The Amyloid beta peptide (Ab) is related to Alzheimer’s disease and is suggested to be the molecular pathogenic species of the disease, probably through the neurotoxic effect of Ab oligomers. Here the results from biophysical studies of Ab and fragments thereof, are presented. Pulsed field gradient NMR diffusion experiments show that Ab exists mainly as an unfolded monomer. In addition, the hydrodynamic radius of Ab suggests that Ab has residual secondary structure propensities. CD experiments reveal that Ab has a high propensity to adopt a polyproline type II (PII) helix at low temperature. NMR diffusion measurements as well as the 3JHNH values show that increasing the temperature from 4 C induces a structure transition from PII propensity to a beta strand propensity around 15 C and to a random coil conformation at higher temperature. The small hydrodynamic radius at low temperature may be explained by the presence of a population of a hairpin conformation as was suggested by MD simulations. 15N relaxation and secondary chemical shifts suggest that Ab consists of 6 structural regions, two regions with high PII propensity are separated by a highly mobile region located in the N-terminal part of the peptide. In the C-terminal part two regions with a propensity to adopt b-strand are located, separated by a mobile region. The structural propensities of soluble monomeric Ab agree well with the structure of the peptide in fibril aggregates as well as in SDS micelles. Ab binds zinc specifically and with high affinity. This interaction was studied using heteronuclear correlation experiments. The metal ligands were determined to be three histidines, 6,13 and 14 and the N-terminus. The Ab peptide also binds b-cyclodextrin and the combined use of NMR diffusion experiments and induced chemical shifts show that Ab has at least two binding sites for b-cyclodextrin, and the dissociation constants of these binding sites were determined.

In natural oxygen-producing photosynthesis solar energy is stored as chemical energy, in carbohydrates, fats and amino acids, using water as electron source. The large transmembrane protein complex, PSII, is the key enzyme in the light-driven reactions. Water oxidation is accomplished by a triad in PSII in which the Mn-cluster plays an important role. In the artificial photosynthetic system, nature’s photosynthesis will be mimicked such that hydrogen, a sustainable energy source, can be produced from solar energy and water alone. Since water oxidiation requires the catalytic activity of a Mn-cluster in photosynthesis, different artificially constructed manganese complexes are investigated. The dinuclear ([Mn2(II,III)L(µ-OAc)2]ClO4), where L is the X-anion of 2-(N,N-Bis(2-methylpyridyl)aminomethyl)-6-(N-(3,5-ditert-butylbenzyl-2-hydroxy)-N-(pyridylmethyl)aminomethyl)-4-methylphenol, an unsymmetric ligand with two coordinating phenolate groups, has been studied. The two Mn-ions are linked via a mono-µ-oxo bridge and two acetate ligands. Q-band Electron Paramagnetic Resonance was conducted on the Unsymmetric Mn2(II,III) Complex. Aquired results show that the complex has a 2600 Gauss broad signal (11 400-14 000 Gauss) with 14-17 lines at g~2 and hyperfines of 120 Gauss. This is consistent with previous X-band studies. Q-band spectra of the Unsymmetric Mn(II,III) display increased hyperfine resolution compared to Qband spectra of the symmetric complex, Mn2(bpmp)(µ-OAC)2. This is noticeable since Unsymmetric Mn2(II,III) and Mn2 (bpmp)(µ-OAC)2 partly overlap in low-frequency experiments (X-band EPR). Further investigations are yet to be expected. Nevertheless, the conducted thesis study provides important knowledge in the futuristic goal of building an artificial super-complex.

Implants are commonly used for orthopaedic and dental applications. There is however a problem with implants; they have a tendency to get loose after 10-15 years of usage. Bone that is not used will get weaker; this can be concluded from studies of people being immobilised or in microgravity. When an implant is put into bone, the surrounding bone does not experience any deformation and it will resorb. This is called stress shielding. Finally the implant will get loose. To avoid this problem we want to give electrical stimulation to the bone surrounding the implant. Electricity has been used before to stimulate bone, and it has been shown that immobilised bone can almost be maintained by using electric stimulation. Piezoelectricity is a property of certain materials that make them generate electricity when they are deformed. When an implant is coated with a piezoelectric material, electrical stimulation can be achieved for the surrounding bone that is stress shielded. In this diploma work, a test-equipment is built to stimulate cells. Cells will be grown on a piezoelectric plate that is bent by the test-equipment. Thus, the cells will be stimulated by both mechanical stress and electric potential since the piezoelectric material generates electricity when it is deformed. Piezoelectric samples and culture wells suitable for bending applications are prepared and tested in the equipment. Some initial cell growth experiments have been performed to see that the material is suitable for cell growth.

