Protein modelling and associated drug design

PhD ThesisPart one covers an investigation into the secondary and tertiary structure of the protein Xylanase found in Pseudomonasfluorescens subspecies cellulosa. Part two documents the Computer Aided Design of Novel Quinazoline Antifolates for the enzyme Thyrnidylate Synthase. Partone Mature Xylanase protein consists of two distinct regions - a cellulose binding domain and a catalytic region, A and B respectively. Computer modelling of tertiary structure from primary sequence and secondary turn information proved difficult in the absence of experimental X-ray crystal data. Consequently,a series of modified proteins bbased on the Xylanase were prepared by Recombinant DNA technology for extraction and purification. The modified proteins were to be used as a bench mark for quantitative and definitive calculation and detennination of the secondary structure of the xylanase. This was to provide an excellent reference point for theoretical modelling of tertiary structure. Part one of the Thesis documents Computer Modelling work and protein purification and extraction of the xylanase. Part two Thymidylate Synthase (TS) exists as dimer with a single active site in each subunit. It has been crystallised in two forms; a "reduced" (major), and "oxidised" (minor) form. The major form of TS contains dUMP covalently bound to cysteine in both active sites and in the presence of CB3717. One active site of the minor form contains dUMP non-covalently bound and in the presence of CB3717 while the other active site contains only inorganic phosphate and CB3717. The active site of TS is a large cavity that binds CB3717 into two possible confirmations. One is seen in the major form and one in the minor form. Part two of my research documents an investigation into enzyme/inhibitor interaction in TS and covers the Computer Aided Design of a series of inhibitors based on the knowledge of the TS active site. Several of these compounds have been put forward as target compounds for synthesis.SERC

Guanosine-borate hydrogels- Form and function

Due to their biocompatibility and stimuli-responsive nature, supramolecular hydrogels derived from natural products are attractive for a number of biomedical applications, including diagnostics, targeted drug delivery and tissue engineering. Nucleosides, the building blocks of nucleic acids, are desirable candidates for forming supramolecular gels as they readily engage in reversible, noncovalent interactions. Guanosine (G 1), in particular, is unique in that it has multiple faces for noncovalent interactions and can self-associate into stable higher-order assemblies, such as G4-quartets and G-quadruplexes. This self-assembly of G 1 and its derivatives into G4-quartets has long been known to induce hydrogelation. However, the requirement of excess salt and the propensity of G 1 to crystallize persist as limitations for G4-hydrogels. Thus, recent interest has focused on developing G4-hydrogels with improved lifetime stabilities and lower salt concentrations. The work described here focuses on a long-lived G4-hydrogel made from G 1 and 0.5 equiv. of KB(OH)4. Gelation occurs through the formation of guanosine-borate (GB) diesters and subsequent assembly into cation-templated G4•K+-quartets. The physical properties and stability of the GB hydrogel can be readily manipulated by varying the gelation components. For example, merely altering the identity of the cation drastically alters the gel’s physical properties. Namely, while GB hydrogels formed with K+ are self-supporting and robust, mixing G 1 with LiB(OH)4 results in a weak gel that readily dissociates upon physical agitation. Small molecules, such as cationic dyes and nucleosides, could be selectively incorporated into the GB hydrogel through reversible noncovalent and covalent interactions. One such dye and known G4-quartet binding ligand, thioflavin T (ThT) fluoresces in the presence of the GB hydrogel. The ThT fluorescence increases as a function of gelator concentration with a sharp increase correlating to the gel point. Thus, this ThT fluorescence assay is a new method for probing the formation of G4-hydrogels. Additionally, ThT acts as a molecular chaperone for Li+ GB hydrogelation. Substoichiometric amounts of ThT results in faster hydrogelation, increased gel strength and improved recovery of a hydrogel destroyed by external stress. Insights gained from this research have implications towards development of biomaterials, biomolecule sensing, and drug delivery

Enzymatic and Bioinspired Systems for Hydrogen Production

The extraordinary potential of hydrogen as a clean and sustainable fuel has sparked the interest of the scientific community to find environmentally friendly methods for its production. Biological catalysts are the most attractive solution, as they usually operate under mild conditions and do not produce carbon-containing byproducts. Hydrogenases promote reversible proton reduction to hydrogen in a variety of anoxic bacteria and algae, displaying unparallel catalytic performances. Attempts to use these sophisticated enzymes in scalable hydrogen production have been hampered by limitations associated with their production and stability. Inspired by nature, significant efforts have been made in the development of artificial systems able to promote the hydrogen evolution reaction, via either electrochemical or light-driven catalysis. Starting from small-molecule coordination compounds, peptide- and protein-based architectures have been constructed around the catalytic center with the aim of reproducing hydrogenase function into robust, efficient, and cost-effective catalysts. In this review, we first provide an overview of the structural and functional properties of hydrogenases, along with their integration in devices for hydrogen and energy production. Then, we describe the most recent advances in the development of homogeneous hydrogen evolution catalysts envisioned to mimic hydrogenases

