In this thesis we present computer modelling studies that were implemented to investigate protein behavior in various environments causing their folding, unfolding and aggregation. Applications related to two important proteins - insulin and apolipoprotein C-II (ApoC-II) are presented. The use of atomistic simulation methodologies based on empirical force fields has enhanced our understanding of many physical processes governing protein structure and dynamics. However, the force fields used in classical modelling studies are often designed for a particular class of proteins and rely on continuous improvement and validation by comparison of simulations with experimental data. In Chapter 4 we present a comprehensive comparison of five popular force fields for simulation of insulin. The effect of each force field on the conformational evolution and structural properties of the protein is analysed in detail and compared with available experimental data. A fundamental phenomenon in nature is the ability of proteins to fold ab initio to their functional native conformation, also known as their biologically active state. Due to the heterogeneity and dimensionality of the systems involved, it is necessary to employ methodologies capable of accelerating rare events, specifically, configurational changes that involve the crossing of large free energy barriers. In Chapter 5, using the recently developed method BE-META we were able to identify the structural transitions and possible folding pathways of insulin. Another interesting phenomenon is the misfolding of proteins causing their aggregation, that may lead to formation of either amorphous compounds or structures of elongated-unbranched morphology known as amyloid fibrils. The deposition of amyloid fibrils in the human body may cause many debilitating diseases such as Alzheimer's and variant Creutzfeldt-Jakob diseases, thus making this field of research important and urgent. The human plasma protein apoC-II serves important roles in lipid transport, and it has been shown to form amyloid-like aggregates in solution. We have performed computational studies to investigate the effect of mutations, such as Met oxidation and the residue substitutions to hydrophobic Val and hydrophilic Gln, on dynamics of apoC-II(60-70) peptide. The conformation features relevant to the amyloidogenic propensities of the peptide were identified and presented in Chapter 6. The involvement of lipids at the various stages of development of amyloid diseases is becoming more evident in recent research efforts. In particular, micellar and sub-micellar concentrations have showed to have different effect on fibril growth and kinetics of native apoC-II and derived peptides. In Chapter 7 we investigated the influences of phospholipids at various concentrations on the structure of apoC-II(60-70) using MD and umbrella sampling methods. The molecular mechanisms of lipid effects on the peptide conformation and dynamics were identified. In Chapter 8 preliminary results on the structural stability of pre-formed oligomeric composites of apoC-II(60-70) peptide of different sizes and arrangements were also presented. The effects of mutation (oxidised Met, Met60Val and Met60Gln) on the most stable cluster was also investigated. To conclude, several ideas for continuation of research in the protein folding and aggregation field are discussed in the Future Work section of this thesis.

A new variant of human apolipoprotein B has been identified in a subject with decreased low density lipoprotein cholesterol and apolipoprotein B concentrations. Although no clinical signs of fat malabsorption were observed the subject was diagnosed, on the basis of his low cholesterol and apolipoprotein B level, as having hypobetalipoproteinaemia. The variant of apolipoprotein B was first identified by Western blot analysis. The analysis revealed an abnormal low molecular weight form of apolipoprotein B as well as normal apolipoprotein B-100 indicating that the subject was heterozygous for a truncated form of apolipoprotein B. The new variant (apo B-32) was a result of a C→T transition at nucleotide 4548 in exon 26 of the apolipoprotein B gene. This mutation changes a CAG codon which codes for glutamine into a TAG stop codon resulting in translation of a truncated apolipoprotein B protein approximately 32% the length of normal apolipoprotein B-100. Although only 32% of the length of apolipoprotein B-100, apo B-32 was still capable of forming lipoprotein particles as indicated by its presence in both the low density and high density lipoprotein fractions. This density distribution is unique since apo B-32 is the shortest known truncated apolipoprotein B to be found in the low density lipoprotein fraction. This finding clearly indicates that the region of apo B-32 is important in the lipid binding characteristics of apolipoprotein B-100. The binding of apo B-32 to heparin confirmed three heparin binding sites previously predicted to be in the amino-terminal 30% of apolipoprotein B-100. Isolated lipoproteins formed from apo B-32 appeared to be similar to high density lipoproteins in size and composition. However, unlike high density lipoproteins, the apo B-32 lipoproteins in plasma were partially precipitated by polyanionlcation reagents normally used to precipitate very low density and low density lipoproteins. The presence of both apolipoproteins Al and E on the apo B-32 lipoproteins suggested that apolipoprotein Al or E may mediate the metabolism of apo B-32 since apo B-32 does not posses the receptor binding region for the low density lipoprotein receptor. Four further subjects were identified as having reduced low density lipoprotein and apolipoprotein B concentrations. However a lack of any truncated apolipoprotein B in their plasma made it difficult to link their hypobetalipoproteinaemia with the apolipoprotein B gene. The cause of the hypobetalipoproteinaemia in these subjects remains uncharacterised although future linkage analysis studies in these individuals and family members will at least establish whether their hypobetalipoproteinaemia is related to the apo B gene.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

