1,721,050 research outputs found
Structural bases of protein kinase CK2 inhibition
No full textProtein kinase CK2 is involved in many fundamental aspects of normal cell life, but it is also able to establish favourable conditions for tumorigenesis. CK2 is elevated in various cancers, it is a potent suppressor of apoptosis, it strongly promotes cell survival, it strengthens the multi-drug resistant phenotype and can be considered a valuable drug target for cancer therapy. In this review, the structural bases of CK2 inhibition deduced from the analysis of crystal structures of CK2alpha-inhibitor complexes are presented and discussed. The best ATP-competitive inhibitors show an adequate hydrophobic character, an excellent shape complementarity with the unique active site of CK2, and the ability to establish polar interactions with both the hinge region and the positive electrostatic area near the conserved water W1 and the Lys68-Glu81 salt bridge. The state of the art of non-ATP-competitive inhibitors is also presented
Different orientations of low-molecular-weight fragments in the binding pocket of a BRD4 bromodomain
No full textBromodomains are involved in the regulation of chromatin architecture and transcription through the recognition of acetylated lysines in histones and other proteins. Many of them are considered to be relevant pharmacological targets for different pathologies. Three crystallographic structures of the N-terminal bromodomain of BRD4 in complex with low-molecular-weight fragments are presented. They show that similar molecules mimicking acetylated lysine bind the bromodomain with different orientations and exploit different interactions. It is also advised to avoid DMSO when searching for low-affinity fragments that interact with bromodomains since DMSO binds in the acetylated lysine-recognition pocket of BRD4
TAP score: torsion angle propensity normalization applied to local protein structure evaluation
Full text linkAbstract Background Experimentally determined protein structures may contain errors and require validation. Conformational criteria based on the Ramachandran plot are mainly used to distinguish between distorted and adequately refined models. While the readily available criteria are sufficient to detect totally wrong structures, establishing the more subtle differences between plausible structures remains more challenging. Results A new criterion, called TAP score, measuring local sequence to structure fitness based on torsion angle propensities normalized against the global minimum and maximum is introduced. It is shown to be more accurate than previous methods at estimating the validity of a protein model in terms of commonly used experimental quality parameters on two test sets representing the full PDB database and a subset of obsolete PDB structures. Highly selective TAP thresholds are derived to recognize over 90% of the top experimental structures in the absence of experimental information. Both a web server and an executable version of the TAP score are available at http://protein.cribi.unipd.it/tap/. Conclusion A novel procedure for energy normalization (TAP) has significantly improved the possibility to recognize the best experimental structures. It will allow the user to more reliably isolate problematic structures in the context of automated experimental structure determination.</p
Active Form of the Protein Kinase CK2 alpha(2)beta(2) holoenzyme Is a Strong Complex with Symmetric Architecture
No full textCK2 is a protein kinase essential for cell viability whose activity is altered in several cancers. Its mechanisms of regulation differ from those common to other eukaryotic protein kinases and are not entirely established yet. Here we present crystal structures of the monomeric form of the alpha(2)beta(2) holoenzyme that allow refining a formerly proposed structural model for activity regulation by oligomerization. Previous crystal structures of the CK2 holoenzyme show an asymmetric arrangement of the two alpha catalytic subunits around the obligate beta(2) regulatory subunits. Asymmetric alpha(2)beta(2) tetramers are organized in trimeric rings that correspond to inactive forms of the enzyme. The new crystal structures presented here reveal the symmetric architecture of the isolated active tetramers. The dimension and the nature of the alpha/beta interfaces configure the holoenzyme as a strong complex that does not spontaneously dissociate in solution, in accordance with the low dissociation constant (similar to 4 nM)
Structural Determinants of Protein Kinase CK2 Regulation by Autoinhibitory Polymerization
No full textCK2 is a Ser/Thr protein kinase essential for cell viability whose activity is anomalously high in several cancers. CK2 is a validated target for cancer therapy with one small molecule inhibitor in phase I clinical trials. This enzyme is not regulated by mechanisms common to other protein kinases, and how its activity is controlled is still unclear. We present a new crystal structure of the CK2 holoenzyme that supports an autoinhibitory mechanism of regulation whereby the β-subunit plays an essential role in the formation of inactive polymeric assemblies. The derived structural model of (down)regulation by aggregation contributes to the interpretation of biochemical and functional data and paves the way for new strategies in the modulation of CK2 activity and for the design of non-ATP-competitive inhibitors targeting the interaction between the α catalytic and the β regulatory subunits
A structural insight into CK2 inhibition
No full textThe acidophilic Ser/Thr protein kinase CK2 displays some unique properties such as high pleiotropicity and constitutive activity. CK2 is involved in many fundamental aspects of the normal cell life, for instance it promotes cell survival and enhances the tumour phenotype under special circumstances. This makes CK2 an appealing target for the development of inhibitors with pharmacological potential. Here we present an overview of our recent studies on inhibitors directed to the CK2 ATP-binding site whose distinctive features are highlighted by the ability to use both ATP and GTP as co-substrates and by its low susceptibility to staurosporine inhibition. We discuss the effects of the binding of different chemical families of fairly selective inhibitors with potency in the nanomolar or low micromolar range. An important common energetic contribution to the binding is due to the hydrophobic interaction with the apolar surface region of the CK2 binding cleft. The analysis of the known CK2 crystal structures reveals the presence of some highly conserved water molecules in this region. These waters reside near Lys68, in an area with a positive electrostatic potential that is able to attract and orient negatively charged ligands. The presence of this positive region and of two unique bulky residues, Ile66 and Ile174, responsible for the reduced dimension of the CK2 active site, play a critical role in determining ligand orientation and binding selectivity
