We have developed a method to study the primary sequence specificities of protein kinases by using an oriented degenerate peptide library. We report here the substrate specificities of eight protein Ser/Thr kinases. All of the kinases studied selected distinct optimal substrates. The identified substrate specificities of these kinases, together with known crystal structures of protein kinase A, CDK2, Erk2, twitchin, and casein kinase I, provide a structural basis for the substrate recognition of protein Ser/Thr kinases. In particular, the specific selection of amino acids at the ؉1 and ؊3 positions to the substrate serine/threonine can be rationalized on the basis of sequences of protein kinases. The identification of optimal peptide substrates of CDK5, casein kinases I and II, NIMA, calmodulin-dependent kinases, Erk1, and phosphorylase kinase makes it possible to predict the potential in vivo targets of these kinases.The essential role of protein kinases in regulating signal transduction was established with the discovery of cyclic AMPdependent protein kinase (PKA) (12). To respond to different extracellular stimuli, distinct groups of protein kinases have evolved. Each protein kinase is thought to phosphorylate a unique set of targets in the cell. The substrate specificities of protein kinases are therefore crucial for the fidelity of signaling events.The classical approach for studying the specificity of a protein kinase is to compare the phosphorylation kinetics of synthetic peptides on the basis of known sequences phosphorylated by the kinase. This procedure is helpful in identifying the amino acids critical for efficient phosphorylation. However, it is not practical to synthesize and study each of the billions of possible variations of sequences that must be considered. Moreover, it is extremely difficult to apply this approach to study the specificity of a protein kinase with no known substrates. To overcome these problems, we developed a method for determining the primary sequence specificities of protein kinases by using an oriented degenerate peptide library (21). Optimal peptide substrates of a given protein kinase are identified by phosphorylation of a pool of degenerate peptides containing billions of different species. The specificities determined for PKA, CDC2, and CDK2 by using this technique were consistent with known substrates of these kinases. The results also allowed the prediction of in vivo kinase substrates. Synthetic peptides based on predicted optimal motifs were shown to act as low-K m substrates for the kinases studied. Therefore, this method is a useful tool for studying substrate specificities of protein kinases.We present here the specificities of eight additional protein Ser/Thr kinases: CDK5, casein kinase I (CKI) ␦ and ␥, casein kinase II (CKII), NIMA, calmodulin-dependent (Cam) kinase II, Erk1, and phosphorylase kinase. Our findings demonstrate that each of these protein kinases has a distinct optimal peptide substrate. Critical determinants for recognition by the protein kinas...

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DYRKs (dual specificity, tyrosine phosphorylation regulated kinases) and CLKs (cdc2-like kinases) are implicated in the onset and development of Alzheimer's disease and Down syndrome. The marine sponge alkaloid leucettamine B was recently identified as an inhibitor of DYRKs/CLKs. Synthesis of analogues (leucettines) led to an optimized product, leucettine L41. Leucettines were cocrystallized with DYRK1A, DYRK2, CLK3, PIM1, and GSK-3β. The selectivity of L41 was studied by activity and interaction assays of recombinant kinases and affinity chromatography and competition affinity assays. These approaches revealed unexpected potential secondary targets such as CK2, SLK, and the lipid kinase PIKfyve/Vac14/Fig4. L41 displayed neuroprotective effects on glutamate-induced HT22 cell death. L41 also reduced amyloid precursor protein-induced cell death in cultured rat brain slices. The unusual multitarget selectivity of leucettines may account for their neuroprotective effects. This family of kinase inhibitors deserves further optimization as potential therapeutics against neurodegenerative diseases such as Alzheimer's disease.

