In this thesis, the structure and stability of globular proteins adsorbed onto nanometer-sized hydrophilic silica particles were investigated using differential scanning calorimetry (DSC), hydrogen/deuterium exchange (HDX), and mass spectrometry (MS). The adsorption process itself was characterized with fluorescence and absorption spectroscopy and surface plasmon resonance (SPR). The combination of these methods offered a unique insight into adsorption-induced changes within proteins related to their adsorption characteristics. DSC contributed with thermodynamic information on the overall structural stability within the protein population. HDX in combination with MS contributed information on the structure and stability of adsorbed proteins with focus on changes within the secondary structure elements. In order to increase the structural resolution in this part of the investigation, proteolysis was performed prior to the MS analyzing step. Knowledge on the protein adsorption process was utilized in a practical approach called ligand fishing. In this approach, SPR was used to monitor the chip-based affinity purification of a protein with MS used for protein identification. Adsorption isotherms revealed that electrostatic interactions play an important role in the adsorption of proteins to hydrophilic surfaces. DSC investigation revealed that the thermal stability of proteins reduces with increasing electrostatic attraction between the protein and the surface and that this effect diminishes at higher surface coverage. The mass-increase due to exchange between protein hydrogen atoms and deuterium atoms in solution was investigated as a function of time. This gave insight into adsorption-induced changes in the structural stability of proteins. By combining DSC and HDX-MS, it was possible to differentiate between adsorption-induced changes in the secondary and tertiary structure. Additionally, if limited proteolysis was performed, the investigations gave insight into the orientation and protein segment specific changes in the stability of proteins adsorbed to silica surfaces. The adsorption of proteins to silica particles also provided the basis for a new experimental design that allows handling of minute amounts of proteins in a ligand fishing application, as used in the field of functional proteomics.

Gold nanoparticles exhibit remarkable optical properties and could prove useful in sensitive biosensing applications. Upon illumination gold nanoparticles produce localized surface plasmons, which influence nearby fluorophores and an enhancement in their fluorescence intensity can be observed. This property makes gold nanoparticles attractive for enhancing optical signals. In this project gold nanoparticles were functionalized with an antibody and immobilized to the surface of an existing biochip platform based on fluorescence. The aim was to investigate the possibility of obtaining an increased fluorescence signal from the gold nanoparticles. Two different conjugation procedures were investigated, direct physisorption and covalent attachment of the antibodies to the particles. Activity of bound antibodies was confirmed in both cases. The on-chip fluorescence intensity produced by the different conjugates was monitored by use a specialized fluorescence reader designed for point-of-care use. AFM and SEM were used to determine the surface concentration of particles. A correlation between the produced fluorescence intensity and the surface concentration could be seen.

The study and understanding of molecular interactions is fundamentally important in today's field of life sciences and there is a demand for well designed surfaces for biosensor applications. The biosensor has to be able to detect specific molecular interactions, while non-specific binding of other substances to the sensor surface should be kept to a minimum.                                                                                                                                                                                The objective of this master´s thesis was to design sensor surfaces based on self-assembled monolayers (SAMs) and evaluate their structural characteristics as well as their performance in Biacore systems. By mixing different oligo (ethylene glycol) terminated thiol compounds in the SAMs, the density of functional groups for bimolecular attachment could be controlled.  Structural characteristics of the SAMs were studied using Ellipsometry, Contact Angle Goniometry, IRAS and XPS. Surfaces showing promising results were examined further with Surface Plasmon Resonance in Biacore instruments.Mixed SAM surfaces with a tailored degree of functional COOH groups could be prepared. The surfaces showed promising characteristics in terms of stability, immobilization capacity of biomolecules, non-specific binding and kinetic assay performance, while further work needs to be dedicated to the improvement of their storage stability. In conclusion, the SAM based sensor surfaces studied in this thesis are interesting candidates for Biacore applications.

A novel process for the fabrication of Long Range Surface Plasmon Polariton (LRSPP) waveguide based biosensors is presented herein. The structure of the biosensor is comprised of Au stripe waveguide devices embedded in thick CYTOP claddings with a SiO2 solvent diffusion barrier and etch-stop layer. The SiO2 layer is introduced to improve the end quality of Au waveguide structures, which previously deformed during the deposit of the upper cladding process and to limit the over-etching of CYTOP to create micro-fluidic channels. The E-beam evaporation method is adapted to deposit a thin SiO2 on the bottom cladding of CYTOP. A new micro-fluidic design pattern is introduced. Micro-fluidic channels were created on selective Au waveguides through O2 plasma etching. The presented data and figures are refractive index measurements of different materials, thickness measurements, microscope images, and AFM images. Optical power cutback measurements were performed on fully CYTOP-cladded symmetric LRSPP waveguides. The end-fire coupling method was used to excite LRSPP modes with cleaved polarization maintaining (PM) fibre. The measured mode power attenuation (MPA) was 6.7 dB/mm after using index-matched liquid at input and output fibre-waveguide interfaces. The results were compared with the theoretical calculations and simulations. Poor coupling efficiency and scattering due to the SiO2 are suspected for off-target measurements.

