A hallmark of Alzheimer's disease (AD) is the accumulation of insoluble senile plaques in the brain.[1] The major component of the insoluble plaques is the amyloid-β peptide (Aβ) that is produced through cleavage of the amyloid-β precursor protein (APP).[2] It is well understood that once the monomeric Aβ is generated, it has the potential to aggregate into soluble oligomers and further into insoluble fibrils. Recently it has been proposed that early oligomers are the main toxic species in the aggregation cascade.[3] However, it has been shown that the formation of toxic early oligomers is inhibited by several endogenous plasma proteins, including albumin and transferrin (Tf). In this investigation we are focusing on the mechanism of inhibition of the Aβ early oligomerization by Tf. Specifically, we have targeted the early stages of Aβ aggregation using a deletion mutant of the Aβ peptide, i.e. the Aβ12-28 fragment, which selectively stabilizes the early Aβ oligomers. Self-association of this peptide was controlled by adding-NaCl to filtered monomeric Aβ samples and the effect of Tf inhibition on these aggregates was probed by 1H relaxation NMR experiments.[4-7] Our data shows that Tf directly targets intermediary Aβ oligomers via a coating mechanism. 1. Kirkitadze, M.D., Condron, M.M. and Teplow, D.B, JMB 2001 312;1103-1119. 2. Stefan F. Lichtenthaler and Christian Haass, JCI 2004 113(10);1384-1387. 3. Necula M., Kayed R., Milton, S. and Glabe C.G, JBC 2007 282(14);10311-10324. 4. Klement K., Wieligmann K., Meinhardt J., Hortschansky P., Richter W., and Fändrich M., JMB 2007 373;1321-1333. 5. Huang H, Milojevic J, Melacini G. J Phys Chem B. 2008 112(18):5795-802. 6. Milojevic J, Esposito V, Das R, Melacini G. JACS. 2007 129(14):4282-90. 7. Milojevic J, Esposito V, Das R, Melacini G. J Phys Chem B. 2006 110(41):20664-70. / Thesis / Master of Science (MSc)

Alzheimer’s disease (AD) is a neurodegenerative disorder which is histopathologically characterised by amyloid plaques and neurofibrillary tangles. Amyloid plaques consist of the amyloid β-peptide (Aβ) that can form aggregates in the brain. Aβ is generated from the amyloid precursor protein (APP) through proteolytic cleavage. APP belongs to a conserved protein family that also includes the two paralogues, APP-like proteins 1 and 2 (APLP1 and APLP2). Despite the immense amount of research on APP, motivated by its implication in AD, the function of this protein family has not yet been determined. In this thesis, we have studied the expression and proteolytic processing of the APP protein family. Our results are consistent with previous findings that suggest a role for APP during neuronal development. Treatment of cells with retinoic acid (RA) resulted in increased synthesis. In addition, we observed that RA treatment shifted the processing of APP from the amyloidogenic to the non-amyloidogenic pathway. The proteins in the APP family have been hard to distinguish both with respect to function and proteolytic processing. However, for development of new drugs with APP processing enzymes as targets this is of great importance. Our studies suggest similarities, but also differences in the mechanism regulating the processing of the different paralogues. We found that brain-derived neurotrophic factor (BDNF) had different impact on the members of the APP family. Most interestingly, we also found that the mechanism behind the increased processing in response to IGF-1 was not identical between the homologous proteins. In summary, our results indicate that in terms of regulation APLP1 and APLP2 differ more from each other than from APP. Our studies open up the possibility of finding means to selectively block Aβ production without interfering with the processing and function of the paralogous proteins.