Protein kinase CK2 is a ubiquitous protein kinase implicated in proliferation and cell survival. Its regulatory ␤ subunit, CK2␤, which is encoded by a single gene in mammals, has been suspected of regulating other protein kinases. In this work, we show that knockout of the CK2␤ gene in mice leads to postimplantation lethality. Mutant embryos were reduced in size at embryonic day 6.5 (E6.5). They did not exhibit signs of apoptosis but did show reduced cell proliferation. Mutant embryos were resorbed at E7.5. In vitro, CK2␤ ؊/؊ morula development stopped after the blastocyst stage. Attempts to generate homozygous embryonic stem (ES) cells failed. By using a conditional knockout approach, we show that lack of CK2␤ is deleterious for mouse ES cells and primary embryonic fibroblasts. This is in contrast to what occurs with yeast cells, which can survive without functional CK2␤. Thus, our study demonstrates that in mammals, CK2␤ is essential for viability at the cellular level, possibly because it acquired new functions during evolution.Protein kinase CK2 is a pleiotropic and highly conserved protein kinase with more than 300 substrates described to date. It seems to be involved in controlling a large panel of normal cellular functions such as gene expression, protein synthesis, cell cycle, and proliferation, as well as pathological processes such as carcinogenesis and viral tumorigenesis (12, 33). Recently, its function in protecting cells against apoptosis has been reported (1).CK2 is a tetrameric holoenzyme generally composed of two catalytic subunits, ␣ and ␣Ј, and two regulatory ␤ subunits which combine to form an ␣␣Ј␤ 2 , ␣ 2 ␤ 2 , or ␣Ј 2 ␤ 2 heterotetramer. The catalytic CK2 subunits ␣ and ␣Ј belong to the eukaryotic protein kinase superfamily. In contrast, the regulatory ␤ subunit is a unique protein encoded by a single gene in mammals (3) and does not belong to a known protein family.CK2␤ has several functions in the holoenzyme complex. Reconstitution experiments with recombinant purified subunits have demonstrated that CK2␤ modulates the activity of CK2. Depending on the substrate, CK2␤ activates or downregulates the activity of the catalytic subunit (24). CK2␤ also confers stability to the holoenzyme complex (18) and seems to mediate interaction with a number of substrates (19).The crystal structure elucidations of the isolated CK2␤ subunit (5) and of the holoenzyme complex (28) indicate that the ␤ subunit exists as a dimer and is the building block of the CK2 holoenzyme bridging the two catalytic subunits. The crystal structure is also consistent with the suggested flexible role of the ␤ subunit as a docking partner for other protein kinases and other interacting partners in the cell (28).Functional and biochemical studies have indicated that fractions of both the catalytic and regulatory subunits may exist separately. A population of CK2␣ that binds to protein phosphatase 2A is free of CK2␤ (16). Moreover, CK2␤ fractions devoid of the catalytic subunit, but probably involved in complexes with other prote...

Protein kinase CK2 is a tetramer composed of two α catalytic subunits and two β regulatory subunits. The structure of a C-terminal truncated form of the human β subunit has been determined by X-ray crystallography to 1.7 Å resolution. One dimer is observed in the asymmetric unit of the crystal. The most striking feature of the structure is the presence of a zinc finger mediating the dimerization. The monomer structure consists of two domains, one entirely α-helical and one including the zinc finger. The dimer has a crescent shape holding a highly acidic region at both ends. We propose that this acidic region is involved in the interactions with the polyamines and/or catalytic subunits. Interestingly, conserved amino acid residues among β subunit sequences are clustered along one linear ridge that wraps around the entire dimer. This feature suggests that protein partners may interact with the dimer through a stretch of residues in an extended conformation. Keywords: MAD method/protein kinase CK2/regulatory subunit/X-ray structure/zinc finger

