<p>The study and understanding of Alzheimer’s disease on protein level is fundamentally important in the search for its treatment and there is a demand for proteins that can be used together with candidate drugs in crystallography trials. The refolding time reaching up to three weeks for beta-site APP cleaving enzyme 1 (BACE1), the proposed disease-generating protein, is presently not optimal and new protein constructs are needed. In attempts to shorten the refolding time the six cysteins in BACE1 were substituted to hydrophobic valine or alanine residues. The proteins, both wild type and mutant BACE1, were expressed in <em>Escherichia coli</em>, refolded for one week and purified by ion exchange chromatography and gel filtration. The final products were characterised by measuring stability, homogeneity and enzyme activity. There was significantly lower protein yield for the mutants compared to the wild type BACE1, indicating that generation of the disulphide bonds are important for correctly folded and stable BACE1. Also, it was found that the three different disulphide bonds are not equally important during refolding, with Cys₂₇₈-Cys₄₄₃being the most important and Cys₂₁₆-Cys₄₂₀ and Cys₃₃₀-Cys₃₈₀ being of less importance. The present work shows that one week of refolding is enough for a sufficient protein yield of wt BACE1 and that the current refolding time for wt BACE1 can be shortened. Furthermore the disulphide bridges in BACE1 are important for forming an active protein with correct fold.</p>

The study and understanding of Alzheimer’s disease on protein level is fundamentally important in the search for its treatment and there is a demand for proteins that can be used together with candidate drugs in crystallography trials. The refolding time reaching up to three weeks for beta-site APP cleaving enzyme 1 (BACE1), the proposed disease-generating protein, is presently not optimal and new protein constructs are needed. In attempts to shorten the refolding time the six cysteins in BACE1 were substituted to hydrophobic valine or alanine residues. The proteins, both wild type and mutant BACE1, were expressed in Escherichia coli, refolded for one week and purified by ion exchange chromatography and gel filtration. The final products were characterised by measuring stability, homogeneity and enzyme activity. There was significantly lower protein yield for the mutants compared to the wild type BACE1, indicating that generation of the disulphide bonds are important for correctly folded and stable BACE1. Also, it was found that the three different disulphide bonds are not equally important during refolding, with Cys278-Cys443 being the most important and Cys216-Cys420 and Cys330-Cys380 being of less importance. The present work shows that one week of refolding is enough for a sufficient protein yield of wt BACE1 and that the current refolding time for wt BACE1 can be shortened. Furthermore the disulphide bridges in BACE1 are important for forming an active protein with correct fold.

No description available.

The use of low-friction coatings on machine elements is steadily increasing, and they are expected to play an important role in the reduction of fuel consumption of future motorized vehicles. Many low-friction coatings function by transformation of the outermost coating layer into tribofilms, which then cover the coating surface and its counter surface. It is within these tribofilms that sliding takes place, and their properties largely determine the performance. The role of the coating is then not to provide low friction, but to supply support and constituents for the tribofilm. In this thesis, the formation of such tribofilms has been studied for a number of different low-friction coatings. The sensitivity of the tribofilm formation towards changes in the tribological system, such as increased surface roughness, varied surrounding atmosphere and reduced availability of the tribofilm constituents has been given special attention. For TaC/aC coatings, the formation of a functioning tribofilm was found to be a multi-step process, where wear fragments are formed, agglomerated, compacted and eventually stabilized into a dense film of fine grains. This formation is delayed by a moderate roughening of the coated surface. Coatings based on tungsten disulphide (WS2) are often able to provide exceptionally low friction, but their use is restricted by their poor mechanical properties and sensitivity to humidity. Large improvements in the mechanical properties can be achieved by addition of for example carbon, but the achievable hardness is still limited. When titanium was added to W-S-C coatings, a carbidic hard phase was formed, causing drastically increased hardness, with retained low friction. Titanium oxides in the tribofilms however caused the friction to be high initially and unstable in the long term. In a study of W-S-N coatings, the effects of humidity and oxygen were studied separately, and it was found that the detrimental role of oxygen is larger than often assumed. Low friction tribofilms may form by rearrangement of coating material, but also by tribochemical reactions between constituents of the coating and its counter surface. This was observed for Ti-C-S coatings, which formed WS2 tribofilms when sliding against tungsten counter surfaces, leading to dramatic friction reductions.