Ubiquitylation is an indispensable post-translational modification system in eukaryotic cells that leads to the covalent attachment of a small ubiquitin (Ub) protein onto a target. The traditional and best-characterized role for ubiquitylation is a fundamental regulatory mechanism whereby target proteins are tagged with a characteristic Lys48-linked Ub chain that signals for their elimination through proteasomal degradation. Challenging this conventional wisdom is the finding that some ubiquitylated proteins are modified by Ub chains linked through Lys63, providing a molecular signal that is thought to be structurally and functionally distinct from Lys48-linked Ub chains. Of further interest and significance is that the Lys63-linked Ub chains are apparently synthesized through a novel biochemical mechanism employing a unique complex formed between a true Ub conjugating enzyme (E2), Ubc13, and an E2-variant (Uev), Mms2 (or Uev1A). The goal of this thesis was to employ structural and functional approaches in order to better characterize the Ubc13-Mms2 Lys63-linked Ub conjugation complex. <p>Error-free DNA damage tolerance (DDT) in the budding yeast is dependent on Lys63-linked Ub chains synthesized by Ubc13-Mms2 and thus provided the opportunity to experimentally test the function of the human UBC13 and MMS2 genes in a simple model organism. Human UBC13 and MMS2 were each shown to function in place of their yeast counterparts and in accordance, human Ubc13 was shown to physically interact with yeast Mms2, and vice versa. Two human MMS2 homologs were also tested and it was determined that UEV1A but not UEV1B can function in place of mms2 in yeast DDT. Physical interactions were observed between Ubc13 and Uev1A, but not between Ubc13 and Uev1B, suggesting that Ubc13-Uev complex formation is required for function. <p>In collaboration with a research group at the University of Alberta, crystal structure and NMR data were used to develop a mechanistic model for the conjugation of Lys63-linked Ub chains by the Ubc13-Mms2 heterodimer, whereby the special orientation of two Ub molecules facilitates a specific Ub-Ub linkage via Lys63. In order to help support the in vitro model and to determine how the Ubc13-Mms2 structure relates to biological function, I used a structure-based approach to direct the creation of point mutations within four key regions of the Ubc13-Mms2 heterodimer; the Ubc13 active-site, the Ubc13-E3 (Ub ligating enzyme) interface, the Mms2-Ub interface, and the Ubc13-Mms2 interface. <p>Underscoring the importance of the Ub conjugation by Ubc13-Mms2, a Ubc13-C87S active-site mutation was created that could bind to Mms2 but was unable to function in DDT. Regarding the Ubc13-E3 interface, a single Ubc13-M64A point mutation had a potent effect on disrupting Ubc13 function in DDT, as well as its physical interaction with Rad5, TRAF6, and CHFR. The results suggest that different RING finger E3s use the same Ubc13 surface to sequester the Ub conjugation activity of Ubc13-Mms2. Two human Mms2 mutations at Ser32 and Ile62, which are contained within the Mms2-Ub interface, were found to reduce the ability of Mms2 to bind Ub. When the corresponding yeast mutations are combined, a synergistic loss in DDT function is observed. The relative orientation of Ser32 and Ile62 suggests that the Mms2 and Tsg101 Uev families use different Uev surfaces to physically interact with Ub. A 200 ìM dissociation constant for the wild-type Mms2-Ub interaction was also determined. The systematic mutagenesis and testing of 14 Ubc13-Mms2 interface residues led to mutants with partial or complete disruption of binding and function. Using this data, a model involving the insertion of a specific Mms2-Phe residue into a unique Ubc13 hydrophobic pocket was created to explain the specificity of Mms2 for Ubc13, and not other E2s. In addition, the dissociation constant for the wild-type Ubc13-Mms2 heterodimer was determined to be approximately 50 nM. <p>The structural and functional studies strongly support the notion that Ubc13-Mms2 complex has the unique ability to conjugate Lys63-linked Ub chains. However, several reported instances of Lys63-linked Ub chains in vivo have not yet been attributed to Ubc13 or Mms2. To address the disparity I was able to demonstrate and map a physical interaction between Mms2 and Rsp5, an E3 implicated in Lys63-linked Ub conjugation. Surprisingly, it was found that MMS2 is not responsible for the RSP5-dependent Lys63-linked Ub conjugation of a plasma membrane protein. A possible explanation for the apparent paradox is presented.

