The cystic fibrosis transmembrane conductance regulator (CFTR) is an ABC transporter family protein that acts as an ion channel. Mutations in CFTR cause the most common genetic disease in Caucasian populations, cystic fibrosis (CF). The high-resolution X-ray crystal structure of CFTR is now needed to aid the design of CFTR-targeted drugs for CF treatment and also to elucidate the molecular mechanisms behind its unique function as an ATP-ligand gated ion channel. However, until now, such structural studies have been severely limited by the lack of sufficient quantities of purified full-length CFTR protein. This thesis reports the novel over-expression and purification of milligram quantities of the chicken orthologue of CFTR protein from a Saccharomyces cerevisiae (yeast) expression system. A green fluorescent protein (GFP) tag fused to the CFTR C-terminus allowed rapid detection of the protein throughout the purification procedure. CFTR was expressed under an inducible promoter and appeared localised at, or near to, the plasma membrane, where it represented around 1 % of total protein after isolation in yeast microsomes. CFTR was solubilised from microsomes and purified using the detergents dodecylmaltoside (DDM) and lyso-phosphatidyl glycerol (LPG), by nickel affinity and size exclusion chromatography (SEC) to yield 1-2 mg of CFTR protein per 18 L fermentation culture. CFTR thermal stability was probed using fluorescent measurements to reveal a two-state cooperative unfolding transition around 40 °C for the DDM-purified protein, but no such transition was observed for the LPG-purified material. Light scattering and electron microscopy techniques revealed that, in LPG, CFTR was a homogenous population of monomeric particles around 60-Å in length that were soluble up to 8 mg/ml protein concentration. In DDM, CFTR was only soluble below 0.4 mg/ml protein concentration where is existed as a very heterogenous population of different sized amorphous particles, including dimeric particles around 180-Å in length. The DDM-purified CFTR protein could be crystallised as monomers in two-dimensional (2D) crystals with similar lattice parameters to 2D crystals of CFTR purified from mammalian cells. The ATPase activity of DDM-purified and reconstituted CFTR was similar to already published rates, at around 13 nmol Pi/min/mg integrated over a reaction time of 60 min, with an apparent affinity Km for ATP of 0.14 mM. Such a low ATPase rate compared to other ABC transporters may be due to the observed rapid run-down of activity with time and correlation with published CFTR channel gating kinetics. CFTR showed reduced ATPase activity after purification in LPG, suggesting a structural destabilisation in this detergent. The protocols presented here can now be used to provide sufficient quantities of purified CFTR protein for novel biochemical and biophysical studies. The tendency of CFTR to aggregate in a mild detergent remains a major obstacle towards 3D crystallisation trials and a high-resolution structure.

abstract: Viral protein U (Vpu) is a type-III integral membrane protein encoded by the Human Immunodeficiency Virus-1 (HIV- 1). It is expressed in infected host cells and plays vital roles in down-regulation of CD4 receptors in T cells and also in the budding of virions. But, there remain key structure/function questions regarding the mechanisms by which the Vpu protein contributes to HIV-1 pathogenesis and thus, it makes for an attractive target to study the structural attributes of this protein by elucidating a structural model with X-ray crystallography. This study describes a multi-pronged approach of heterologous over-expression of Vpu. The strategies of purification and biophysical/ biochemical characterization of the different versions of the protein to evaluate their potential for crystallization are also detailed. Furthermore, various strategies employed for the crystallization of Vpu by both in surfo and in cubo techniques, and the challenges faced towards the structural studies of this membrane protein by characterization with solution Nuclear magnetic resonance (NMR) spectroscopy are also described. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2016

The MdfA is a 410 amino acid-long integral membrane protein, which belongs to the Major Facilitator superfamily of multidrug transporters. It is predicted to consist of 12 transmembrane helices. MdfA uses the energy of the transmembrane proton gradient to pump a variety of toxic compounds out of E. coli cells. No high resolution structure of MdfA is available. The goals of this research project were to develop a practical method for purification of MdfA, to evaluate the feasibility of structure determination by Nuclear Magnetic Resonance (NMR) and X-ray crystallography, and to develop an activity assay for purified MdfA. To this end, MdfA, with a hexa-histidine tag attached to facilitate protein purification, was successfully expressed and incorporated into the cell membrane using an E. coli expression system. MdfA was extracted from the cell membrane with the detergents 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), n-dodecyl-B-D-maltoside (DDM), and 1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LMPG) and purified by affinity chromatography on nickel-nitrilotriacetic acid agarose. Pure protein was found to be monodisperse in DHPC, DDM and LMPG micelles. To achieve simple amino acid selective isotope labeling for high-resolution NMR studies, MdfA was expressed in a cell-free translation system. To determine if the purified protein was properly folded, 19F NMR experiments were carried out on 5-fluoro-tryptophan-labeled MdfA while titrating the MdfA substrates ethidium bromide and chloramphenicol into the fluoro-tryptophan-labeled MdfA sample. An activity assay was developed for MdfA incorporated into liposomes using the fluorescent dye 9-amino-6-chloro-2-methoxyacridine (ACMA) to detect proton translocation coupled to substrate transport. Results from both the 19F NMR and the transport activity assay indicated that the purified MdfA was properly folded and functional. NMR experiments with pure MdfA yielded spectra of insufficient quality for high-resolution structure determination but did indicate that structural studies of MdfA by NMR are feasible. Crystallization trials yielded crystals that are likely to contain protein and will serve as a starting point for further optimization of crystallization conditions for X-ray structure determination.

The MdfA is a 410 amino acid-long integral membrane protein, which belongs to the Major Facilitator superfamily of multidrug transporters. It is predicted to consist of 12 transmembrane helices. MdfA uses the energy of the transmembrane proton gradient to pump a variety of toxic compounds out of E. coli cells. No high resolution structure of MdfA is available. The goals of this research project were to develop a practical method for purification of MdfA, to evaluate the feasibility of structure determination by Nuclear Magnetic Resonance (NMR) and X-ray crystallography, and to develop an activity assay for purified MdfA. To this end, MdfA, with a hexa-histidine tag attached to facilitate protein purification, was successfully expressed and incorporated into the cell membrane using an E. coli expression system. MdfA was extracted from the cell membrane with the detergents 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), n-dodecyl-B-D-maltoside (DDM), and 1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LMPG) and purified by affinity chromatography on nickel-nitrilotriacetic acid agarose. Pure protein was found to be monodisperse in DHPC, DDM and LMPG micelles. To achieve simple amino acid selective isotope labeling for high-resolution NMR studies, MdfA was expressed in a cell-free translation system. To determine if the purified protein was properly folded, 19F NMR experiments were carried out on 5-fluoro-tryptophan-labeled MdfA while titrating the MdfA substrates ethidium bromide and chloramphenicol into the fluoro-tryptophan-labeled MdfA sample. An activity assay was developed for MdfA incorporated into liposomes using the fluorescent dye 9-amino-6-chloro-2-methoxyacridine (ACMA) to detect proton translocation coupled to substrate transport. Results from both the 19F NMR and the transport activity assay indicated that the purified MdfA was properly folded and functional. NMR experiments with pure MdfA yielded spectra of insufficient quality for high-resolution structure determination but did indicate that structural studies of MdfA by NMR are feasible. Crystallization trials yielded crystals that are likely to contain protein and will serve as a starting point for further optimization of crystallization conditions for X-ray structure determination.