The thesis presents experimental studies of device characteristics and vibrational properties of atomic layer thin graphene and molybdenum disulphide (MoS2). We carried out Raman spectroscopic studies on field effect transistors (FET) fabricated from these materials to investigate the phonons renormalized by carrier doping thus giving quantitative information on electron-phonon coupling. Below, we furnish a synoptic presentation of our work on these systems. Chapter1: Introduction Chapter1, presents a detailed introduction of the systems studied in this the¬sis, namely single layer graphene (SLG), bilayer graphene (BLG) and single layer molybdenum disulphide (MoS2). We have mainly discussed their electronic and vibrational properties in the light of Raman spectroscopy. A review of the Raman studies on graphene layers is presented. Chapter2: Methodology and Experimental Techniques Chapter 2 starts with a description of Raman instrumentation. The steps for isolating graphene and MoS 2 flakes and the subsequent device fabrication procedures involving lithography are discussed in detail. A brief account of the top gated field effect transistor (FET) using solid polymer electrolyte is presented. Chapter3: Band gap opening in bilayer graphene and formation of p-n junction in top gated graphene transistors: Transport and Raman studies In Chapter3 the bilayer graphene (BLG) field effect transistor is fabricated in a dual gate configuration which enables us to control the energy band gap and the Fermi level independently. The gap in bilayer energy spectrum is observed through different values of the resistance maximum in the back gate sweep curves, each taken at a fixed top gate voltage. The gate capacitance of the polymer electrolyte is estimated from the experimental data to be 1.5μF/cm2 . The energy gap opened between the valence and conduction bands using this dual-gated geometry is es¬timated invoking a simple model which takes into account the screening of gate induced charges between the two layers. The presence of the controlled gap in the energy band structure along with the p-n junction creates a new possibility for the bilayer to be used as possible source of terahertz source. The formation of p-n junction along a bilayer graphene (BLG) channel is achieved in a electrolytically top gated BLG FET, where the drain-source voltage VDS across the channel is continuously varied at a fixed top gate voltage VT(VT>0). Three cases may arise as VDS is varied keeping VT fixed: (i) for VT-VDS0, the entire channel is doped with electron, (ii) for VT-VDS= 0, the drain end becomes depleted of carriers and kink in the IDS vs VDS curve appears, (iii) for VT-VDS « 0, carrier reversal takes place at the drain end, accumulation of holes starts taking place at the drain end while the source side is still doped with electrton. The verification of the spatial variation of carrier concentration in a similar top gated single layer graphene (SLG) FET device is done using spatially resolved Ra¬man spectroscopy. The signature 2D Raman band in a single layer graphene shows opposite trend when doped: 2D peak position decreases for electron doping while it increases for hole doping. On the other hand, the G mode response being symmetric in doping can act as a read-out for the carrier concentration. We monitor the peak position of the G and the 2D bands at different locations along the SLG FET channel. For a fixed top gate voltage V T , both G and the 2D band frequencies vary along the channel. For a positive VTsuch that VT-VDS= 0, the peak frequencies ωGand ω2DωG/2D occur at the undoped frequency (ωG/2D)n=0 near the drain end while the source end corresponds to non-zero concentration. When VT-VDS<0, Raman spectra from hole doped regions (drain end) in the channels show an blue-shift in ω2Dwhile from the electron doped regions (near source) ω2Dis softened. Chapter4: Mixing Of Mode Symmetries In Top Gated Bilayer And Multilayer Graphene Field Effect Devices In Chapter4, the effect of gating on a bilayer graphene is captured by using Raman spectroscopy which shows a mixing of different optical modes belonging to differ¬ent symmetries. The zone-center G phonon mode splits into a low frequency (Glow) and a high frequency (Ghigh) mode and the two modes show different dependence on doping. The two G bands show different trends with doping, implying different electron-phonon coupling. The frequency separation between the two sub-bands in¬creases with increased doping. The mode with higher frequency, termed as Ghigh, shows stiffening as we increase the doping whereas the other mode, Glow, shows softening for low electron doping and then hardening at higher doping. The mode splitting is explained in terms of mixing of zone-center in-plane optical phonons rep¬resenting in-phase and out-of-phase inter-layer atomic motions. The experimental results are combined with the theoretical predictions made using density functional theory by Gava et al.