A novel process for the fabrication of Long Range Surface Plasmon Polariton (LRSPP) waveguide based biosensors is presented herein. The structure of the biosensor is comprised of Au stripe waveguide devices embedded in thick CYTOP claddings with a SiO2 solvent diffusion barrier and etch-stop layer. The SiO2 layer is introduced to improve the end quality of Au waveguide structures, which previously deformed during the deposit of the upper cladding process and to limit the over-etching of CYTOP to create micro-fluidic channels. The E-beam evaporation method is adapted to deposit a thin SiO2 on the bottom cladding of CYTOP. A new micro-fluidic design pattern is introduced. Micro-fluidic channels were created on selective Au waveguides through O2 plasma etching. The presented data and figures are refractive index measurements of different materials, thickness measurements, microscope images, and AFM images. Optical power cutback measurements were performed on fully CYTOP-cladded symmetric LRSPP waveguides. The end-fire coupling method was used to excite LRSPP modes with cleaved polarization maintaining (PM) fibre. The measured mode power attenuation (MPA) was 6.7 dB/mm after using index-matched liquid at input and output fibre-waveguide interfaces. The results were compared with the theoretical calculations and simulations. Poor coupling efficiency and scattering due to the SiO2 are suspected for off-target measurements.

This thesis describes a number of novel experiments contributing to the understanding of protein adsorption from both a fundamental and applied perspective. The first three papers involve the use of the localized surface plasmon resonance of gold nanospheres to measure protein conformational dependencies during heat and acid denaturation. Thermal denaturation of BSA is shown to proceed differently depending on the size of nanosphere to which it is conjugated. Activation energies are extracted for thermal denaturing on nanoparticles. These energies decrease with decreasing radius of curvature. Under pH perturbation in the acid region, the multiple transition states of bulk BSA are suppressed, and only one apparent transition around pH 4 is evident. Smaller spheres (diameter < 20nm) do not exhibit any transition. A significant finding of all three studies is that the state and stability of BSA depends strongly upon local curvature. The last two papers investigate protein adsorption relevant to the biomaterial field. Investigation of protein adsorption to polyHEMA hydrogels is carried out using a quartz crystal microbalance. Single and mixed protein adsorption kinetics for BSA, lysozyme and lactoferrin are extracted and interpreted. Selected commercial cleaning solutions are shown to be no more effective than simple buffer solution. Examination of commercial lenses indicates that the morphology of adsorption is material dependent and that siloxane-based hydrogels only deposit low levels of protein. A unique fibril-like morphology is identified on galyfilcon A. Protein morphology is discussed in terms of bare lens morphology, roughness, and surface composition.

We introduce an approach to implement full coherent control on nanometer length scales. It is based on spatiotemporal modulation of the surface plasmon polariton (SPP) fields at the thick edge of a nanowedge. The SPP wavepackets propagating toward the sharp edge of this nanowedge are compressed and adiabatically concentrated at a nanofocus, forming an ultrashort pulse of local fields. The profile of the focused waveform as a function of time and one spatial dimension is completely coherently controlled. We establish the principal limits for the nanoconcentration of the terahertz (THz) radiation in metal/dielectric waveguides and determine their optimum shapes required for this nanoconcentration. We predict that the adiabatic compression of THz radiation from the initial spot size of vacuum wavelength R λ 300 μm 0 0 ≈ ≈ to the unprecedented final size of R = 100 − 250 nm can be achieved, while the THz radiation intensity is increased by a factor of 10 to 250. This THz energy nanoconcentration will not only improve the spatial resolution and increase the signal/noise ratio for THz imaging and spectroscopy, but in combination with the recently developed sources of powerful THz pulses, will allow the observation of nonlinear THz effects and a variety of nonlinear spectroscopies (such as two-dimensional spectroscopy), which are highly informative. This should find a wide spectrum of applications in science, engineering, biomedical research and environmental monitoring. We also develop a theory of the spoof plasmons propagating at the interface between a dielectric and a real conductor. The deviation from a perfect conductor is introduced through a finite skin depth. The possibilities of guiding and focusing of spoof plasmons are considered. Geometrical parameters of the structure are found which provide a good guiding of such modes. Moreover, the limit on the concentration by means of planar spoof plasmons in case of non-ideal metal is established. These properties of spoof plasmons are of great interest for THz technology.

