Some studies on chlorocuprates

The work in this thesis is concerned with alkylammonium chlorocuprates and their solid solutions. The stoichiometries and structures of various chlorocuprate anions are considered in terms of the influence of the size and shape of the cation on the compounds formed. The determination of the structure of (Me3NH)3 Cu2 C17 by X-ray crystallography is described; it is unusual because it contains two distinct chlorocuprate anions, CUC14 2-tetrahedra and (CUC13-)n chains. The symmetry of the CuC142- tetrahedron is approximately C3v, and this is attributed to the effect of the packing of (CuC13-)n chains, together with interactions between CuC142- and the cations. The CuC12- 2- 2- 4 ion in this compound is replaceable by CoC14 and ZnC14 ' while the (CuC13-)n chains are not disturbed. This led to a consideration of the possible effects of replacing the Jahn-Teller distorted ion in simple tetrachlorocuprates by ions not affected by this distortion, and hence to the preparation of solid 'solutions A2 (M,M' )C14. The formation of solid solutions from a system of two salts having a common ion and a solvent is discussed, with particular emphasis on systems which deviate from ideal behaviour. The preparations of solid solutions (Me4N)2(Cu,Co)C14, (Me4N)2(Cu,Zn)C14 and Me4N)2(Co,Zn)Cl4 from ethanol and water are described, and related to the general conditions for solid solution formation. Solid solutions (Me3NH)3Cu(Cu,Co)C17 are also given. Differential scanning calorimetry has been used in an attempt to elucidate the nature of the thermal transitions in (Me4N)2MC14 and in the solid solutions. The crystal structures of (Me4N)2CuC14, and (Me4N)2(Cu,Co)C14 (Cu:Co = 1:1) have been determined, and compared with that of (Me4N)2CoC14' It has been . 2- 2- shown that CuC14 and CoC14 each retain their characteristic configuration in the solid solution, so that CuC142- is the more distorted, because of the Jahn-Teller effect

Structure and Chemical Inhibition of the Ret Tyrosine Kinase Domain.

The RET proto-oncogene encodes a receptor tyrosine kinase for the glial cell line-derived neurotrophic factor family of ligands. Loss-of-function mutations in RET are implicated in Hirschsprung disease, whereas activating mutations in RET are found in human cancers, including familial medullar thyroid carcinoma and multiple endocrine neoplasias 2A and 2B. We report here the biochemical characterization of the human RET tyrosine kinase domain and the structure determination of the non-phosphorylated and phosphorylated forms. Both structures adopt the same active kinase conformation competent to bind ATP and substrate and have a pre-organized activation loop conformation that is independent of phosphorylation status. In agreement with the structural data, enzyme kinetic data show that autophosphorylation produces only a modest increase in activity. Longer forms of RET containing the juxtamembrane domain and C-terminal tail exhibited similar kinetic behavior, implying that there is no cis-inhibitory mechanism within the RET intracellular domain. Our results suggest the existence of alternative inhibitory mechanisms, possibly in trans, for the autoregulation of RET kinase activity. We also present the structures of the RET tyrosine kinase domain bound to two inhibitors, the pyrazolopyrimidine PP1 and the clinically relevant 4-anilinoquinazoline ZD6474. These structures explain why certain multiple endocrine neoplasia 2-associated RET mutants found in patients are resistant to inhibition and form the basis for design of more effective inhibitors

Oncogenic RET Kinase domain mutations perturb the autophosphorylation trajectory by enhancing substrate presentation in trans

To decipher the molecular basis for RET kinase activation and oncogenic deregulation, we defined the temporal sequence of RET autophosphorylation by label-free quantitative mass spectrometry. Early autophosphorylation sites map to regions flanking the kinase domain core, while sites within the activation loop only form at later time points. Comparison with oncogenic RET kinase revealed that late autophosphorylation sites become phosphorylated much earlier than wild-type RET, which is due to a combination of an enhanced enzymatic activity, increased ATP affinity, and surprisingly, by providing a better intermolecular substrate. Structural analysis of oncogenic M918T and wild-type RET kinase domains reveal a cis-inhibitory mechanism involving tethering contacts between the glycine-rich loop, activation loop, and αC-helix. Tether mutations only affected substrate presentation but perturbed the autophosphorylation trajectory similar to oncogenic mutations. This study reveals an unappreciated role for oncogenic RET kinase mutations in promoting intermolecular autophosphorylation by enhancing substrate presentation

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Discovery of inhibitors of the pentein superfamily protein dimethylarginine dimethylaminohydrolase (DDAH), by virtual screening and hit analysis

Original article can be found at: http://www.sciencedirect.com/science/journal/0960894X--Copyright Elsevier Ltd. DOI : 10.1016/j.bmcl.2007.04.095Peer reviewe

Structure of mouse 7S NGF: a complex of nerve growth factor with four binding proteins

Background: Nerve growth factor (NGF) is a neurotrophic factor that promotes the differentiation and survival of certain populations of neurons in the central and peripheral nervous systems. 7S NGF is an α2β2γ2 complex in which the β-NGF dimer (the active neurotrophin) is associated with two α-NGF and two γ-NGF subunits, which belong to the glandular kallikrein family of serine proteinases. The γ-NGF subunit is an active serine proteinase capable of processing the precursor form of β-NGF, whereas α-NGF is an inactive serine proteinase. The structure of 7S NGF could be used as a starting point to design inhibitors that prevent NGF binding to its receptors, as a potential treatment of neurodegenerative diseases. Results: The crystal structure of 7S NGF shows that the two γ-NGF subunits make extensive interactions with each other around the twofold axis of the complex and have the C-terminal residues of the β-NGF subunits bound within their active sites. The ‘activation domain’ of each of the α-NGF subunits is in an inactive (zymogen-like) conformation and makes extensive interactions with the β-NGF dimer. The two zinc ions that stabilize the complex are located at the relatively small interfaces between the α-NGF and γ-NGF subunits. Conclusions: The structure of 7S NGF shows how the twofold axis of the central β-NGF dimer organizes the symmetry of this multisubunit growth factor complex. The extensive surface of β-NGF buried within the 7S complex explains the lack of neurotrophic activity observed for 7S NGF. The regions of the β-NGF dimer that contact the α-NGF subunits overlap with those known to engage NGF receptors. Two disulphide-linked loops on α-NGF make multiple interactions with β-NGF and suggest that it might be possible to design peptides that inhibit the binding of β-NGF to its receptors

Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition

The XPF/Mus81 structure-specific endonucleases cleave double-stranded DNA (dsDNA) within asymmetric branched DNA substrates and play an essential role in nucleotide excision repair, recombination and genome integrity. We report the structure of an archaeal XPF homodimer alone and bound to dsDNA. Superposition of these structures reveals a large domain movement upon binding DNA, indicating how the (HhH)(2) domain and the nuclease domain are coupled to allow the recognition of double-stranded/single-stranded DNA junctions. We identify two nonequivalent DNA-binding sites and propose a model in which XPF distorts the 3′ flap substrate in order to engage both binding sites and promote strand cleavage. The model rationalises published biochemical data and implies a novel role for the ERCC1 subunit of eukaryotic XPF complexes