[PRB 80, 155422 (2009)]. Similar G band splitting is observed in the Raman spectra from multilayer graphene showing influence of stacking on the symmetry properties. Chapter5: Anomalous dispersion of D and 2D modes in graphene and doping dependence of 2D ′and 2D+G bands Chapter 5 consists of two parts: Part A titled “Doping dependent anomalous dispersion of D and 2D modes in graphene” describes the tunability of electron-phonon coupling (EPC) associated with the highest optical phonon branch (K-A) around the zone corner K using a top gated single layer graphene field effect transistor. Raman D and 2D modes originate from this branch and are dispersive with laser excitation energy. Since the EPC is proportional to the slope of the phonon branch, doping dependence of the D and 2D modes is carried out for different laser energies. The dispersion of the D mode decreases for both the electron and the hole doping, in agreement with the recent theory of Attaccalite et. al [Nano Letters, 10, 1172 (2010)]. In order to observe D-band in the SLG samples, low energy argon ion bombardment was carried out. The D peak positions for variable carrier concentration using top-gated FET geometry are determined for three laser energies, 1.96 eV, 2.41 eV and 2.54 eV. However, the dispersion of the 2D band as a function of doping shows an opposite trend. This most curious result is quantitatively explained us¬ing a fifth order process rather than the usual fourth order double resonant process usually considered for both the D and 2D modes. Part B titled “Raman spectral features of second order 2D’ and 2D+G modes in doped graphene transistor” deals with doping dependence of 2D’ and 2D+G bands in single layer graphene transistor. The phonon frequency blue shifts for the hole doping and whereas it red shifts for electron doping, similar to the behaviour of the 2D band. The linewidth of the 2D+G combination mode too follows the 2D trend increasing with doping while that of 2D’ mode remains invariant. Chapter6: New Raman modes in graphene layers using 2eV light Unique resonant Raman modes are identified at 1530 cm−1 and 1445 cm−1 in single, bi, tri and few layers graphene samples using 1.96 eV (633 nm) laser excitation energy (EL). These modes are absent in Raman spectra using 2.41 eV excitation energy. In addition, the defect-induced D band which is observed only from the edges of a pristine graphene sample, is observed from the entire sample region using E L = 1.96 eV. Raman images with peak frequencies centered at 1530 cm−1, 1445 cm−1 and D band are recorded to show their correlations. With 1.96 eV, we also observe a very clear splitting of the D mode with a separation of ∼32 cm−1, recently predicted in the context of armchair graphene nanoribbons due to trigonal warping effect for phonon dispersion. All these findings suggest a resonance condition at ∼2eVdue to homo-lumo gap of a defect in graphene energy band structure. Chapter7: Single and few layer MoS2: Resonant Raman and Phonon Renormalization Chapter 7 is divided into two parts. In Part A “Layer dependent Resonant Raman scattering of a few layer MoS2”, we discuss resonant Raman scattering from single, bi, four and seven layers MoS2. As bulk crystal of MoS2is thinned down to a few atomic layers, the indirect gap widens turning into a direct gap semiconductor with a band gap of 1.96 eV in its monolayer form. We perform Raman study from MoS 2 layers employing 1.96 eV laser excitation in order to achieve resonance condition. The prominent Raman modes for MoS 2 include first order E12g mode at ∼383 cm−1 and the A1gmode at ∼408 cm−1 which are observed under both non resonant and resonant conditions. A1gphonon involves the sulphur atomic vibration in opposite direction along the c axis (perpendicular to the basal plane) whereas for E12g mode, displacement of Mo and sulphur atoms are in the basal plane. With decreasing layer thickness, these two modes shifts in opposite direction, the E12g mode shows a blue shift of ∼2cm−1 while the A1gis red shifted by ∼4cm−1 . Under resonant condi¬tion, apart from E12g and A1gmodes, several new Raman spectral features, which are completely absent in bulk, are observed in single, bi and few layer spectra pointing out the importance of Raman characterization. New Raman mode attributed to the longitudinal acoustic mode belonging to the phonon branch at M along the Γ-M direction of the Brillouin zone is seen at ∼230 cm−1 for bi, four and seven layers. The most intense region of the spectrum around 460 cm−1 is characterized by layer dependent frequencies and spectral intensities with the band near 460 cm−1 becoming asymmetric as the sample thickness is increased. In the high frequency region between 510-630 cm−1, new bands are seen for bi, four and seven layers. In Part B titled “Symmetry-dependent phonon renormalization in monolayer MoS2transistor”, we show that in monolayer MoS2the two Raman-active phonons, A1g and E21 g, behave very differently as a function of doping induced by the top gate voltage in FET geometry. The FET achieves an on-off ratio of ∼ 105 for electron doping. We show that while E12g phonon is essentially unaffected, the A1gphonon is strongly influenced by the level of doping. We quantitatively understand our experimental results through the use of first-principles calculations to determine frequencies and electron-phonon coupling for both the phonons as a function of carrier concentration. We present symmetry arguments to explain why only A1g mode is renormalized significantly by doping. Our results bring out a quantitative under¬standing of electron-phonon interaction in single layer MoS2.