Amyloidogenic diseases, such as Alzheimer's disease (AD) and Type II Diabetes (T2D), are characterized by the accumulation of amyloid aggregates. Despite having very different amino-acid sequences, the underlying amyloidogenic proteins form similar supramolecular fibril structures that are highly stable and resistant to physical and chemical denaturation. AD is characterized by two toxic lesions: extracellular amyloid β-peptide (Aβ) plaques and intracellular neurofibrillary tangles composed of microtubule-associated protein tau. Similarly, a feature of T2D is the deposition of islet amyloid polypeptide (IAPP) aggregates in and around the pancreas. The mechanisms by which Aβ, tau, and IAPP aggregate, and cause cell death is unknown; thus, gaining greater insight into the stabilizing forces and initial unfolding events is crucial to our understanding of these amyloidogenic diseases. This work uses molecular dynamics (MD) simulations to study the secondary, tertiary, and quaternary structure of Aβ, tau, and IAPP. Specifically, this work used the Drude polarizable force field (FF), which explicitly represents electronic polarization allowing charge distributions to change in response to perturbations in local electric fields. This model allows us to describe the role charge plays on protein folding and stability and how perturbations to the charge state drive pathology. Studies were conducted to address the following questions: 1) What are the stabilizing forces of fibril and oligomeric structures? 2) How do charge-altering mutations modulate the conformational ensemble and thermodynamic properties of Aβ? 3) How do charge-altering post-translational modifications of Aβ and tau modulate changes in the conformational ensembles? These studies establish that shifts in local microenvironments play a role in fibril and oligomer stability. Furthermore, these studies found that changes in protein sequence and charge are sufficient to disrupt and change the secondary and tertiary structure of these amyloidogenic proteins. Overall, this dissertation describes how charge modulates protein unfolding and characterizes the mechanism of those changes. In the long term, this work will help in the development of therapeutics that can target these changes to prevent protein aggregation that leads to cell death. / Doctor of Philosophy / Protein aggregation is the hallmark of many chronic diseases, such as Alzheimer's disease (AD) and Type II Diabetes (T2D). The formation of two toxic aggregates: amyloid β-peptide (Aβ) plaques and neurofibrillary tangles composed of microtubule-associated protein tau are some of the key characteristics of AD. In addition, the formation of islet amyloid polypeptide (IAPP) aggregates in the pancreas is thought to play a role in the development of T2D. The pathways by which the proteins Aβ, tau, and IAPP aggregate are unknown; thus, gaining a greater insight into the properties that may cause these diseases is necessary to develop treatments. By studying these proteins at the atomistic level, we can understand how small changes to these proteins alter how they misfold in a way that promotes toxicity. Herein, we used a computational technique called molecular dynamics (MD) simulations to gain new insights into how protein structure changes. We explored the dynamics of these proteins and investigated the role that charge plays in protein folding and described how charge modulates protein folding and characterized the mechanism of those changes. This work serves as a characterization of protein folding and sets the ground for future structural studies and drug development.

Studies presented in this dissertation were conducted to gain more insight into the role of phospholipid asymmetry and amyloid-β (Aβ)-induced oxidative stress in brain of subjects with amnestic mild cognitive impairment (aMCI) and Alzheimer disease (AD). AD is a largely sporadic, age-associated neurodegenerative disorder clinically characterized by the vast, progressive loss of memory and cognition commonly in populations over the age of ~65 years, with the exception of those with familial AD, which develop AD symptoms as early as ~30 years-old. Neuropathologically, both AD and FAD can be characterized by synapse and neuronal cell loss in conjunction with accumulation of neurofibrillary tangles and senile plaques. Elevated levels of oxidative stress and damage to brain proteins, lipids, and nucleic acids are observed, as well. Likewise, aMCI, arguably the earliest form of AD, displays many of these same clinical and pathological characteristics, with a few exceptions (e.g., no dementia) and to a lesser extent. Studies in this dissertation focused on the contributions of oxidative stress to the exposure of phosphatidylserine (PtdSer) to the outer-leaflet of the lipid membrane, how and when PtdSer asymmetric collapse contributes to the progression of aMCI, AD, and FAD, and the role played by methionine-35 (Met-35) of Aβ in oxidative stress and damage, as measured in a transgenic mouse model of Aβ pathology. Normally, the PtdSer is sequestered to the cytosolic, inner-leaflet of the bilayer by the adenosine triphosphate (ATP)-dependent, membrane-bound translocase, flippase, which unidirectionally transports PtdSer inward against its concentration gradient. Oxidative stress-induced modification of flippase and/or PtdSer, however, leads to prolonged extracellular exposure of PtdSer on the outer membrane leaflet, a known signal for both early apoptosis and selective recognition and mononuclear phagocytosis of dying cells. Within the inferior parietal lobule (IPL) of subjects with aMCI and AD, a significant collapse in PtdSer asymmetry was found in association with increased levels of both pro- and anti-apoptotic proteins, Bax, caspase-3, and Bcl-2. Moreover, a significant collapse in PtdSer asymmetry was also found in whole brain of human double-mutant knock-in mouse models of Aβ pathology, together with significantly reduced Mg2+ATPase activity, representing flippase activity, and increased levels of pro-apoptotic caspase-3. Significant PtdSer externalization corresponded to the age at which significant soluble Aβ(1-42) deposition occurs in this particular mouse model (9 months), and not of plaque deposition (12 months), suggesting that elevated levels of Aβ(1-42), together with increasing oxidative stress and apoptosis, may contribute to altered PtdSer membrane localization. Also in this dissertation, transgenic mice carrying Swedish and Indiana mutations on the human amyloid precursor protein (APPSw,In) and APPSw,In mice carrying a Met35Leu mutation on Aβ were derived to investigate the role of Met-35 in Aβ(1-42)-induced oxidative stress in vivo. Oxidative stress analyses revealed that Aβ-induced oxidative stress requires the presence of Met-35, as all indices of oxidative damage (i.e., protein carbonylation, nitration, and protein-bound 4-hydroxy-2-trans-nonenal [HNE]) in brain of Met35Leu mice were completely prevented. Moreover, immunohistochemical analyses indicated that the Met35Leu mutation influences plaque formation, as a clear reduction in Aβ-immunoreactive plaques in Met35Leu mice was found in conjunction with a significant increase in microglial activation. In contrast, behavioral analyses suggested that spatial learning and memory was independent of Met-35 of Aβ, as Met35Leu mice demonstrated inferior water-maze performance compared to non-transgenic mice. Differential expression and redox proteomic analyses to pinpoint proteins significantly altered by the APPSw,In and Met35Leu mutations was performed, as well. Expression proteomics showed significant increases and decreases in APPSw,In and Met35Leu mouse brain, respectively, in proteins involved in cell signaling, detoxification, structure, metabolism, molecular chaperoning, protein degradation, mitochondrial function, etc. Redox proteomics found many of these same proteins to be oxidatively modified (i.e., protein carbonylation and nitration) in both APPSw,In and Met35Leu mouse brain, providing additional insights into the critical nature of Met-35 of Aβ for in vivo oxidative stress in a mammalian species brain, and strongly suggesting similar importance of Met-35 of Aβ(1-42) in brain of subjects with aMCI and AD. Taken together, studies presented in this dissertation demonstrate the role of oxidative stress-induced alteration of PtdSer asymmetry and Met-35 in Aβ-induced oxidative stress in aMCI, AD, and FAD brain.

De nombreuses protéines associées aux maladies neurodégénératives humaines sont intrinsèquement désordonnées. Ce sont des protéines qui sont dépourvues de structure tertiaire ou secondaire stable dans des conditions physiologiques. Plus précisément, les protéines intrinsèquement désordonnées (IDPs) subissent diverses changements conformationnels entre la pelote aléatoire, des conformations hélicoïdales et des structures en feuillet-β, ces deux dernières étant généralement impliquées dans la reconnaissance protéine-protéine. Parmi une vingtaine de peptides amyloïdogènes connus liés aux maladies dégénératives humaines, notre étude porte sur deux protéines désordonnées: le peptide Amyloïde-β (Aβ) associé à la maladie d'Alzheimer et l'Islet Amyloid Polypeptide (IAPP) impliqué dans le diabète de type II. Aβ possède deux alloformes courants de 40 et 42 résidus, tandis que IAPP est une hormone peptidique de 37 résidus. Les agrégats de Aβ sont toxiques pour les cellules du cerveau, tandis que la fibrillisation de IAPP affecte les cellules-β du pancréas. Le mécanisme d'agrégation de ces deux peptides reste encore mal connu, mais il a été proposé qu’en solution, ces peptides visitent différentes conformations, l'une d'entre elles étant riche en feuillets-β. Cela conduirait à l’oligomérisation de ces peptides, par le biais d’interactions feuillet-β / feuillet-β et, éventuellement, à la formation de fibrilles. Le but de notre étude est de mieux caractériser la dynamique conformationnelle de ces deux peptides, dans leur forme monomérique et oligomérique. Comprendre les premières étapes de leur agrégation est