Influenza infections continue to be a global health concern that causing both seasonal epidemics and unpredictable pandemics. Hemagglutinin (HA) and Neuraminidase (NA) are the two major surface glycoproteins of influenza viruses, which are important for their host cell sialic acid (Sia) receptor binding and cleaving activities. Although numerous methods have been developed to study the HA and NA interactions with sialic acid, x-ray crystallography remained the only method to provide detailed information at atomic resolution. The aim of this study is to develop and evaluate a novel strategy for the investigation of influenza virus-receptor interactions, which is able to provide information about an interaction down to atomic resolution. Influenza virus-like particles (VLPs) containing HA and NA separately were developed and it was reported here for the first time that sole expression of NA in mammalian cell led to VLP formation. Characterization of these VLPs demonstrated that they are non-infectious, but morphologically and biochemically mimic the native viruses. Therefore the VLPs can be regarded as an ideal research model to study the HA-Sia interaction without the interference of NA, or vice versa. Saturation transfer difference (STD) NMR spectroscopy is a state-of-the-art technology to determine how a binding-ligand interacts with its target protein. Modification of STD-NMR methodology was performed to adapt the technique to influenza VLP system. HA-Sia interaction was investigated in great detail and group epitope mapping of the interacting ligands was performed by analyzing the STD-NMR spectra. The data obtained are in a good agreement with the well established crystallography technique, reflecting the reliability of the STD-NMR technology. Regarding the NA-Sia interaction, my data demonstrated that substrate-hydrolysis specificity of NA is dependent on the binding of NA to those ligands. In addition, using competition experiments with NA inhibitor, a secondary sialic acid binding site was detected. It is the first direct experimental evidence that confirms avian, seasonal human and human pandemic swine-origin influenza virus N1 neuraminidases exhibit a distinct secondary binding site. In conclusion, here I presented a novel interdisciplinary strategy using VLP and NMR technology to study the interaction of influenza virus with its receptor. This method is unique in its ability to provide detailed information on the HA and NA interactions with sialic acid leading to group epitope mapping of the binding ligands, which will help us not only to understand the virus tropism but also to define new therapeutic targets. / published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy

Influenza virus has long been a major threat to public health worldwide. The virus can be highly deadly because of antigenic shift. Since the H5N1 outbreak in Hong Kong in 1997, avian flu is regarded as the next pandemic threat. For combating the disease, it is essential to investigate more on the influenza virus, in particular H5N1. Nucleoprotein (NP) is a major component of the ribonucleoprotein complex (RNP) in the influenza virus. NP exhibits both structural and functional roles for influenza virus assembly and propagation and is involved in mediating the transcription-replication process. The NP of the virus binds the RNA genome and acts as a key adapter between the virus and the host cell. It therefore plays important roles and represents an attractive drug target. Recently, the X-ray structure of H5N1 NP was solved to a resolution of 3.3 Å , which provides valuable clues on how NP carries out its functions. However, the N-terminal 1-20 residues were not resolved in the H5N1 NP crystal structure. This N-terminal region is thought to contain a nuclear localization signal (NLS), a cellular splicing factor BAT1/UAP56 binding site, and a nuclear export signal. It has been suggested that the N-terminal NLS binds to importin (a cytosolic protein) for the nuclear import of NP. In the present study, the solution structure of H5N1 NP N-terminal peptide (NP20) in membrane mimetic solvent condition was determined using Circular Dichroism (CD) and Nuclear Magnetic Resonance (NMR) spectroscopies. The CD results show that NP20 adopted an α-helical conformation. The NMR data indicate that NP20 formed a single α-helix spanning from residues Gly5 to Gly16. Surface electrostatic potentials further showed that the NP20 peptide is amphipathic in nature, which may be important for its binding with importin. NMR titration experiments have been carried out between NP20 and importin. Addition of importin into the solution of NP20 peptide caused significant broadening of the NMR signals of NP20 and progressive changes of the chemical shifts of NOE cross-peaks at increasing importin concentration confirm that NP20 could bind with importin. Therefore, the present study supports that NP20 region is the binding site of importin mediating the import of NP into the host cell nucleus. In conclusion, the knowledge gained from this study provides a better understanding on the structure of NP20 and its interaction with the host importin protein, and may serve as a template for the development of novel antiviral drug targeting NP with improved therapeutic index. / published_or_final_version / Chemistry / Master / Master of Philosophy

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Calmodulin (CaM) is a highly conserved protein able to bind Ca2+. When Ca2+ is bound the protein can bind and activate further proteins with several individual functions. CaM switches to a more open conformation when Ca2+-bound and is able to do so at a high rate. Little is known about the conformational switches between apo and Ca2+-bound states. A hypothesis suggests that protonation/deprotonation of a histidine side-chain is part of the answer and thus the dynamics of CaM would be pH dependent. This was further investigated in this thesis. Methods to carry out the project included protein expression of isotope labelled CaM-TR2C E140Q, standard protein purification and protein adapted Nuclear Magnetic Resonance (NMR) spectroscopy. The results suggest that CaM-TR2C E140Q is likely to depend on pH and that histidine 107 (H107) may have a central role in the conformational changes observed. At lower pH it was also suggested that CaM-TR2C E140Q obtained a more open conformation with weakened intramolecular interactions and that the tertiary structure of CaM-TR2C E140Q may have been disrupted. / Calmodulin (CaM) är ett, till hög grad konserverat protein med möjlighet att binda in Ca2+. Då Ca2+ är bundet kan proteinet binda och aktivera ytterligare protein med olika enskilda funktioner. CaM byter med hög hastighet till en mer öppen konformation då Ca2+ binder. Lite vetskap finns kring hur konformationsändringarna mellan apo-form och Ca2+-bunden form går till. En hypotes föreslår att protonering/deprotonering av en histidin-sidokedja kan vara en del av svaret och att CaMs dynamik därför bör vara beroende av pH. Detta undersöktes vidare i detta examensarbete. Metoder som användes för att genomföra projektet inkluderar proteinuttryck av isotopinmärkt CaM-TR2C E140Q, standardiserad proteinrening och proteinanpassad kärnmagnetisk resonans (NMR) spektroskopi. Resultaten föreslår att konformationsändringarna av CaM-TR2C E140Q troligen är pH-beroende och att histidin 107 (H107) kan ha en central roll vid dessa ändringar. Vid lägre pH föreslås att CaM-TR2C E140Q antar en mer öppen konformation med försvagade intramolekylära interaktioner och att tertiärstrukturen av CaM-TR2C E140Q kan ha blivit upplöst.

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In this dissertation I explain the theoretical and experimental details of nuclear magnetic resonance force microscopy (NMRFM). I report the data that I have collected on ammonium hexafluorophosphate at room temperature using NMRFM. This experiment measured cantilever deflection as a function of applied magnetic field. I also report on the progress of a new dynamical room-temperature NMRFM microscope. I describe the new probe and its advantages over the previous generation probe and I show the current calibration measurements. / text

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

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