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 (serinearginine) 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.phosphorylation ͉ RS domain ͉ SR protein ͉ transportin-SR2 P osttranslational modifications of proteins are of immense importance in molecular biology because of their ability to control the functions of a host of proteins (1). These processes have been studied in great detail, but many of their structural implications are not well understood. Although there are only 20 amino acid residues genetically encoded for mammalian cells, nature has found ways of adding to the variety by modifying the side chain of some existing residues after the translational process. There are several forms of posttranslational modification of protein residues that are vital for biological functions such as methylation and glycosylation. Among them, the most widely known and well studied form of reversible posttranslational modification is phosphorylation of the hydroxyl group of serine, threonine, or tyrosine by protein kinases.Phosphorylation of proteins is known to act as a signaling mechanism, either by direct changes of the binding properties with its recognition partners or by conformational switching to alter functions. Once a protein is phosphorylated or dephosphorylated, it can trigger a cascade of signaling pathways that eventually lead to the alteration of enzyme activity or gene expression (1-3). The underlying molecular consequence of phosphorylation could be the recognition of the phosphate group by another protein or a change in the native unphosphorylated conformations of the protein by rearranging the freeenergy landscape. The landscape of a protein could be changed in variety of ways because of phosphorylat...

Graphlet Kernels for Prediction of Functional Residues in Protein Structures

“…This hypothesis has been validated in recent experimental studies (Collins, et al, 2008; Gsponer, et al, 2008) and in several cases disorder-to-order transition upon phosphorylation has been predicted (Espinoza-Fonseca, et al, 2007; Hamelberg, et al, 2007; Hegedus, et al, 2008). Furthermore, it has recently been shown that disordered proteins are substrates of twice as many kinases as are ordered proteins (Gsponer, et al, 2008).…”

Multisite Phosphorylation Disrupts Arginine-Glutamate Salt Bridge Networks Required for Binding of Cytoplasmic Linker-associated Protein 2 (CLASP2) to End-binding Protein 1 (EB1)

“…4). In addition, the formation of similar stable R-pS salt bridges has been proposed in hyperphosphorylated RS dipeptide repeat motifs (50).…”

Redirecting SR Protein Nuclear Trafficking through an Allosteric Platform

“…Although RRMs bind pre-mRNA and are generally well-characterized at the structural level, RS domain structure and function is still not fully understood. RS domains are disordered but they become more rigid upon phosphorylation based on NMR studies 9, 11 . However, owing to their poor solubility and self-association, no high-resolution structure of a full-length SR protein has been reported.…”