crucial pour le développement de nouvelles molécules thérapeutiques efficaces contre ces protéines amyloïdes. / Many proteins associated with human neurodegenerative diseases are intrinsically disordered. They are proteins which lack stable tertiary or secondary structure under physiological conditions. More specifically, intrinsically disordered proteins (IDPs) undergo various structural conversions between random coil, helical conformations and β-strand structures, these two latter being generally involved in protein-protein recognition. Among about twenty known amyloidogenic peptides related to human degenerative diseases, we focus our study on two disordered proteins: the Amyloid-β peptide (Aβ) associated to the Alzheimer’s disease and the Islet Amyloid Polypeptide (IAPP) involved in type II diabetes. Aβ has two common alloforms of 40 and 42 residues in length, meanwhile IAPP is a 37-residues peptide hormone. Aggregates of Aβ are toxic to the brain cells, meanwhile IAPP fibrillization affects the pancreatic β-cells. The aggregation mechanism of these two peptides is not known in detail, but it was proposed that in solution, these peptides visit various conformations, one of them being rich in β-strands. This would lead to peptide oligomerization, through β-strand / β-strand interactions and eventually to the fibril formation. The aim of our study is to provide insights into the conformational dynamics of these two peptides in monomeric and oligomeric forms. Understanding the early steps of their aggregation is crucial for the development of new effective therapeutic molecules against these amyloid proteins.De nombreuses protéines associées aux maladies neurodégénératives humaines sont intrinsèquement désordonnées. Ce sont des protéines qui sont dépourvues de structure tertiaire ou secondaire stable dans des conditions physiologiques. Plus précisément, les protéines intrinsèquement désordonnées (IDPs) subissent diverses changements conformationnels entre la pelote aléatoire, des conformations hélicoïdales et des structures en feuillet-β, ces deux dernières étant généralement impliquées dans la reconnaissance protéine-protéine. Parmi une vingtaine de peptides amyloïdogènes connus liés aux maladies dégénératives humaines, notre étude porte sur deux protéines désordonnées: le peptide Amyloïde-β (Aβ) associé à la maladie d'Alzheimer et l'Islet Amyloid Polypeptide (IAPP) impliqué dans le diabète de type II. Aβ possède deux alloformes courants de 40 et 42 résidus, tandis que IAPP est une hormone peptidique de 37 résidus. Les agrégats de Aβ sont toxiques pour les cellules du cerveau, tandis que la fibrillisation de IAPP affecte les cellules-β du pancréas. Le mécanisme d'agrégation de ces deux peptides reste encore mal connu, mais il a été proposé qu’en solution, ces peptides visitent différentes conformations, l'une d'entre elles étant riche en feuillets-β. Cela conduirait à l’oligomérisation de ces peptides, par le biais d’interactions feuillet-β / feuillet-β et, éventuellement, à la formation de fibrilles. Le but de notre étude est de mieux caractériser la dynamique conformationnelle de ces deux peptides, dans leur forme monomérique et oligomérique. Comprendre les premières étapes de leur agrégation est crucial pour le développement de nouvelles molécules thérapeutiques efficaces contre ces protéines amyloïdes.

Alzheimer’s disease is an incurable neurodegenerative disorder linked to the amyloid β (Aβ) peptide, a 38-43 residue peptide. The detailed molecular disease mechanism(s) is (are) unknown, but oligomeric Aβ structures are proposed to be involved. In common for the papers in this thesis is interactions; interactions between Aβ(1-40) and selected molecules and metal ions. The purpose has been to find out more about the structural states that Aβ can adopt, in particular the β-sheet state, which probably is linked to the oligomeric structures. The methods used have been nuclear magnetic resonance (NMR), circular dichroism (CD) and fluorescence spectroscopy using Thioflavin T (ThT). Upon addition of SDS/LiDS detergent or Congo red (CR) to Aβ(1-40), the initial random coil/PII-helix state was transformed into β-sheet and, in the case of detergent, a final α-helical state. In contrast to SDS/LiDS and CR, the dimeric Affibody molecule locks monomeric Aβ(1-40) in a β-hairpin state. It was found that by truncating the flexible N-terminal end of the Affibody molecule its affinity to Aβ was improved. The aggregation of Aβ(1-40) was further studied in the presence of a β-cyclodextrin dimer by a kinetic assay using ThT. Although having a weak dissociation constant in the millimolar range, the β-cyclodextrin dimer modified the aggregation pathways of Aβ. Finally Aβ(1-40) was studied in presence of Cu2+ and Zn2+ at physiological and low pH. Cu2+ was observed to maintain its specific binding to Aβ when decreasing the pH to 5.5 while Zn2+ behaved differently. This could be of importance in the Alzheimer’s disease brain in which the environment can become acidic due to inflammation.        