We introduce an approach to implement full coherent control on nanometer length scales. It is based on spatiotemporal modulation of the surface plasmon polariton (SPP) fields at the thick edge of a nanowedge. The SPP wavepackets propagating toward the sharp edge of this nanowedge are compressed and adiabatically concentrated at a nanofocus, forming an ultrashort pulse of local fields. The profile of the focused waveform as a function of time and one spatial dimension is completely coherently controlled. We establish the principal limits for the nanoconcentration of the terahertz (THz) radiation in metal/dielectric waveguides and determine their optimum shapes required for this nanoconcentration. We predict that the adiabatic compression of THz radiation from the initial spot size of vacuum wavelength ~300 μm to the unprecedented final size of 100-250 nm can be achieved, while the THz radiation intensity is increased by a factor of 10 to 250. This THz energy nanoconcentration will not only improve the spatial resolution and increase the signal/noise ratio for THz imaging and spectroscopy, but in combination with the recently developed sources of powerful THz pulses, will allow the observation of nonlinear THz effects and a variety of nonlinear spectroscopies (such as two-dimensional spectroscopy), which are highly informative. This should find a wide spectrum of applications in science, engineering, biomedical research and environmental monitoring. We also develop a theory of the spoof plasmons propagating at the interface between a dielectric and a real conductor. The deviation from a perfect conductor is introduced through a finite skin depth. The possibilities of guiding and focusing of spoof plasmons are considered. Geometrical parameters of the structure are found which provide a good guiding of such modes. Moreover, the limit on the concentration by means of planar spoof plasmons in case of non-ideal metal is established. These properties of spoof plasmons are of great interest for THz technology.

A Mie-based code is developed for multilayer concentric spheres. The code is used in conjunction with a finite-element package to investigate the plasmonic and optical properties of micro- and nanostructures. For plasmonic nanostructures, gold-silica-gold multilayer nanoshells are computationally investigated. A plasmon hybridization theory is used to interpret the optical tunability. The interaction between the plasmon modes on the inner core and the outer shell results in dual resonances. The low-energy dipole mode is red-shifted by reducing the spacing ( i.e. , the intermediate silica layer) between the core and the shell. This extra tunability allows the plasmon resonance of a multilayer nanoshell to be tuned to the near-infrared region from a visible silica-gold nanoshell whose gold shell cannot be further reduced in thickness. For multilayer nanoshells with reduced geometrical symmetry ( i.e. , the inner core is offset from the center), modes of different orders interact. The mixed interaction introduces the dipolar (bright) characteristic into the higher-order (dark) modes and improves their coupling efficiency to the excitation light. The excitation of the dark modes attenuates and red-shifts the dipole mode and gives it higher-order characteristics. For non-plasmonic structures, simulations have demonstrated that multilayered structures can either reduce or enhance the scattering of light. By adding an anti-reflection layer to as microsphere made of a high-index material, the scattering force can be dramatically reduced. The reduced scattering allows optical trapping of high-index particles. Additionally, the improved trapping is not largely sensitive to the refractive index or the thickness of the coating. The technique has the practical potential to lower the requirement on the numerical aperture of the microscope objectives, making possible the integration of the imaging and optical trapping systems. While the anti-reflection coating reduces scattering, the photothermal bubble (PTB) generated by gold nanoparticles by and large enhances the scattering of light. Transient PTBs are generated by super-heating gold nanoparticles with short laser pulses. Mie-based simulations predict that the scattering of PTBs strongly depends on the transient environment immediately surrounding the nanoparticles. A scattering enhancement of two-to-four orders of magnitude from PBT is demonstrated from both calculations and experiments. Lastly, the near-field coupling between different plasmonie structures for surface-enhanced Raman scattering is investigated. A gold-coated silicon-germanium nanocone substrate has been fabricated and characterized. Finite-element simulations reveal that individual nanocones generate strong tip enhancement with axially polarized light ( i.e. , light polarized along the vertical axis of the nanocone) while the enhancement from transversely polarized light ( i.e. , light polarized in the plane of the substrate) is relatively weak. By simply filling the valleys between nanocones with plasmonic gold nanoparticles, the performance of the substrate is improved with in-plane excitation. Simulations reveal strong coupling between nanoparticles and adjacent nanocones with transverse exactions. An over one order-of-magnitude improvement has been experimentally observed.