Zinc is the second most abundant transition metal in biological systems. This cation is required for the catalytic activity of hundreds of enzymes which mediate protein synthesis, DNA replication and cell division. Despite the central importance of zinc in cellular homeostasis, the mechanism of zinc uptake, compartmentalization and efflux is unknown. Recently, a family of proteins, called ZIP, has been shown to control zinc uptake. Mutations in one of the genes coding for these proteins (ZIP4) can lead to potentially life-threatening diseases like Acrodermatitis Enteropathica and high levels of ZIP4 have been detected in patients suffering from pancreatic cancer. Therefore our goal is to investigate the mechanism of ZIP4 transport and regulation. It was previously shown that the intracellular loop between transmembrane III and IV (M3M4) of ZIP4 is ubiquitinated in the presence of high intracellular zinc which lead to protein degradation. Our initial hypothesis was that the large intracellular domain of ZIP4 (M3M4) is a sensor which detects the intracellular concentration of zinc and regulates the surface expression of ZIP4. In order to test this hypothesis we expressed and purified the M3M4 domain to examine the ability of M3M4 to bind zinc. Our results have demonstrated that M3M4 binds zinc with a 2:1 zinc:protein stoichiometry with nanomolar affinity. We have also shown that upon binding of zinc, M3M4 undergoes a large conformational change.

Montamos um espectrômetro o qual nos permite obter dados de atividade ótica Dispersão Rotatória (DRO) e Dicroísmo Circular (DC) simultaneamente. O sistema ótico consiste de uma fonte de luz, um monocromador, um suporte para amostra, um analisador gigante e um detector de luz. O analisador girante é sustentado por um mancal pneumático e gira usando um motor de passo, o qual é controlado por um microcomputador. Um outro motor de passo também controlado por microcomputador é usado para girar a grade de difração do monocromador. Para obter os espectros de DRO e DC, o monocromador pára em um certo comprimento de onda, enquanto o eixo de transmissão do analisador é posicionado em &#946= 0&#176, 45&#176, 90&#176 e -45&#176 relativo ao eixo de transmissão do polarizador. O microcomputador através do detector de luz lê as quatro intensidades de luz e usando um formalismo desenvolvido por nós, relaciona-as à elipticidade e a rotação ótica naquele comprimento de onda. O monocromador é então girado a um novo comprimento de onda e o procedimento é repetido. No final, os espectros de DC e DRO podem ser mostrados em uma Tabela ou com um Gráfico. Além de funcionar como um espectropolarímetro, o equipamento pode ser usado também como um espectrofotômetro, para acompanhar cinética de reação, para medir dicroísmo linear, etc... Devido à relação sinal/ruído, temos nos ângulos medidos, uma resolução de 1&#186 / We have assembled a spectrometer which provides the optical activity data Optical Rotatory Dispersion (ORD) and Circular Dichroism (CD) simultaneously. The Optical System consists of a source of light, a monochromator, a polarizer, a sample holder, a rotating analyzer and a light detector. The rotating analyzer is supported by a pneumatic bearing and rotates using a step motor which is controlled by a microcomputer. Another spet motor also controlled by the microcomputer is used to rotate the diffraction grating of the monochromator. To obtain the ORD and CD spectra, the monochromator stops at a certain wave length, while the transmission axis of the analyzer is positioned at &#946= 0&#176, 45&#176, 90&#176 e -45&#176 relative to the transmission axis of the polarizer. The microcomputer through the light detector reads the four light intensities and using the formalism developed by us relates them to the elipticity and optical rotation at that wavelength. The monochromator is then rotated to a new wavelength and the procedure is repeated. At the end the CD and ORD spectra can be shown in a Table or as a graph. Besides functioning as a spectropolarimeter, the equipment can be use also as a regular spectrometer, to follow kinetic of recreations, to measure linear dichroism, etc Due to the signal/noise ratio we have in the measured angles a resolution of 1&#176