In conclusion the results show that Aβ(1-40) is very sensitive to its environment, responding by adopting different conformations and aggregating in aqueous solutions. The β-sheet state is induced by varying molecules with different properties, properties that govern the final Aβ state. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Manuscript. Paper 5: Manuscript.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Memory is considered to be a process that has several stages, including acquisition, consolidation and retrieval. Memory impairment occurs when important synapses are modified. Alzheimer s disease (DA) is the most common cause of dementia. DA is characterized by cognitive damage, accumulation of the pathogenic amyloid-β (Aβ) peptide, and cholinergic dysfunction. Moreover, oxidative stress is associated with DA. Therapies used for dementia are still palliative rather than curative. Consequently, new therapies are urgently required. Biological effects of tellurium compounds have been studied, leading to a set of interesting and promising applications. Accordingly, 2-phenylethinyl-butyltellurium (PEBT), an organotellurium compound, has been reported as antioxidant. The purpose of this study was to characterize PEBT as a promising alternative for memory improvement and prevention of cognitive deficits, using experimental models of DA in mice. Initially, the present study was conducted to evaluate the effect of a single oral administration (p.o.) of PEBT at a dose of 10 mg/kg on memory, employing the step-down inhibitory avoidance task. PEBT administered 1 h before training, immediately after training or 1 h before the test session of the step-down inhibitory avoidance task increased the step-down latency time in comparison to the control mice, improving acquisition, consolidation, and retrieval of memory, respectively. The glutamate uptake, but not glutamate release, by cerebral cortex and hippocampal slices of mice was inhibited after 1 h of treatment with PEBT. After 24 h of PEBT exposure, the inhibition of cerebral cortex glutamate uptake disappeared. The improvement of memory by PEBT seems most likely to be mediated through an interaction with the amino acid transporters of the glutamatergic system. Thereafter, a subchronic PEBT treatment (1 mg/kg, p.o., for 10 days) after injection of Aβ(25-35) (3 nmol/3 μl/per site, intracerebroventricular) reversed Aβ-induced learning and memory deficits in the Morris water maze and step-down inhibitory avoidance tasks. In addition, PEBT (10 mg/kg, p.o.), administered 30 min before scopolamine (1 mg/kg, intraperitoneal), ameliorated memory deficit induced by this amnesic agent in the Morris water maze. Further, scopolamine was given 30 min before training and test or immediately post-training of step-down inhibitory avoidance task, inducing damage on acquisition, retrieval, and consolidation of memory, respectively. PEBT, administered 30 min before scopolamine, improved consolidation and retrieval stages, but not acquisition. General locomotor and exploratory activities, evaluated in the open-field test, were similar in all mice. Finally, the antiapoptotic effect of PEBT was evaluated. Human retinal pigment epithelial cells (ARPE-19 cell line) were exposed to in vitro oxidative stress by 10 ng/ml tumor necrosis factor-α and 600 μM H2O2. One hour PEBT incubation at concentrations of 7.5 and 10 μM attenuated the apoptosis induced by oxidative stress. This effect lasted up to 6 hours after oxidative stress induction. PEBT (5 and 10 μM) inhibited oxidative stress-induced poly (ADP-ribose) polymerase (PARP) cleavage and restored extracellular-signal-related kinase (ERK) phosphorylation decreased by oxidative stress. The protective mechanism exerted by PEBT against oxidative stress may involve PARP cleavage, regulation of ERK pathway, as well as its known antioxidant properties. In conclusion, the finds of the present thesis point out the ameliorative effect of PEBT on memory stages (acquisition, consolidation and retrieval). Likewise, PEBT improved memory impairment in mice. These effects seem to be due to strengthen the physiological glutamatergic tonus by PEBT and the antiapoptotic effect of PEBT. Therefore, PEBT could be considered a candidate for the prevention of memory deficits such as those observed in DA. / memória inclui pelo menos três tipos de processamento relacionados entre si: aquisição, consolidação e evocação. A memória é afetada quando as sinapses encarregadas de fazer ou evocar memórias encontram-se alteradas. A doença de Alzheimer (DA) é a causa mais comum de demência. A DA é caracterizada por danos cognitivos, acúmulo de peptídeo β-amiloide (Aβ) e disfunção colinérgica. Além disso, o estresse oxidativo está associado à DA. Uma vez que ainda não há cura para a DA e as terapias atuais são apenas paliativas, torna-se importante a busca de novos compostos para melhorar danos cognitivos. Com o estudo dos efeitos biológicos de compostos de telúrio, muitas aplicações estão sendo descobertas. Neste sentido, o