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X-ray crystallography studies, as well as live-cell fluorescent imaging, have recently challenged the traditional view of protein kinase CK2. Unbalanced expression of catalytic and regulatory CK2 subunits has been observed in a variety of tissues and tumours. Thus the potential intersubunit flexibility suggested by these studies raises the likely prospect that the CK2 holoenzyme complex is subject to disassembly and reassembly. In the present paper, we show evidence for the reversible multimeric organization of the CK2 holoenzyme complex in vitro. We used a combination of site-directed mutagenesis, binding experiments and functional assays to show that, both in vitro and in vivo, only a small set of primary hydrophobic residues of CK2beta which contacts at the centre of the CK2alpha/CK2beta interface dominates affinity. The results indicate that a double mutation in CK2beta of amino acids Tyr188 and Phe190, which are complementary and fill up a hydrophobic pocket of CK2alpha, is the most disruptive to CK2alpha binding both in vitro and in living cells. Further characterization of hotspots in a cluster of hydrophobic amino acids centred around Tyr188-Phe190 led us to the structure-based design of small-peptide inhibitors. One conformationally constrained 11-mer peptide (Pc) represents a unique CK2beta-based small molecule that was particularly efficient (i) to antagonize the interaction between the CK2 subunits, (ii) to inhibit the assembly of the CK2 holoenzyme complex, and (iii) to strongly affect its substrate preference.

The presence of fibroblast growth factor-2 (FGF-2) in the nucleus has now been reported both in vitro and in vivo, but its nuclear functions are unknown. Here, we show that FGF-2 added to nuclear extract binds to protein kinase CK2 and nucleolin, a CK2 natural substrate. Added to baculovirus-infected cell extracts overexpressing CK2 or its isolated subunits, FGF-2 binds to the enzyme through its regulatory ␤ subunit. Using purified proteins, FGF-2 is shown to directly interact with CK2 and to stimulate CK2 activity toward nucleolin. Furthermore, a mitogenic-deficient FGF-2 mutant protein has an impaired ability to interact with CK2 and to stimulate CK2 activity using nucleolin as substrate. We propose that in growing cells, one function of nuclear FGF-2 is to modulate CK2 activity through binding to its regulatory ␤ subunit.The fibroblast growth factors (FGFs) 1 family includes nine polypeptides of which FGF-1 and FGF-2 (acidic and basic FGF) are prototype members (reviewed in Refs. 1 and 2). FGF-2 exerts its pleiotropic effects in cell growth and differentiation through a dual receptor system consisting of four different high-affinity transmembrane receptor tyrosine kinases and low-affinity binding sites corresponding to heparan sulfate proteoglycans (reviewed in Refs. 2 and 3). In addition, FGF-1 and FGF-2 are translocated from outside the cell to the nucleus (reviewed in Ref.2). Many other growth factors have been detected in the cell nucleus (reviewed in Refs. 4 and 5). In the case of Schwannomaderived growth factor and FGF-1, nuclear localization is necessary for mitogenic activity (6 -8). For FGF-2, nuclear translocation is correlated to cell proliferation, since it is no longer recovered in the nucleus of confluent cells (9, 10). Therefore, these data strongly suggest that FGF-2, as well as other growth factors, plays specific, but still unknown, nuclear functions in addition to classical signaling through cell surface receptors.We reported previously that in synchronized ABAE growing cells, a large increase of ribosomal genes transcription is tightly correlated to the nuclear translocation of FGF-2 and especially to an accumulation of the growth factor in the nucleolus. In contrast, in quiescent cells ribosomal genes transcription is 20-fold lower, and FGF-2 is exclusively found in the cytoplasm (9, 10). Upon addition of FGF-2 to nuclei of serum-starved cells, a 6-fold increase of ribosomal genes transcription is observed together with an increase in phosphorylation of nuclear proteins, essentially of nucleolin (9, 11); These data suggest that a nuclear function of FGF-2 could be to regulate ribosomal genes transcription by modulating the phosphorylation level of nuclear and nucleolar proteins as nucleolin. Nucleolin that is the major component of nucleolus is also a major substrate for protein kinase CK2 in rapidly proliferating tissues, and its phosphorylation level is correlated to the rate of ribosome biogenesis (reviewed in Ref. 12). CK2 is a serine/threonine protein kinase present in both the cyt...