<p>Microcontact printing using elastomeric stamps is a technique used in finding new and efficient ways to produce biodetection chips. Microcontact printed, with poly(dimetylslioxane) (PDMS) stamps, patterns of antibodies have been evaluated using fluorescence microscopy, imaging ellipsometry and atomic force microscopy. Fluorescent conjugated polyelectrolytes form non-covalent molecular complexes with Immunoglobulin-γ type antibodies, antigen binding to the tagged antibody result in spectroscopic shifts. Four different conjugated polyelectrolytes (POWT, POMT, PTT, PTAA) in complex with human serum albumin antibodies (aHSA) have been tested with fluorescence spectroscopy. Complexes of POWT and aHSA gave rise to thelargest wavelength shift when exposed to human serum albumin.</p><p>Several types of commercially available fluorescent antibodies and antigens were used to test the specificity of microcontact printed antibodies to different antigen solutions. Using fluorescence microscopy it could not be shown that printed antibody patterns promote specific adsorption of corresponding antigen. It is proposed however that changed surface characteristics of the substrate due to PDMS residues transferred during printing is the main driving force behind antigen adsorption.</p><p>POMT - poly (3-[(s)-5-amino-5-methoxylcarboxyl-3-oxapentyl]-2,5-thiophenylenehydrochloride)</p><p>POWT - poly (3-(s)-5-amino-5-carboxyl-3-oxapentyl]-2,5-thiophenylenehydrochloride)</p><p>PTAA - polytiophene acetic acid</p><p>PTT - poly (3-[2,5,8-trioxanonyl] thiophene)</p>

Microcontact printing using elastomeric stamps is a technique used in finding new and efficient ways to produce biodetection chips. Microcontact printed, with poly(dimetylslioxane) (PDMS) stamps, patterns of antibodies have been evaluated using fluorescence microscopy, imaging ellipsometry and atomic force microscopy. Fluorescent conjugated polyelectrolytes form non-covalent molecular complexes with Immunoglobulin-γ type antibodies, antigen binding to the tagged antibody result in spectroscopic shifts. Four different conjugated polyelectrolytes (POWT, POMT, PTT, PTAA) in complex with human serum albumin antibodies (aHSA) have been tested with fluorescence spectroscopy. Complexes of POWT and aHSA gave rise to thelargest wavelength shift when exposed to human serum albumin. Several types of commercially available fluorescent antibodies and antigens were used to test the specificity of microcontact printed antibodies to different antigen solutions. Using fluorescence microscopy it could not be shown that printed antibody patterns promote specific adsorption of corresponding antigen. It is proposed however that changed surface characteristics of the substrate due to PDMS residues transferred during printing is the main driving force behind antigen adsorption. POMT - poly (3-[(s)-5-amino-5-methoxylcarboxyl-3-oxapentyl]-2,5-thiophenylenehydrochloride) POWT - poly (3-(s)-5-amino-5-carboxyl-3-oxapentyl]-2,5-thiophenylenehydrochloride) PTAA - polytiophene acetic acid PTT - poly (3-[2,5,8-trioxanonyl] thiophene)

In this thesis, the folding process of the de novo designed polypeptide chignolin was elucidated through atomic-scale Molecular Dynamics (MD) computer simulations. In a series of long timescale and replica exchange MD simulations, chignolin’s folding and unfolding was observed numerous times and the native state was identified from the computed Gibbs free-energy landscape. The rate of the self-assembly process was predicted from the replica exchange data through a novel algorithm and the structural fluctuations of an enzyme, lysozyme, were analyzed. DNA’s structural flexibility was investigated through experimental structure determination methods in the liquid and gas phase. DNA nanostructures could be maintained in a flat geometry when attached to an electrostatically charged, atomically flat surface and imaged in solution with an Atomic Force Microscope. Free in solution under otherwise identical conditions, the origami exhibited substantial compaction, as revealed by small angle X-ray scattering. This condensation was even more extensive in the gas phase. Protein folding is highly reproducible. It can rapidly lead to a stable state, which undergoes moderate fluctuations, at least for small structures. DNA maintains extensive structural flexibility, even when folded into large DNA origami. One may reflect upon the functional roles of proteins and DNA as a consequence of their atomic-level structural flexibility. DNA, biology’s information carrier, is very flexible and malleable, adopting to ever new conformations. Proteins, nature’s machines, faithfully adopt highly reproducible shapes to perform life’s functions robotically.