composto orgânico de telúrio 2-feniletinil-butiltelúrio (PEBT) apresenta efeito antioxidante. O objetivo deste estudo foi caracterizar o PEBT como uma alternativa promissora para a melhora e prevenção de danos cognitivos, usando modelos experimentais da DA em camundongos. Primeiramente, avaliou-se o efeito de uma única dose oral (p.o) de PEBT (10 mg/kg) na memória, utilizando a tarefa da esquiva inibitória. O tratamento com PEBT 1 h antes do treino, imediatamente após o treino ou 1 h antes do teste da esquiva inibitória aumentou a latência comparada com os animais controles, melhorando a aquisição, consolidação e evocação da memória, respectivamente. A captação de glutamato, mas não a liberação deste neurotrasmissor, foi inibida em córtex e hipocampo de camundongos após 1 h de tratamento com PEBT. Após 24 h, a inibição da captação de glutamato no córtex não foi mais evidenciada. A melhora da memória causada pelo PEBT parece ser mediada através da interação com os transportadores de glutamato. Além disso, o tratamento subcrônico com PEBT (1 mg/kg, p.o., por 10 dias) após a injeção de Aβ(25-35) (3 nmol/3 μl/per site, intracerebroventricular) reverteu o prejuízo no aprendizado e na memória causados por Aβ nas tarefas do labirinto aquático de Morris e na esquiva inibitória. O PEBT (10 mg/kg, p.o.), adminstrado 30 min antes da escopolamina (1 mg/kg, intraperitoneal), também protegeu do dano de memória causado por este agente anticolinérgico no labirinto aquático de Morris. Quando a escopolamina foi administrada 30 min antes do treino ou teste, ou imediatamente após o treino da esquiva inibitória houve dano na aquisição, evocação e consolidação da memória, respectivamente. O PEBT, administrado 30 min antes da escopolamina, protegeu do dano na consolidação e evocação da memória, mas não na aquisição. Não houve diferença nas atividades locomotora e exploratória dos animais tratados com o PEBT no teste do campo aberto. Finalmente, o efeito antiapoptótico do PEBT foi avaliado. Células do epitélio pigmentado da retina humana (linhagem ARPE-19) foram expostas ao estresse oxidativo induzido pelo fator de necrose tumoral-α (10 ng/ml) e H2O2 (600 μM). O PEBT (7.5 e 10 μM), quando pré-incubado por 1 h, protegeu contra a apoptose induzida pelo estresse oxidativo e este efeito permaneceu até 6 h após a indução. O PEBT (5 e 10 μM) inibiu a clivagem da poli(ADP-ribose) polimerase (PARP) induzida por estresse oxidativo e, também, restaurou a fosforilação da quinase regulada por sinal extracelular (ERK). O efeito protetor do PEBT contra o estresse oxidativo parece envolver a clivagem da PARP e a regulação da fosforilaçao de ERK, além de sua atividade antioxidante. Nesse sentido, os resultados apresentados nesta tese destacam o efeito do PEBT na melhora das três fases da memória, bem como em modelos de dano cognitivos em camundongos. Estes resultados parecem estar relacionados ao aumento do tônus glutamatérgico causado pelo PEBT e seu efeito antiapoptótico. Assim sendo, estes dados sugerem que o PEBT poderá, futuramente, ser considerado candidato para a prevenção de danos de memória, como aqueles observados na DA.

Mass spectrometry has in recent years been established as the standard method for protein identification and characterization in proteomics with excellent intrinsic sensitivity and specificity. Fourier transform ion cyclotron resonance is the mass spectrometric technique that provides the highest resolving power and mass accuracy, increasing the amount of information that can be obtained from complex samples. This thesis concerns how useful information on proteins of interest can be extracted from mass spectrometric data on different levels of protein structure and how to obtain this data experimentally. It was shown that it is possible to analyze complex mixtures of protein tryptic digests by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and identify abundant proteins by peptide mass fingerprinting. Coupling on-line methods such as liquid chromatography and capillary electrophoresis increased the number of proteins that could be identified in human body fluids. Protein identification was also improved by novel statistical methods utilizing prediction of chromatographic behavior and the non-randomness of enzymatic digestion. To identify proteins by short sequence tags, electron capture dissociation was implemented, improved and finally coupled on-line to liquid chromatography for the first time. The combined techniques can be used to sequence large proteins de novo or to localize and characterize any labile post-translational modification. New computer algorithms for the automated analysis of isotope exchange mass spectra were developed to facilitate the study of protein structural dynamics. The non-covalent interaction between HIV-inhibitory peptides and the oligomerization of amyloid β-peptides were investigated, reporting several new findings with possible relevance for development of anti-HIV drug therapies and understanding of fundamental mechanisms in Alzheimer’s disease.