Thesis (M.Sc.). / Written for the Dept. of Microbiology and Immunology. Title from title page of PDF (viewed 2008/05/28). Includes bibliographical references.

Thesis (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2005. / Embargoed. Vita. Bibliography: 92-104.

Thesis (Ph. D.)--University of California, San Diego and San Diego State University, 2007. / Title from first page of PDF file (viewed May 30, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 116-127).

Disputats, Umeå universitet, 2006. / Härtill 3 uppsatser.

Η αθηρωματική νόσος είναι η κύρια αιτία καρδιαγγειακών νοσημάτων (CVD). Σύμφωνα με τον WHO το 2004 οι θάνατοι λόγω CVD ήταν 17.1 εκατομμύρια, το 29% των θανάτων παγκοσμίως. Η παθογένεια της νόσου είναι πολυπαραγοντική και οφείλεται σε περιβαλλοντικά και γενετικά αίτια, ένα από τα οποία είναι οι λιπιδαιμικές διαταραχές. Μελέτες τόσο in vitro όσο και in vivo σε ανθρώπους και πειραματόζωα καταδεικνύουν την απολιποπρωτεΐνη Ε (ApoE) ως κομβικό μόριο στη μεταφορά και το μεταβολισμό των λιποπρωτεϊνών, οι οποίες αποτελούν τα μεταφορικά μέσα των λιπιδίων. Η ΑpoE εκφράζεται σε ποικίλους ιστούς, όπως ο λιπώδης ιστός, τα ενδοθηλιακά κύτταρα, τα μακροφάγα και ο εγκέφαλος, αν και η κύρια θέση παραγωγής της είναι το ήπαρ. Στις δράσεις της ΑpoE περιλαμβάνονται η ηπατική πρόσληψη των λιποπρωτεϊνών, η ενεργοποίηση ενζύμων που συμμετέχουν στον μεταβολισμό των λιποπρωτεϊνών (LCAT, CETP, HL) η μεταφορά χοληστερόλης από περιφερικούς ιστούς στο ήπαρ με στόχο την κάθαρση και τελικώς τη ρύθμιση της ομοιόστασης του ισοζυγίου της χοληστερόλης στο αίμα. Η απομάκρυνση VLDL και υπολειμμάτων χυλομικρών από την κυκλοφορία μέσω της αγρίου τύπου (wt) ΑpoE προϋποθέτει την ύπαρξη λειτουργικών υποδοχέων LDLr. Στους ανθρώπους μεταλλάξεις ή πλήρης έλλειψη έκφρασης του LDLr οδηγεί στη εμφάνιση Οικογενής υπερχοληστερολαιμίας (FH). Στην περίπτωση της ομόζυγης Οικογενής υπερχοληστερολαιμίας (HoFH) οι ήδη υπάρχουσες φαρμακολογικές προσεγγίσεις είναι αναποτελεσματικές, με συνέπεια οι ασθενείς να καταλήγουν πρόωρα. Παρά τις ωφέλιμες δράσεις της wt ApoE στο μεταβολισμό των λιποπρωτεϊνών, η θεραπευτική της αξία είναι περιορισμένη καθώς σε συγκεντρώσεις άνω των φυσιολογικών επιπέδων στο πλάσμα επάγει συνδυαστική υπερλιπιδαιμία. Η διερεύνηση της δομής και των λειτουργικών θέσεων της ΑpoΕ οδήγησε στην κατασκευή μιας τεχνητά μεταλλαγμένης μορφής, της ΑpoE4mut1 , η οποία όχι μόνο δεν προκαλεί διαταραχή λιπιδίων αλλά έχει και βελτιωμένες δράσεις σε σχέση με την wt ΑpoE. Η έρευνα που αναλύεται στην εργασία αυτή ξεκίνησε με σκοπό να μελετηθεί η αναγκαιότητα έκφρασης λειτουργικού υποδοχεά LDLr για την εκδήλωση των βελτιωμένων βιολογικών δράσεων της ΑpoE4mut1. Συγκεκριμένα, σε υπερχοληστερολαιμικά ποντίκια με ταυτόχρονη έλλειψη στην ΑpoE και τον LDLr (ApoE-/- x LDLr-/-) χορήγηση της μεταλλαγμένης μορφής ΑpoE4mut1 μέσω αδενοϊών οδήγησε σε μείωση των επιπέδων χοληστερόλης στο αίμα τους. Το γεγονός αυτό καταδεικνύει μια νέα ιδιότητα της ΑpoE4mut1 πολλά υποσχόμενη όσον αφορά στην ανακάλυψη νέων θεραπευτικών κατευθύνσεων για την ομόζυγη οικογενή υπερχοληστερολαιμία (ΗoFH). / Atherosclerosis is a focal disease that constitutes the main cause of coronary heart disease (CHD) and cardiovascular diseases (CVD). According to WHO an estimated 17.1 million people died from CVDs in 2004, representing 29% of all global deaths. The initial formation and progression of atheromatic lesions involves a complex interplay of both genetic and environmental factors, such as dyslipidemias. In vitro and in vivo studies, both in animal models and humans, have established that apolipoprotein E has a key role in the metabolism of lipoproteins, which are the main transport vehicles of the lipids in the circulation. ApoE is mainly synthesized by the liver