Structural and functional determinants of protein kinase CK2 alpha: facts and open questions
No full textSer/Thr protein kinase CK2 is involved in several fundamental processes that regulate the cell life, such as cell cycle progression, gene expression, cell growth, and differentiation and embryogenesis. In various cancers, CK2 shows a markedly elevated activity that has been associated with conditions that favor the onset of the tumor phenotype. This prompts to numerous studies aimed at the identification of compounds that are able to inhibit the catalytic activity of this oncogenic kinase, in particular, of ATP-competitive inhibitors. The many available crystal structures indicate that this enzyme owns some regions of remarkable flexibility which were associated to important functional properties. Of particular relevance is the flexibility, unique among protein kinases, of the hinge region and the following helix alpha D. This study attempts to unveil the structural bases of this characteristic of CK2. We also analyze some controversial issues concerning the functional interpretation of structural data on maize and human CK2 and try to recognize what is reasonably established and what is still unclear about this enzyme. This analysis can be useful also to outline some principles at the basis of the development of effective ATP-competitive CK2 inhibitors
Structural bases of protein kinase CK2 function and inhibition.
No full textCK2, a member of the family of eukaryotic protein kinases (ePK), is ubiquitously present in eukaryotic cells and essential for their viability. With hundreds of sub- strates, the enzyme is implicated in many fundamental cellular processes. in particular, it is essential for cellular homeostasis: downregulation of CK2 leads to apoptosis, and abnormal over-activation has been found coupled to several diseases, in particular to cancer. the mechanism of regulation of CK2 is not firmly established yet; however, it is clear that it differs from those commonly utilized by other protein kinases. almost 15 years of intense crystallographic efforts, with dozens of crystal structures determined, have disclosed the structural bases of many key biochemical and functional properties of this enzyme. in this chapter, we review the progression in the structural biology of CK2 from the early discoveries to the current knowledge, giving our reasoned view of the state-of-art knowledge of the field. the basic structural features of the main CK2 entities—the catalytic subunit CK2α, the regulatory subunit CK2β, and the tetrameric α2β2 CK2 holoenzyme—are analyzed, in the broader context of the eukaryotic protein kinase family. from such an analysis, the picture of an anomalous protein kinase, “challenging the canons” proper of the vast majority of ePKs, clearly emerges. We further examine the issue of CK2 inhibition, a field fostered particularly by the involvement of CK2 in many pathologies and part of the wider topic of protein kinases inhibition, of particular interest for both the academia and pharmaceutical companies. Principles of CK2 inhibition by type I ATP-competitive inhibitors are now well established, and are reviewed and analyzed by means of several examples. the current state in the development of non-ATP-competitive inhibitors, which is very promising but still in an immature state, is also examined. alongside the critical review of the established knowledge, we finally address the still open questions, the perspectives, and the possible forthcoming developments in the field of CK2 structural biology
Synthesis of a heterotrimeric triple helical „mini-collagen“ with a C-terminal disulfide knot for induction of the correct register.
No full textInhibitors of protein kinase CK2: structural aspects
No full textProtein kinase CK2 is one of the most challenging members of the kinase superfamily. Although this protein has been the subject of intensive studies over the last 50 years, very little is known about its precise biological function and mode of regulation. The CK2 holoenzyme is composed of two catalytic α- and two regulatory β-subunits and is classified as an acidophilic Ser/Thr kinase. Unique properties of the catalytic α-subunit are its intrinsic activity and high pleiotropicity. CK2 is supposed to be involved in many fundamental aspects of the normal cell life as well as in degenerative processes that can lead to cancer or tumor pathologies. This makes CK2 an interesting target for the development of inhibitors with pharmacological perspectives. The inhibitors studied are directed to the CK2 ATP-binding site that, among the known kinases, carries some distinctive features as indicated by its ability to use both ATP and GTP as co-substrates and the low susceptiveness to staurosporine inhibition. On the basis of three-dimensional crystal structures, we describe and discuss the effects of the binding to CK2 of inhibitors with a potency in the low micromolar range belonging to different chemical families, i.e., benzotriazoles, anthraquinones, and quinazolinones. The overall structure of the protein is poorly affected by the binding of these small molecules. In the proximity of the binding site, the most affected residues are Asn118, His160, Met163, and those of the glycine-rich loop. Two of the inhibitors, namely tetrabromo-2-benzotriazolo (TBB) and the indoloquinazolinone IQA, display a significant selectivity among panels of tens of different kinases. An important common energetic contribution to the inhibitors' binding is ascribed to the hydrophobic interaction with the apolar surface region of the CK2 binding cleft. The shape and the reduced dimension of the CK2 active site in comparison with other kinases are essential in explaining the selectivity of these inhibitors as well as the anomalous low potency of staurosporine
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