The work presented in this thesis deals with the structural and functional properties of peptides at surfaces. The interaction of peptides with surfaces is an ever so common occurrence in our every day life, from the bug squashed on the windshield of our car to the barnacle on our boat, and from the blood plasma used in the hospital to the proteins in our cells. The effect these occurrences has on our lives is diverse, the bug is annoying whereas the barnacle settlement of ship hull is costly for marine transportation, the blood plasma contains components of vital importance for our immunological defense system and the proteins in our cells are crucial for regulatory processes and life.One part of this thesis, performed as a part of the EU-founded project AMBIO, deals with the concept of marine biofouling. A number of short peptides have been designed, synthesized, and used to investigate their effect on the settlement on marine biofoulers, such as the Ulva linza algae and the Navicula diatom, on template surfaces coated with thin layers of these molecules. The surfaces have been thoroughly investigated with respect of their physio-chemical properties before and after submersion in artificial seawater and ultimately in suspensions containing the organisms. The most interesting results were obtained with an arginine-rich peptide coating that when introduced to Ulva linza zoospores, displayed extensive settlement, compared to reference surfaces. In addition, a large fraction of the settled spores had an abnormal morphology.The other part of this thesis is focused on designed peptides that when adsorbed on a negatively charged surface adopts a well-defined secondary structure, either α-helical or β-sheet. Precisely placed amino acids in the peptides will strongly disfavor structure in solution, primarily due to electrostatic repulsion, but when the peptides are adsorbed on the negatively charged surfaces, they adopt a well-defined secondary structure due to ion pair bonding. These interactions have been thoroughly investigated by systematic variations of the side-chains. In order to determine the factors contributing to the induced structure, several peptides with different amino acid sequences have been synthesized. Factors that have been investigated include 1) the positive charge density, 2) distribution of positive charges, 3) negative charge density, 4) increasing hydrophobicity, and 5) incorporating amino acids with different helix propensities. Moreover, pH dependence and the effect of different interaction partners have also been investigated. It has also been shown that the system can be modified to incorporate a catalytic site that is only active when the helix is formed. This research will increase our understanding of peptide-surface interactions and might be of importance for both bionanotechnology and medicine.

All biological processes are fundamentally inter-molecular interactions. In order to understand, and hence control, biomolecular structure and function, methods are required that probe biological systems at the molecular level, ideally with those molecules being in their native environment. The research summarized herein has at its core the development and application of ultra violet (UV)-visible spectrophotometric techniquies for this prupose, in particular circular dichrosim (CD) and linear dichrosim (LD) but also absorbance, fluorescence and resonance light scattering. The spectroscopy is complemented by fundamental theoretical work on molecular structure and reactivity that forms the basis for designing molecules to bind to biomolecules for a particular structural or functional effect. A brief summary of the contributions of the listed publications to our understanding of 'Molecular aspects of biololecule structure and function' is given below under five headings: Circular dichroism theory Molecular geometry and reactivity Small molecule-macromolecule interactions: spectroscopic probes of inter-molecular geometries Molecular design for nucleic acid structure and control Spectroscopic probes of biomolecule structure: instrumentation and application In general terms these correspond to successive phases of the research programme, however, all areas have been present since the first publications in 1983 and can be traced weaving through all subsequent activity.