and secondary by other tissues, such as fat tissue, macrophages, brain. The protein is involved in the efficient hepatic uptake of lipoprotein particles, the activation of enzymes, such as LCAT, CETP, which participate to metabolic pathways of lipoproteins, and the stimulation of reverse cholesterol transport from peripheral tissues to the liver. Therefore, ApoE is capable of regulating cholesterol homeostasis in plasma. The expression of functional LDLr is required by wild type ApoE, in order to perform the clearance of lipoprotein particles. In humans mutations or total deficiency in LDLr result in a disease called Familial Hypercholesterolemia (FH). Homozygote patients with FH (HoFH) do not benefit from the conventional therapies and die prematurely. Despite the central role of wt ApoE in the metabolism of lipoprotein particles, its therapeutic value is reduced due to the limitation that at concentrations higher than physiological, plasma ApoE induces combined hyperlipidemia. Studies on the structure-function relationship of the protein resulted in the generation of a mutant variant ApoE4mut1, which has improved functions regarding wt ApoE4 and does not induce hypertriglyceridemia. The present study was initiated in order to determine whether the improved functions of ApoE4mut1 require the expression of LDLr. The results demonstrated new possible interventions for the treatment of HoFH. In particular, hypercholesterolemic mice with deficiency both in ApoE and LDLr genes (ApoE-/- x LDLr-/-), which expressed through adenovirusmediated gene transfer the mutant ApoE4mut1, showed a decrease in the cholesterol levels. This finding may lead to important therapeutic applications as a new treatment for HoFH when gene therapy becomes a reality in the future.

BACKGROUND & AIMS - Metabolic syndrome (MetS), characterized by abdominal obesity, atherogenic dyslipidemia, elevated blood pressure, and insulin resistance is a major public health concern in the United States. The effect of Apolipoprotein E (Apo E) polymorphism has been relatively well studied in relation to cardiovascular disease; however, its effects on MetS are not well established. METHODS - We conducted a cross-sectional study consisting of 1,551 participants from the National Heart, Lung, and Blood Institute (NHLBI) Family Heart Study to assess the relation of Apo E polymorphism with the prevalence of MetS. Information on the different Apo E genotypes was extracted from the database and we defined MetS according to the AHA-NHLBI-IDF-WHO Harmonized Criteria. We used generalized estimating equations to estimate adjusted odds ratios for prevalent MetS and the Bonferroni correction to account for multiple testing in the secondary analysis. RESULTS – Our study population had a mean age (SD) of 56.5 (11.0) years and 49.7% had MetS. There was no association between the Apo E genotypes and MetS. The multivariable adjusted ORs (95% CI) were 1.00 (reference), 1.26 (0.31-5.21), 0.89 (0.62- 1.29), 1.13 (0.61-2.10), 1.13 (0.88-1.47) and 1.87 (0.91-3.85) for the *e3/e3, *e2/e2, *e2/e3, *e2/e4, *e3/e4 and *e4/e4 genotype respectively. In a secondary analysis, the *e2/e3 genotype was associated with lower HDL levels, with the multivariable adjusted ORs (95% CI) of 0.59 (0.36-0.95) when compared to the reference *e3/e3 genotype. CONCLUSIONS - Our findings do not support an association between Apo E polymorphism and MetS in a multi-center population based study of predominantly white US men and women. The *e2/e3 genotype was associated with lower HDL levels as compared to the *e3/e3 genotype. KEY WORDS: Apolipoprotein E (Apo E) polymorphism, metabolic syndrome, blood pressure, glucose, waist circumference, triglycerides, high-density lipoprotein cholesterol

