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The design and creation of a functional metalloanti body is presented. A survey of metalloprotein structures was carried out to determine the common structural features of metal binding sites. Metal ligands were then introduced into hypervariable loop 11 of the anti-lysozyme antibody HyHEL-5 and the site comprehensively modelled. The final model was used as a basis for site-directed mutagenesis and mutant antibodies were produced using a Xenopus laevis oocyte expression system. Antigen binding studies showed the mutants to have an affinity for lysozyme equivalent to the parent antibody, while subsequent metal binding experiments have shown the new site to be capable of binding the transition metals cobalt, nickel, copper, zinc and cadmium. A method for the rapid prediction and design of metal binding sites in proteins is described. A protein structure is screened for the location of putative metal sites by template matching. After the introduction of suitable liganding residues, the metal binding potential at each site is evaluated using hydrophobicity contrast. A point representing the metal ion within a new site may be optimised with-respect-to the ligands using multidimensional minimisation. The method has been tested on known metalloprotein structures. It was routinely able to identify the metal binding sites and position a metal point in the site to within 0.6A of the actual metal ion.

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This project applies structure-activity relationship (SAR), structure-based and database mining approaches to study ligand-protein interactions. To support these studies, we have developed a relational database system called EDinburgh University Ligand Selection System (EDULISS 2.0) which stores the structure-data files of +5.5 million commercially available small molecules (+4.0 million are recognised as unique) and over 1,500 various calculated molecular properties (descriptors) for each compound. A user-friendly web-based interface for EDULISS 2.0 has been established and is available at http://eduliss.bch.ed.ac.uk/. We have utilised PubChem bioassay data from an NMR based screen assay for a human FKBP12 protein (PubChem AID: 608). A prediction model using a Logistic Regression approach was constructed to relate the assay result with a series of molecular descriptors. The model reveals 38 descriptors which are found to be good predictors. These are mainly 3D-based descriptors, however, the presence of some predictive functional groups is also found to give a positive contribution to the binding interaction. The application of a neural network technique called Self Organising Maps (SOMs) succeeded in visualising the similarity of the PubChem compounds based on the 38 descriptors and clustering the 36 % of active compounds (16 out of 44) in a cluster and discriminating them from 95 % of inactive compounds. We have developed a molecular descriptor called the Atomic Characteristic Distance (ACD) to profile the distribution of specified atom types in a compound. ACD has been implemented as a pharmacophore searching tool within EDULISS 2.0. A structure-based screen succeeded in finding inhibitors for pyruvate kinase and the ligand-protein complexes have been successfully crystallised. This study also discusses the interaction of metal-binding sites in metalloproteins. We developed a database system and web-based interface to store and apply geometrical information of these metal sites. The programme is called MEtal Sites in Proteins at Edinburgh UniverSity (MESPEUS; http://eduliss.bch.ed.ac.uk/MESPEUS/). MESPEUS is an exceptionally versatile tool for the collation and abstraction of data on a wide range of structural questions. As an example we carried out a survey using this database indicating that the most common protein types which contain Mg-OATP-phosphate site are transferases and the most common pattern is linkage through the β- and γ-phosphate groups.

Friedreich Ataxia (FRDA) is an autosomal recessive degenerative disorder. It is caused by an abnormal expansion of GAA trinucleotide repeats in the first intron of the gene encoding frataxin. Since rates of cell division have been linked to oxidative stress, we have examined several parameters of oxidative stress in a FRDA primary fibroblast cell line that had a dramatically different growth rate. In the FRDA fibroblasts, the high level of reactive oxygen species (ROS) indicated elevated oxidative stress. The elevated glutathione peroxidase (Gpx) activity in the ROS defense system may represent an adaptive response to the high oxidative stress. The increased mitochondrial membrane potential (MMP) likely contributed to increased oxidant production, which could be contributed by elevated ROS. This increased oxidant production might be responsible for increased rate of progression through the cell cycle.<p> Furthermore, the elevated oxidative stress is also associated with progressive neural pathology of FRDA. In FRDA, pathology is first seen in the dorsal root ganglia and the dorsal columns of the spinal cord. Due to the abnormal metal distribution seen in the FRDA spinal cord and medulla, we hypothesized that metal binding proteins were abnormally distributed in FRDA. In our FRDA samples, we observed the well established histopathology of FRDA and examined the distribution of some metal binding proteins (frataxin, ferritin and metallothionein) through immunohistochemistry. Our results showed demyelination and loss of axons in the degeneration areas of the two FRDA cases. In addition, we found that the metal binding proteins were abnormally distributed in the FRDA spinal cord and the medulla. The abnormal distributions of the metal binding proteins were characterized by low expressions of iron binding proteins, especially frataxin and cytosolic ferritin, and undetectable expression of the copper and zinc binding protein, metallothionein. In summary, the rapid cell growth is a feature of FRDA fibroblast cell lines. We also tested Gpx activity, measured oxidant levels and determined the MMP in a FRDA primary fibroblast cell line that had a dramatically fast growth rate. The FRDA histopathology studies showed the metal binding proteins including frataxin, ferritin and metallothionein were abnormally distributed in the spinal cord and the medulla.