This thesis is focussed on structural and functional studies of a novel glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes. GpdQ is highly promiscuous and is the first known phosphatase which is capable of degrading all three classes of phosphate esters (mono-, di- and triesters). Remarkably, GpdQ is also able to hydrolyse stable aliphatic phosphate esters and has been shown to degrade the hydrolysis product of the nerve agent VX. For these reasons, GpdQ has been realised to have potential as a powerful bioremediator for the removal of organophosphate pesticides and nerve agents. GpdQ is a binuclear metallohydrolase in which one of the metal ions is very weakly bound. Chapter 1 introduces the catalytic mechanisms of binuclear metallohydrolases by examining two related phosphate ester-degrading enzymes. Since one of the main features of catalysis addressed in this thesis are the differential metal binding affinities of GpdQ, Chapter 1 also canvasses a range of other binuclear metallohydrolases with similar behaviour. Chapter 2 examines the structural and evolutionary relationship between GpdQ and a number of other related enzymes. Using genome database searches, the two most closely related enzymes are identified. In performing these searches, a novel, putative binuclear metallohydrolase from Homo sapiens is also discovered. This enzyme, Hsa_aTRACP, is most closely related to PAPs, however construction of a homology model indicates that the active site tyrosine residue of PAP is replaced by histidine. In this respect, it may represent an evolutionary link to Ser/Thr protein phosphatases and GpdQ. The biology and chemistry of this putative enzyme is discussed. PAPs are the only binuclear enzymes with an established heterovalent active site of the type Fe(III)-M(II) (where M=Fe, Zn or Mn) whereas the majority of enzymes in this family have homovalent metal centres, including GpdQ and Ser/Thr protein. This is brought about due to the nature of the coordination sphere imposed by the enzyme. The activity of GpdQ can be reconstituted in the presence of Co(II), Zn(II), Mn(II) and Cd(II). Chapter 3 examines the kinetic properties of a binuclear homovalent system by studying the kinetic properties of Cd(II)-substituted GpdQ and a corresponding model complex. This comparative study leads to the identification of a terminal hydroxide molecule as the likely reaction-initiating nucleophile in Cd(II)-GpdQ with a pKa of 9.4. In Chapter 4, a detailed study of the structural, kinetic and spectroscopic behaviour of Co(II)-substituted GpdQ is presented. This chapter specifically probes the formation of the binuclear active site, the role of the metal ions in catalysis, the identity of the nucleophile and the potential role of any first or second coordination sphere residues in the regulation of enzyme activity, proton donation and metal ion coordination. Based on these findings, a detailed reaction mechanism is proposed in which the substrate itself promotes the formation of the catalytically competent binuclear centre and phosphorolysis occurs following nucleophilic attack by a terminal hydroxide molecule. A potential role of Asn80 (a ligand of one of the metal ions) in regulating both substrate and metal binding, and the role of the bridging hydroxide molecule in the activation of the terminal nucleophile is proposed. Chapter 5 employs a combination of kinetic and spectroscopic techniques to probe the proposed catalytic mechanism of GpdQ in depth. The formation of the catalytically competent binuclear centre is observed in pre-steady state studies, an integral first step in the catalytic mechanism. The dissociation and rate constants associated with formation of the binuclear centre are quantified. The rate of substrate turnover in GpdQ is relatively modest but is enhanced by a structural rearrangement involving the flexible Asn80 ligand. This structural change fine-tunes the reaction mechanism, leading to optimal reactivity. The steady-state kinetic properties of a series of metal ion derivatives (Co(II), Cd(II) and Mn(II)) of GpdQ and their reactivity towards a number of substrates are also compared. These findings lead to the conclusion that the reaction mechanism of GpdQ is modulated by both substrate and metal ion. In this respect, GpdQ is adaptive to the environmental conditions to which it is exposed by employing a flexible mechanistic strategy to achieve catalysis. Chapter 6 correlates the electronic and geometric structure of the binuclear centre in GpdQ as a means to probe specific aspects of the mechanism. This study uses the wild type enzyme and a site-directed mutant (Asn80Asp) to examine the structure of the metal ions at two stages of catalysis. The role of the bridging hydroxide molecule in nucleophilic activation is specifically addressed by monitoring changes in the electronic exchange interaction and other structural parameters as a result of phosphate binding. Also, the coordination environment of the metal ions in both the free enzyme and the phosphate-bound enzyme of wild type and Asn80Asp GpdQ were assessed against the currently proposed structures. The findings in this chapter corroborate the proposed catalytic mechanism of GpdQ. In summary, this project led to a detailed understanding of the mechanism of GpdQ, and provided insight into how both the metal ion composition and the identity of the substrate may modulate this mechanism. The knowledge gained may lead to the design of catalytically more efficient derivatives (mutants) of GpdQ for application in bioremediation.