Efficient model chemistries for peptides. I. Split-valence Gaussian basis sets and the heterolevel approximation in RHF and MP2

We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries (MCs) used are constructed as homo- and heterolevels involving possibly different RHF and MP2 calculations for the geometry and the energy. The basis sets used belong to a sample of 39 selected representants from Pople's split-valence families, ranging from the small 3-21G to the large 6-311++G(2df,2pd). The reference PES to which the rest are compared is the MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, is the more accurate PES of a dipeptide in the literature. The aim of the study presented is twofold: On the one hand, the evaluation of the influence of polarization and diffuse functions in the basis set, distinguishing between those placed at 1st-row atoms and those placed at hydrogens, as well as the effect of different contraction and valence splitting schemes. On the other hand, the investigation of the heterolevel assumption, which is defined here to be that which states that heterolevel MCs are more efficient than homolevel MCs. The heterolevel approximation is very commonly used in the literature, but it is seldom checked. As far as we know, the only tests for peptides or related systems, have been performed using a small number of conformers, and this is the first time that this potentially very economical approximation is tested in full PESs. In order to achieve these goals, all data sets have been compared and analyzed in a way which captures the nearness concept in the space of MCs.Comment: 54 pages, 16 figures, LaTeX, AMSTeX, Submitted to J. Comp. Che

Wet adhesion properties of oilseed proteins stimulated by chemical and physical interactions and bonding

Doctor of PhilosophyDepartment of Grain Science and IndustryX. Susan SunThe ecological and public health liabilities related with consuming petroleum resources have inspired the development of sustainable and environmental friendly materials. Plant protein, as a byproduct of oil extraction, has been identified as an economical biomaterial source and has previously demonstrated excellent potential for commercial use. Due to the intrinsic structure, protein-based materials are vulnerable to water and present relatively low wet mechanical properties. The purpose of this study focuses on increasing protein surface hydrophobicity through chemical modifications in order to improve wet mechanical strength. However, most of the water sensitive groups (WSG), such as amine, carboxyl, and hydroxyl groups, are also attributed to adhesion. Therefore, the goal of this research is to reduce water sensitive groups to an optimum level that the modified soy protein presents good wet adhesion and wet mechanical strength. In this research, we proposed two major approaches to reduce WSG: 1). By grafting hydrophobic chemicals onto the WSGs on protein surface; 2). By interacting hydrophobic chemicals with the WSGs. For grafting, undecylenic acid (UA), a castor oil derivative with 11-carbon chain with a carboxyl group at one end and naturally hydrophobic, was used. Carboxyl groups from UA reacted with amine groups from protein and converted amines into ester with hydrophobic chains grafting on protein surface. The successful grafting of UA onto soy protein isolate (SPI) was proved by both Infrared spectroscopy (IR) and ninhydrin test. Wood adhesive made from UA modified soy protein had reached the highest wet strength of 3.30 ± 0.24 MPa with fiber pulled out, which was 65% improvement than control soy protein. Grafting fatty acid chain was verified to improve soy protein water resistance. For interaction approach, soy oil with three fatty acid chains was used to modify soy protein. Soy oil was first modified into waterborne polyurethanes (WPU) to improve its compatibility and reactivity with aqueous protein. The main forces between WPU and protein were hydrogen bonding, hydrophobic interactions, and physical entanglement. Our results showed that WPU not only increased protein surface hydrophobicity with its fatty acid chains but also enhanced the three-dimensional network structure in WPU-SPI adhesives. WPU modification had increased wet adhesion strength up to 3.81 ± 0.34 MPa with fiber pulled out compared with 2.01 ± 0.46 MPa of SPI. Based on IR and thermal behavior changes observed by DSC, it was inferred that a new crosslinking network formed between WPU and SPI. To exam if the UA and WPU technologies developed using soy protein are suitable for other plant proteins, we selected camelina protein because camelina oil has superior functional properties for jet fuels and polymers. Like soy protein, camelina protein is also highly water sensitive. However, simply applied UA and WPU to camelina protein following the same methods used for soy proteins, we did not obtain the same good adhesion results compared to what we achieved with soy protein. After protein structure analysis, we realized that camelina protein is more compact in structure compared to soy protein that made it weak in both dry and wet adhesion strength. Therefore, for camelina protein, we unfolded its compact structure with Polymericamine epichlorohydrine (PAE) first to improve flexible chains with more adhesion groups for future reaction with UA or WPU. PAE with charged groups interacted camelina protein through electrostatic interaction and promoted protein unfolding to increase reactivity within protein subunits and between protein and wood cells. Therefore, the wet adhesion strength of camelina protein was improved from zero to 1.30 ± 0.23 MPa, which met the industrial standard for plywood adhesives in terms of adhesion strength. Then the wet adhesion strength of camelina protein was further improved after applying UA and WPU into the PAE modified camelina protein. In addition, we also found PAE unfolding significantly improved the dry adhesion strength of camelina protein from 2.39 ± 0.52 to 5.39 ± 0.50 MPa with 100% wood failure on two-layer wood test. Camelina meal which is even more economical than camelina protein was studied as wood adhesive. Through a combination of PAE and laccase modification method, the wet adhesion strength of camelina meal was improved as high as 1.04 ± 0.19MPa, which also met industrial standards for plywood adhesives. The results of this study had proven successful modification of oilseed protein to increase water resistance and wet mechanical strength. We have gained in-depth understanding of the relationship between protein structure and wet adhesion strength. The successful modification of plant proteins meeting the industrial needs for bio-adhesives will promote the development of eco-friendly and sustainable materials