The amyloid-β peptide is an amphiphilic peptide that exhibits self-aggregating properties, forming the amyloid fibrils that can be found in the brains of Alzheimer patients. Today it is believed that it is the soluble Aβ oligomers rather than the mature fibrils that are the main neurotoxic species. These small peptide assemblies are known to associate with lipid membranes and form pores that can transport Ca2+ into the cell, which in part could be responsible for their neurotoxic properties. However, most biophysical methods that have been developed to study Aβ target either the monomer or the mature fibrils, and not the low abundance and polydisperse oligomers. In this work, a soft ionization mass spectrometry method that retains non-covalent oligomer interactions in the gas phase has been developed. Using this method, monomeric and oligomeric Aβ (1-40) from dimers up to octamers, except heptamers, were detected in vitro. It was also possible to detect and study the effects of peptide modifications such as methionine-35 oxidation. As mass spectrometry is a non-averaging technique the aggregation kinetics for reduced and oxidized peptides are followed simultaneously, and the results showed that the oxidized form of Aβ(1-40) aggregates slower and forms lower amounts of soluble oligomers than the reduced form. Additionally, Aβ(1-40) interactions with zwitterionic SB3-14 detergent micelles were studied in the gas phase, and it was demonstrated that Aβ-micelle complexes can survive in the mass spectrometer and be identified. Detergent head group charges seem to be essential for peptide-micelle interaction, both in the gas phase and in solution as no structure induction is observed upon addition of the non-ionic detergent DDM. Overall gas phase and solution properties agree well, which is encouraging for future gas phase studies of Aβ interactions with membrane mimetics.

Alzheimer’s disease (AD) is a devastating neurodegenerative disease that affect millions of people worldwide. Aggregation of Amyloid-β (Aβ) monomers create toxic oligomers that can interact with cellular membranes and disturb cellular functions, resulting in cell death and neurological dysfunction. Increased levels of oxidative stress have been shown in the brains of AD patients, something that besides the obvious cell and tissue toxicity, also favors the amyloidogenic pathway and generates more Aβ monomers. Here we show that Edaravone, a free radical scavenger can affect the aggregation rate of different lengths of Aβ. We show that Aβ-40 that is more commonly found in vivo aggregates faster with addition of Edaravone, while Aβ-42 aggregates slower or not at all. These findings add up to previous findings where free radical scavengers and antioxidants such as Edaravone have been suggested as a potential treatment in Alzheimer’s disease.

Existing cancer treatments, while perhaps proving effective in being destructive of tumours, can also cause significant damage to surrounding healthy tissue. This can cause severe side effects which one would wish to avoid. In order to improve the localisation of the inflicted damage in the tumours, as well as increase the actual damage itself when using X-rays as therapy, the potential effect of attaching a high Z atom into the DNA of the cancer cells as markers or antenna for the X-rays is investigated. The larger size and higher absorption cross section of the iodine makes it favourable for this purpose, as it becomes more sensitive to the X-rays. This has been studied for a single stranded DNA molecule which is three bases long, loaded with iodine, using quantum mechanical/molecular dynamical simulations in SIESTA. The purpose was to study in what way the presence of the iodine affected and possibly increased the fragmentation of the molecule due to ionisation of the 2p orbital and the following Auger cascade, as well as use the results to better interpret mass over charge spectra from experiments. If the molecule fragments more, it becomes more difficult for the cell to repair it and thus perform effective DNA replication. It has been found that by matching the X-rays to above the 2p orbital of the iodine, the parent molecule fragments into much more and smaller remains, than when matching the X-rays to below this edge, meaning an increased damage when using the high Z atom. In addition to this, the results in this thesis provide a complement to existing experimental data, contributing with detailed information about specific fragmentation pathways of the molecule, facilitating the interpretation of mass over charge spectra from experiments.

<p>The four-electron reduction of dioxygen to water is the most exothermic non-photochemical reaction available to biology. A detailed molecular description of this reaction is needed to understand oxygen-based redox processes. Horseradish peroxidase (HRP) is a haem-containing redox enzyme capable of catalysing the reduction of dioxygen to water. We developed instrumentation and experimental methodology to capture and characterise by X-ray crystallography transient reaction intermediates in this reaction. </p><p>An instrument was designed (“the vapour stream system”) to facilitate reaction initiation, monitoring and intermediate trapping. In combination with single crystal microspectrophotometry, it was used to obtain conditions for capturing a reactive dioxygen complex in HRP. X-ray studies on oxidised intermediates can be difficult for various reasons. Electrons re-distributed in the sample through the photoelectric effect during X-ray exposure can react with high-valency intermediates. In order to control such side reactions during data collection, we developed a new method based on an angle-resolved spreading of the X-ray dose over many identical crystals. Composite data sets built up from small chunks of data represent crystal structures which received different X-ray doses. As the number of electrons liberated in the crystal is dose dependent, this method allows us to observe and drive redox reactions electron-by-electron in the crystal, using X-rays.</p><p>The methods developed here were used to obtain a three-dimensional movie on the X-ray-driven reduction of dioxygen to water in HRP. Separate experiments established high resolution crystal structures for all intermediates, showing such structures with confirmed redox states for the first time. </p><p>Activity of HRP is influenced by small molecule ligands, and we also determined the structures of HRP in complex with formate, acetate and carbon monoxide.</p><p>Other studies established conditions for successfully trapping the M-intermediate in crystals of mutant bacteriorhodopsin, but the poor diffraction quality of these crystals prevented high-resolution structural studies.</p>