Distinctive binding and structural properties of piscine transthyretin

AbstractThe thyroid hormone binding protein transthyretin (TTR) forms a macromolecular complex with the retinol-specific carrier retinol binding protein (RBP) in the blood of higher vertebrates. Piscine TTR is shown here to exhibit high binding affinity for L-thyroxine and negligible affinity for RBP. The 1.56 Å resolution X-ray structure of sea bream TTR, compared with that of human TTR, reveals a high degree of conservation of the thyroid hormone binding sites. In contrast, some amino acid differences in discrete regions of sea bream TTR appear to be responsible for the lack of protein–protein recognition, providing evidence for the crucial role played by a limited number of residues in the interaction between RBP and TTR. Overall, this study makes it possible to draw conclusions on evolutionary relationships for RBPs and TTRs of phylogenetically distant vertebrates

Crystal structure of the B subunit of Escherichia coli heat-labile enterotoxin carrying peptides with anti-herpes simplex virus type 1 activity.

Two chimeric proteins, consisting of the B subunit of Escherichia coli heat-labile enterotoxin with different peptides fused to the COOH-terminal ends, have been crystallized and their three-dimensional structure determined. The two extensions correspond to (a) a nonapeptide representing the COOH-terminal sequence of the small subunit of herpes simplex virus type 1 ribonucleotide reductase and (b) a 27-amino acid long peptide, corresponding to the COOH-terminal end of the catalytic subunit (POL) of DNA polymerase from the same virus. Both proteins crystallize in the P41212 space group with one pentameric molecule per asymmetric unit, corresponding to a solvent content of about 75%. The overall conformation of the B subunit pentamer in the two chimeric proteins, which consists of five identical polypeptide chains, is very similar to that in the native AB complex and conforms strictly to 5-fold symmetry. On the contrary, the peptide extensions are essentially disordered: in the case of the nonapeptide, only 5 and 6 amino acids were, respectively, positioned in two monomers, while in the other three only 2 residues are ordered. The extension is fully confined to the surface of the pentamer opposite to the face that interacts with the membrane and consequently it does not interfere with the ability of the B subunit to interact with membrane receptors. Moreover, the conformational flexibility of the two peptide extensions could be correlated to their propensity for proteolytic processing and consequent release of a biologically active molecule into cultured cells

Structural biology of Helicobacter pylori type IV secretion system

Helicobacter pylori chronically infects the gastric mucosa of millions of people annually worldwide: it has been estimated that over 50% of the world population carries this infection. H. pylori has been associated with the development of several diseases, like chronic gastritis, gastric and duodenal ulcer, gastric adenocarcinoma and mucosa-associated lymphoma [1-3]. The complete genome sequence of two different isolates of H. pylori (J99 and 26995) is known. The strains that contain a 37 kb foreign DNA region, called cag pathogenicity island (cag-PAI), cause the most severe form of virulence [4]. The cag-PAI encodes for a functional type IV secretion apparatus homologous to the VirB/D4 Type IV Secretion System (T4SS) of the plant pathogen Agrobacterium tumefaciens and other Gram-negative bacteria [5]. T4SSs are involved in conjugal DNA transfer, in the DNA delivery to (or uptake from) the environment, for instance the release of oncogenic DNA into infected plant cells by A. tumefaciens, or in the translocation of effector proteins [6,7]. The T4SS encoded by the cag-PAI of H. pylori is responsible for the translocation into the host cell of the protein CagA, a major antigenic virulence factor encoded within the cag-PAI. Once secreted into the gastric epithelial cells, CagA induces cellular modifications, such as elongation and spreading of host cells [8]. The aim of this structural genomic project is to determine the three-dimensional structure of most of the proteins encoded by the cag-PAI, a task that will allow to elucidate the function and the organization of the entire T4SS of such a relevant pathogenic bacterium [9]

Structural bases of protein kinase CK2 inhibition

Protein 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

Structural bases of protein kinase CK2 function and inhibition.

CK2, 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\u2014the catalytic subunit CK2\u3b1, the regulatory subunit CK2\u3b2, and the tetrameric \u3b12\u3b22 CK2 holoenzyme\u2014are analyzed, in the broader context of the eukaryotic protein kinase family. from such an analysis, the picture of an anomalous protein kinase, \u201cchallenging the canons\u201d 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

TAP score: torsion angle propensity normalization applied to local protein structure evaluation

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

Different orientations of low-molecular-weight fragments in the binding pocket of a BRD4 bromodomain

Bromodomains 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

Structural and functional determinants of protein kinase CK2 alpha: facts and open questions

Ser/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