Class pi glutathione S-transferase: unfolding and conformational stability in the absence and presence of G-site ligands

A thesis submitted to the Faculty of Science, University of the Witwatersrand, in fulfilment of the requirements for the degree of Doctor of Philosophy, Johannesburg, 1996The glutathione S-transferases (GST) are a supergene family of h0111o-or heterodimeric Phase II detoxification enzymes which catalyse the S-conjugation between glutathione and an electrophilic substrate. The active site can be divided into two adjacent functional regions; a highly specific Gssite for binding the physiological substrate glutathione and a nonspecific If-site for binding nonpolar electrophilic substrates. Unfolding of porcine class Pi isoenzyme (pGSTPl~l) was monitored under equilibrium conditions using different physicochemical parameters. The coincidence of unfolding curves obtained with functional and structural probes, the absence of thermodynamically stable intermediates such as a folded monomer, and the dependence of pGSTPl··l stability upon protein concentration, indicate a cooperative and concerted two-state unfolding transition between native dimeric pGSTPl-l and unfolded monomeric enzyme. Equilibrium and kinetic unfolding experiments employing tryptophan fluorescence and enzyme activity measurements were preformed to study the effect of ligand binding to the G-site on the unfolding and stability of the porcine class pi glutathione S-transferase against urea. The presence of glutathione caused a shift in the equilibrium-unfolding curves towards lower urea concentrations and enhanced the first-order rate constant for unfolding suggesting a destabilisation of the pGSTPl-l structure against urea. The presence of either glutathione sulphonate or S-hexylglutathione, however, produced the opposite effect in that their binding to the G-site appeared to exert a stabilising effect against urea. The binding of these glutathione analogues also reduced significantly the degree of cooperativity of unfolding indicating a possible change in the protein's unfolding pathway.MT201

Characterization of the linkage between xyloglucan and pectin in Arabidopsis thaliana culture cell walls

Xyloglucan, a major cross-linking glycan in the primary cell wall of most eudicots, has been considered to be independent of the pectic network. However, several groups have found strong evidence for a covalent attachment to pectin in walls of cell cultures. There has only been speculation on the nature of the linkage between xyloglucan and pectin. Isolation of a crosslinking fragment between pectin and xyloglucan has been elusive. The Mort lab has been working on this for thirty years with limited success. We isolated the pectin-associated xyloglucan from Arabidopsis thaliana suspension cell cultures using anion exchange chromatography. Endo-arabinanase was then used to release xyloglucan from the pectin. An arabinose residue was found in dissociated xyloglucan and found to be at the reducing end instead of sidechains of the released xyloglucan. A similar arabinose-containing linkage was also found in the pectin-unbound free xyloglucan, possibly existing as an intermediate of xyloglucan-pectin conjugation. Part of the pectin-associated xyloglucan was not covalently linked to the pectin. Such a tight non-covalent interaction survived strong alkali, heat, and concentrated salt elution. Debranching rhamnogalacturonan-I with exo-arabinosidase or heating at 80 degrees C could release much of the non-covalently bound xyloglucan. Much remains to be learned about the interactions between pectins and xyloglucans and their roles in cell wall function

Biochemical requirements for the maturation of mitochondrial c-type cytochromes

AbstractCytochromes c are metalloproteins that function in electron transfer reactions and contain a heme moiety covalently attached via thioether linkages between the co-factor and a CXXCH motif in the protein. Covalent attachment of the heme group occurs on the positive side of all energy-transducing membranes (bacterial periplasm, mitochondrial intermembrane space and thylakoid lumen) and requires minimally: 1) synthesis and translocation of the apocytochromes c and heme across at least one biological membrane, 2) reduction of apocytochromes c and heme and maintenance under a reduced form prior to 3) catalysis of the heme attachment reaction. Surprisingly, the conversion of apoforms of cytochromes c to their respective holoforms occurs through at least three different pathways (systems I, II and III). In this review, we detail the assembly process of soluble cytochrome c and membrane-bound cytochrome c1, the only two mitochondrial c-type cytochromes that function in respiration. Mitochondrial c-type cytochromes are matured in the intermembrane space via the system I or system III pathway, an intriguing finding considering that the biochemical requirements for cytochrome c maturation are believed to be common regardless of the energy-transducing membrane under study