Neste trabalho realizou-se um estudo espectroscópico vibracional do dissulfeto de carbono, CS2, puro e em misturas binárias com diferentes solventes moleculares, a fim de investigar as interações soluto/soluto e soluto/solvente. Os solventes utilizados para esse estudo foram diclorometano (CH2Cl2), clorofórmio (CHCl3), clorofórmio deuterado (CDCl3), benzeno (C6H6) e tetracloreto de carbono (CCl4); e as técnicas utilizadas foram as espectroscopias Raman e infravermelho (IV). A análise das bandas Raman do CS2 que formam o dubleto de Fermi (v1-2v2) permite determinar uma série de valores empíricos, chamados de parâmetros de ressonância de Fermi, dentre os quais, o coeficiente de acoplamento de Fermi (W) foi o mais utilizado neste trabalho. Os diferentes valores de W nos diferentes meios são consequência das forças das interações intermoleculares existentes entre CS2/CS2 e CS2/solvente. Os experimentos demonstraram que os valores de W em todas as misturas binárias investigadas aumentam à medida que a fração molar de CS2 diminui. Isto sugere que quando o CS2 é solvatado por diferentes moléculas, há um aumento da anarmonicidade, dependendo do tipo de interação. A análise da banda atribuída ao modo de deformação angular do CS2, v2, realizada a partir dos espectros no infravermelho sugere que em misturas binárias existem dois regimes de solvatação na solução, uma referente às interações CS2/ CS2, onde as moléculas de CS2 estão preferencialmente solvatadas por moléculas de CS2 e outro regime de solvatação referente às interações CS2/solvente, onde CS2 está solvatado por moléculas do solvente em questão. / In this work has performed a vibrational spectroscopic investigation of carbon disulphide, CS2, neat and in binary mixtures with different molecular solvents, aiming at understanding the solute/solute and solute/solvent interactions. The solvents considered for this study were dichloromethane (CH2Cl2), chloroform (CHCl3), deuterated chloroform (CDCl3), benzene (C6H6) and carbon tetrachloride (CCl4); and the techniques used were Raman and infrared (IR) spectroscopies. The analysis of the Raman bands that compose the Fermi doublet (v1-2v2) allows the determination of a series of empirical values, including the coefficient of Fermi coupling (W), used along this work. The different values of W within the different solvents are consequence of the intermolecular forces between CS2/CS2 and CS2/solvent. The experimental data showed that the W values in all investigated binary mixtures increase as the CS2 molar fraction decreases. It suggests that when CS2 is solvated by different molecules, there is an increase of the anarmonicity, depending on the type of the interaction. The analysis of the band assigned to the CS2 bending mode, v2, performed from infrared spectra, suggests that in the binary mixtures there are two solvation regimes in solution, one related to the CS2/CS2 interactions, where the CS2 molecule is preferentially solvated by CS2 molecules, and one where the CS2 is solvated by the respective solvent molecules.