In dieser Arbeit wurden die Möglichkeiten und Grenzen für Zirkulardichroismus-Messungen mit Synchrotronstrahlung untersucht. Dazu wurde ein Messaufbau für Zirkulardichroismus-Messungen an zwei Strahlrohren am Berliner Elektronenspeicherring für Synchrotronstrahlung eingesetzt, die für Messungen im Bereich des ultravioletten Lichts geeignet sind. Eigenschaften der Strahlrohre und des Messaufbau wurden in einigen wichtigen Punkten mit kommerziellen Zirkulardichroismus-Spektrometern verglichen. Der Schwerpunkt lag auf der Ausdehnung des zugänglichen Wellenlängenbereichs unterhalb von 180 nm zur Untersuchung des Zirkulardichroismus von Proteinen in diesem Bereich. In diesem Bereich ist es nicht nur die Lichtquelle sondern vor allem die Absorption des Lichts durch Wasser, die den Messbereich bei der Messung biologischer Proben in wässriger Lösung einschränkt. Es wurden Bedingungen gefunden, unter denen der Messbereich auf etwa 160 nm, in einigen Fällen bis auf 130 nm ausgedehnt werden konnte. Dazu musste die Pfadlänge deutlich reduziert werden und verschieden Probenküvetten wurden getestet. Der Einfluss der dabei auftretenden Spannungsdoppelbrechung in den Probenküvetten auf das Messsignal konnte mit einem alternativen Messaufbau deutlich reduziert werden. Systematische Fehler im Messsignal und auftretende Strahlenschäden begrenzen jedoch die Zuverlässigkeit der gemessenen Spektren. Bei Proteinfilmen schränkt die Absorption von Wasser den Messbereich kaum ein. Es wurden jedoch meist deutliche Unterschiede zwischen den Spektren von Proteinfilmen und den Spektren von Proteinen in wässriger Lösung festgestellt. Solange diese Unterschiede nicht minimiert werden können, stellen Proteinfilme keine praktikable Alternative zu Messungen in wässriger Lösung dar. / The possibilities and limitations for synchrotron radiation circular dichroism measurements were investigated in this thesis. Therefore an experimental setup to measure circular dichroism was used at two beamlines at the “Berliner Elektronenspeicherring für Synchrotronstrahlung”(BESSY), which were suitable in the ultraviolet range of light. Properties of the beamlines and the experimental setup were compared to those of commercial circular dichroism spectrometer in some important points. The focus was on the extension of the accessible wavelength range below 180 nm, with the aim to investigate the circular dichroism of proteins in that range. It is not only the light source that limits measurements with aqueous solutions in that range, but mainly the absorption of the light by water. Conditions were found under which the wavelength range was extended to about 160 nm, in some cases even to 130 nm. To achieve this, a significant reduction of the pathlength was necessary. Several sample cells were tested for their usability. The effect of birefringence within the sample cells on the circular dichroism signal could be reduced strongly with an alternative experimental setup. However systematic errors in the circular dichroism signal and appearing radiation damage of the proteins limits the reliability of the measured spectra. By using protein films, the light absorption by water is not a problem anymore. However, significant differences between the circular dichroism spectra of protein films and proteins in aqueous solution occurred in most of the cases. Unless these differences can be eliminated, measuring protein films is not an alternative to measurements in aqueous solution.

