level. The color code is the same as in Fig. 2: blue, helical; gray, disordered; red, strand. Only the last one-fifth of the entire simulation is shown.

Fig. 4.

The time series of the structures color-coded at the residue resolution level are shown for several peptides, from a totally unphosphorylated form to partial and fully phosphorylated forms. The color code is the same as in Figs. 2 and 3: blue, helical; gray, disordered; red, strand. Only the last one-fifth of the entire simulation is shown.

Fig. 5.

An arginine claw structure in which six arginines form contacts with a centered phosphoserine. In this particular claw, the center serine is the third serine residue.

Fig. 6.

A zoomed-in view of the claw shows the hydrogen bonds formed between the phosphate group of the serine residue and the guanidinium moieties of the arginine residues that are stabilizing the claw structure.