Neste trabalho realizou-se um estudo espectroscópico vibracional do dissulfeto de carbono, CS2, puro e em misturas binárias com diferentes solventes moleculares, a fim de investigar as interações soluto/soluto e soluto/solvente. Os solventes utilizados para esse estudo foram diclorometano (CH2Cl2), clorofórmio (CHCl3), clorofórmio deuterado (CDCl3), benzeno (C6H6) e tetracloreto de carbono (CCl4); e as técnicas utilizadas foram as espectroscopias Raman e infravermelho (IV). A análise das bandas Raman do CS2 que formam o dubleto de Fermi (v1-2v2) permite determinar uma série de valores empíricos, chamados de parâmetros de ressonância de Fermi, dentre os quais, o coeficiente de acoplamento de Fermi (W) foi o mais utilizado neste trabalho. Os diferentes valores de W nos diferentes meios são consequência das forças das interações intermoleculares existentes entre CS2/CS2 e CS2/solvente. Os experimentos demonstraram que os valores de W em todas as misturas binárias investigadas aumentam à medida que a fração molar de CS2 diminui. Isto sugere que quando o CS2 é solvatado por diferentes moléculas, há um aumento da anarmonicidade, dependendo do tipo de interação. A análise da banda atribuída ao modo de deformação angular do CS2, v2, realizada a partir dos espectros no infravermelho sugere que em misturas binárias existem dois regimes de solvatação na solução, uma referente às interações CS2/ CS2, onde as moléculas de CS2 estão preferencialmente solvatadas por moléculas de CS2 e outro regime de solvatação referente às interações CS2/solvente, onde CS2 está solvatado por moléculas do solvente em questão. / In this work has performed a vibrational spectroscopic investigation of carbon disulphide, CS2, neat and in binary mixtures with different molecular solvents, aiming at understanding the solute/solute and solute/solvent interactions. The solvents considered for this study were dichloromethane (CH2Cl2), chloroform (CHCl3), deuterated chloroform (CDCl3), benzene (C6H6) and carbon tetrachloride (CCl4); and the techniques used were Raman and infrared (IR) spectroscopies. The analysis of the Raman bands that compose the Fermi doublet (v1-2v2) allows the determination of a series of empirical values, including the coefficient of Fermi coupling (W), used along this work. The different values of W within the different solvents are consequence of the intermolecular forces between CS2/CS2 and CS2/solvent. The experimental data showed that the W values in all investigated binary mixtures increase as the CS2 molar fraction decreases. It suggests that when CS2 is solvated by different molecules, there is an increase of the anarmonicity, depending on the type of the interaction. The analysis of the band assigned to the CS2 bending mode, v2, performed from infrared spectra, suggests that in the binary mixtures there are two solvation regimes in solution, one related to the CS2/CS2 interactions, where the CS2 molecule is preferentially solvated by CS2 molecules, and one where the CS2 is solvated by the respective solvent molecules.

<p>Proteins are among the most abundant biological macromolecules. The cellular machinery is coupled to exact structural shape and properties of the more than 100 000 different proteins. Still, proteins can sometimes completely change their character and as a result trigger neuro degenerative disease. Exactly what happens is yet poorly understood but misfolding and aggregation leading to toxic gain of function is probable causes, i.e. the protein adopts new noxious properties. In 1993 the protein superoxide dismutase (SOD) was found to be associated with the neuro degenerative disease ALS. Up to date more than 100 mutations in SOD have been associated with ALS. However, the mutations are scattered all over the structure and no common denominator for the disease mechanism has been found. </p><p>This work has been focused on the molecular mechanism of the toxic gain-of - function of mutant SOD from the perspective of protein folding and structural stability. To facilitate the studies of SOD and its ALS associated mutations, an expression system resulting in increased copper content was developed. Coexpression with the copper chaperone for superoxide dismutase (yCCS) leads to increased expression levels, especially for the destabilised ALS mutants. Through thermodynamic studies, I show that with the exception of the most disruptive mutations the holo protein is only marginally destabilised, whereas all mutations show a pronounced destabilisation on the apo protein. Kinetic studies suggest further that the dimeric apoSOD folds via a three-state process where the dimerisation proceeds via a marginally stable monomer. The apoSOD monomer folds by a two-state process. The disulphide bond is not critical for the folding of the apoSOD monomer although it contributes significantly to its stability. Interestingly, in the absence of metals, reduction of the disulphide bond prevents the formation of the dimer. A mutation can affect the protein stability in various ways: either from destabilisation of the monomer (case 1), weakening of the dimer interface (case 2) or, in the worst case, from a combination of both (case 1+2). Thus, therapeutic strategies to prevent the noxious effects of mutant SOD must include both mechanisms. An important finding in this study is that we can see a correlation between the stability for each mutation and the mean survival time. This could be an opening in the development of therapeutic substances that counteract the defect in SOD upon mutation.</p>