Les interactions protéine-ligand interviennent dans de nombreux processus biochimiques et permettent notamment à certaines protéines sanguines d’assurer leur rôle de transport. Parmi ces protéines figurent notamment l’albumine, protéine la plus abondante du plasma, ou l’apolipoprotéine A1 (ApoA1), majoritaire au sein des lipoprotéines de haute densité (HDL). Dans un contexte diabétique, la glycation des protéines induit des modifications structurales affectant ainsi leur potentiel d’interaction.Le premier objectif de ce travail de thèse visait à déterminer l’impact de la glycation de l’albumine sur sa liaison au liraglutide, un médicament de plus en plus utilisé dans le traitement du diabète de type 2. Ensuite, la seconde partie de ce travail a consisté en la production d’une ApoA1 humaine recombinante fonctionnelle afin d’étudier ses propriétés d’interaction, sous forme libre ou associée aux phospholipides. La technique RMN (résonance magnétique nucléaire) a été utilisée sur les protéines préalablement marquées au fluor (pour le liraglutide) ou aux isotopes stables 13C/15N (pour l’ApoA1). La titration microcalorimétrique isotherme (ITC), méthode complémentaire à la RMN a été appliquée pour l’étude des interactions avec l’avantage de ne nécessiter aucun marquage. Différentes stratégies de clonage ont été explorées pour la surexpression de l’ApoA1 en bactérie Clearcoli.Les résultats obtenus démontrent une altération de l’affinité de l’albumine pour le liraglutide in vitro et in vivo, dépendante du degré de glycation. Ces résultats, enrichis d’une analyse lipidomique et peptidique, permettent d’expliquer les observations cliniques concernant la baisse de l’efficacité de médicaments liant l’albumine chez les patients ayant un diabète mal contrôlé. Concernant l’ApoA1, le choix de l’étiquette de fusion reste à optimiser, mais sa surexpression de manière soluble et abondante a été obtenue pour l’ApoA1 marquée et non marquée. / Protein-ligand interactions are involved in many biochemical processes. They are notably implicated in the role of transporter proteins in blood. Albumin, the most abundant plasma protein, and apolipoprotein A1 (ApoA1), which is the main component of high-density lipoprotein (HDL) belong to this class of proteins. In the context of diabetes, proteins are altered by glycation which leads to structural modifications and potentially affect their interactions.The first objective of this work was to determine the impact of albumin glycation on its binding to liraglutide, a drug increasingly used in the treatment of type 2 diabetes. Then, the second part of this work involved the production of recombinant functional human ApoA1 in order to study its interaction properties, in its lipid-free form or associated with phospholipids. The NMR (nuclear magnetic resonance) technique has been used on proteins previously labeled with fluorine (for liraglutide) or stable 13C/15N isotopes (for ApoA1). In addition, isothermal titration microcalorimetry (ITC), has been applied to the study of interactions with the advantage of not requiring any labeling. Various cloning strategies have been explored for the overexpression of ApoA1 in Clearcoli bacteria.The results demonstrate an alteration of the affinity of albumin for liraglutide in vitro and in vivo, depending on the degree of glycation. These results, supported by a lipidomic and peptide analysis, explain clinical observations concerning the decrease of efficacy of albumin-binding drugs in patients with poorly controlled diabetes. Regarding ApoA1, the choice of the fusion tag remains to be optimized, but both labeled and unlabeled ApoA1 were successfully overexpressed at high yields in a soluble form.