The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins

Uversky, Vladimir N

Histone-interacting proteins. Since histones are polycations, they are known to be involved in interactions with several polyanionic proteins, particularly with proteins containing glutamic which are located outside the catalytic domain, with respectively 44, 32, 53, 59 and 39 glutamates, aspartates, prolines, serines and threonines being found in the non-catalytic region (residues 294-780). Finally, among the 460 residues of the human PTP-HSCF (BDP1/PTP20/PTP-K1/FLP1/PTPN18), there are 27 glutamic acids, 21 aspartic acids, 32 prolines, 29 serines and 25 threonines. Importantly, glutamate-rich, non-catalytic regions of all these PTPs are known to be involved in interactions with multiple binding partners. For example, PTP-LYP is involved in interaction with Grb2, c-Cbl, and the C-terminal Src kinase (Csk), which is the inhibitory protein tyrosine kinase (PTK). The interaction between the PTP-LYP and Csk is mediated by the proline-rich motif in PEP and by the Src homology 3 (SH3) domain of Csk. 186 PTP-PEST promiscuously associates with various proteins involved in the organization of the cytoskeleton, such as Cas (and Cas-related proteins Sin and CasL), paxillin (and paxillin-related polypeptides Hic-5 and leupaxin) and the PTKs FAK and Pyk2. This protein also associates with Shc, Grb2 and Csk. 186 Finally, PTP-HSCF is involved in association with Csk and Tec. 186 Multifarious functions of glutamic acid-rich proteins. Delta factor. In addition to γ-PGA, Bacillus subtilis produces another important polyanion, delta factor, which is an important component of the bacterial RNA polymerase. 188 This delta factor is a 20.4 kDa highly acidic (pI = 3.6) protein that contains two distinct regions, a 13 kDa N-terminal domain with uniform charge distribution and a Glu-Asp-rich C-terminal region. The overall contents of glutamic and aspartic acids in delta factor are 20.8% and 17.9% respectively, whereas these numbers increase to 34.3% and 37.3% in the Glu-Asp-rich C-terminal domain. The ordered N-terminal domain contains 32% α-helix and 16% β-sheet, whereas the C-terminal 8.5 kDa domain is highly charged (net charge of −47) and therefore is largely unstructured. 188 Importantly, the C-terminal intrinsically disordered domain has an important biological function, since the ability of delta factor to displace RNA from RNA polymerase requires the activities of both the N-terminal core-binding domain and the polyanionic C-terminal region. 188 MARCKS. Myristoylated alanine-rich C kinase substrate (MARCKS) is an abundant 32 kDa protein which is unusually rich in alanine and glutamic acid, with glutamic acid and alanine in this proteins accounting for 16.0% and 30.7% residues, respectively. MARCKS is a very prominent cellular substrate for protein kinase C (PKC), and its 22 serine residues and 2 threonines are phosphorylated. Human MARCKS is an acidic protein with a pI of 4.46 which in addition to Ala-Glu enriched N-and C-terminal domains possesses a compact "effector domain" (ED), which is responsible for interaction with calmodulin, is located near the middle of the sequence and is enriched in lysines, serines and phenylalanines. 189 MARCKS is a typical IDP with a labile conformation and little ordered structure. In addition to calmodulin this protein can interact with synapsin and actin, and can serve as filamentous actin (F-actin) cross-linking protein. Furthermore, being myristoylated, MARCKS is able to interact with membrane and serves as a cytoske