Proteins are among the most abundant biological macromolecules. The cellular machinery is coupled to exact structural shape and properties of the more than 100 000 different proteins. Still, proteins can sometimes completely change their character and as a result trigger neuro degenerative disease. Exactly what happens is yet poorly understood but misfolding and aggregation leading to toxic gain of function is probable causes, i.e. the protein adopts new noxious properties. In 1993 the protein superoxide dismutase (SOD) was found to be associated with the neuro degenerative disease ALS. Up to date more than 100 mutations in SOD have been associated with ALS. However, the mutations are scattered all over the structure and no common denominator for the disease mechanism has been found. This work has been focused on the molecular mechanism of the toxic gain-of - function of mutant SOD from the perspective of protein folding and structural stability. To facilitate the studies of SOD and its ALS associated mutations, an expression system resulting in increased copper content was developed. Coexpression with the copper chaperone for superoxide dismutase (yCCS) leads to increased expression levels, especially for the destabilised ALS mutants. Through thermodynamic studies, I show that with the exception of the most disruptive mutations the holo protein is only marginally destabilised, whereas all mutations show a pronounced destabilisation on the apo protein. Kinetic studies suggest further that the dimeric apoSOD folds via a three-state process where the dimerisation proceeds via a marginally stable monomer. The apoSOD monomer folds by a two-state process. The disulphide bond is not critical for the folding of the apoSOD monomer although it contributes significantly to its stability. Interestingly, in the absence of metals, reduction of the disulphide bond prevents the formation of the dimer. A mutation can affect the protein stability in various ways: either from destabilisation of the monomer (case 1), weakening of the dimer interface (case 2) or, in the worst case, from a combination of both (case 1+2). Thus, therapeutic strategies to prevent the noxious effects of mutant SOD must include both mechanisms. An important finding in this study is that we can see a correlation between the stability for each mutation and the mean survival time. This could be an opening in the development of therapeutic substances that counteract the defect in SOD upon mutation.

ATP binding cassette (ABC) transporters constitute one of the largest families of transport proteins. The occurrence of multidrug resistance (MDR) in human cancer cells has been correlated with the over expression of human ABC, P-glycoprotein (Pgp). Streptomyces peucetius produces two anticancer agents, doxorubicin and daunorubicin, that belong to the anthracycline family of antibiotics. The organism is self-resistant to the potent effects of the antibiotics it produces due to the action of an efflux pump, DrrAB. Both Pgp and DrrAB carry out similar functions, but in two different cell types. An understanding of the bacterial drug transporter DrrAB is thus expected to help in obtaining a better understanding of the function and evolution of the multidrug transporter P-glycoprotein. In DrrAB, the catalytic and membrane domains are present on separate subunits, DrrA and DrrB respectively. How the catalytic ATP-binding domains and the membrane domains in transporters interact with each other, or how energy is transduced between them, is not well understood. We introduced several single cysteine substitutions in DrrB and then by using a cysteine to amine hetero-bifunctional cross-linker showed that DrrA interacts predominantly with the N-terminal cytoplasmic tail of DrrB. Within this region of DrrB, we also identified a sequence with similarities to the EAA motif found in importers of the ABC family of proteins, thus leading to the proposal that the EAA or the EAA-like motif may be involved in forming a generalized interface between the ABC and the TMD of both uptake and export systems. By using a combination of approaches, including point mutations and disulfide cross-linking analysis, we show here that the Q-loop region of DrrA plays an important role in dimerization of DrrA as well as in interactions with DrrB. Furthermore, we also show that the interaction of the Q-loop with the N-terminus of DrrB is involved in transmitting conformational changes between DrrA and DrrB. The scope of the present study further extends into identifying the factors involved in the biogenesis of the DrrAB pump. We have identified two accessory proteins namely, FtsH and GroEL that may be involved in proper folding and assembly of the transporter.