The pathogenesis of Alzheimer’s disease (AD), the most common senile dementia, is a complex process. A crucial event in AD is the aggregation of amyloid-β protein (Aβ), a cleavage product from the Amyloid Precursor Protein (APP). Aβ40, a common component in amyloid plaques found in patients, aggregates in vitro at concentrations, much higher than the one found in vivo. But in the presence of charged lipid membranes, aggregations occurs at much lower concentration in vitro compared to the membrane-free case. This can be understood due to the ability of Aβ to get electrostatically attracted to target membranes with a pronounced surface potential. This electrostatically driven process accumulates peptide at the membrane surface at concentrations high enough for aggregation while the bulk concentration still remains below threshold. Here, we elucidated the molecular nature of this Aβ-membrane process and its consequences for Aβ misfolding by Circular Dichroism Spectroscopy, Differential Scanning Calorimetry and Nuclear Magnetic Resonance Spectroscopy. First, we revealed by NMR that Aβ40 peptide does indeed interact electrostatically with membranes of negative and positive surface potential. Surprisingly, it even binds to nominal neutral membranes if these contain lipids of opposite charge. Combined NMR and CD studies also revealed that the peptide might be shielded from aggregation when incorporated into the membrane. Moreover, CD studies of Aβ40 added to charged membranes showed that both positively and negatively membranes induce aggregation albeit at different kinetics and finally that macromolecular crowding can both speed up and slow down aggregation of Aβ.

More than one-third of all Magnetic Resonance Imaging (MRI) scans employ image-enhancing contrast agents to increase the differential signal intensity between diseased and normal tissue. Because current clinical contrast agents exhibit low relaxivity (mM-1 s-1), low dose efficiency, and rapid secretion, we have designed a group of protein-based MRI contrast agents with multiple gadolinium binding sites. In this study, the developed purification method for Class ProCA-3 agents allows for a quick and cost-effective way to abstract up to 109 mg of pure, soluble protein from a 1L E. Coli cell pellet devoid of DNA or RNA “contamination” for extensive animal studies. Circular dichroism far-UV spectra ensure the metal stability of the agents, revealing maintenance of their native α-helical structure in the presence and absence of metal ions. Furthermore, substantial evidence supports the high dose efficiency of these agents, exhibiting up to five folds higher relaxivity than their analogous commercial competitors.

This work presents first-principles calculations of long-range intermolecular dispersion energies between two atoms or molecules and of electronic circular dichroism spectra of chiral molecules. The former is expressed in terms of the C6 dipole-dipole dispersion coefficients Δε, and the latter is given in terms of the extinction coefficient. In a series of publications, the complex linear polarization propagator method has been shown to be a powerful tool to provide accurate ab initio and first-principles density functional theory results. This was the case not only for the C6 dispersion coefficients but also for the electronic circular dichroism at an arbitrary wavelength ranging from the optical to the X-ray regions of the spectrum. The selected samples for the investigation of dispersion interactions in the electronic ground state are the noble gases, n-alkanes, polyacenes, azabenzenes, alkali-metal clusters, and C60. It is found that the values of C6 for the sodium-cluster-to-fullerene interactions are well within the error bars of the experiment. The proposed method can also be used to determine dispersion energies for species in their respective excited electronic states. The C6 dispersion coefficients for the first π → π* excited state of the azabenzene molecules have been obtained with the adopted method in the multiconfiguration self-consistent field approximation. The dispersion energy of the π → π* excited state is smaller than that of the ground state. It is found that the characteristic frequencies ω1 defined in the London approximation of n-alkanes vary in a narrow range which makes it possible to construct a simple structure-to-property relationship based on the number of π-bonds for the dispersion interaction in these saturated compounds. However, this simple approach is not applicable to the interactions of the π-conjugated systems since, depending on the systems, their characteristic frequencies ω1 can vary greatly. In addition, an accomplishment of calculations of the electronic circular dichroism spectra in the near-edge X-ray absorption has been demonstrated.

In order to investigate the effects of C-terminus modification of Dragon Grouper Nervous Necrosis Virus capsid protein on the virus particle formation, we used E. coli expression system to express DGNNV capsid protain with different truncations at C-teminus fused with six or three histidines (His-Tag). These poly-His tagged clones, including ¡µC334-C6H, ¡µC335-C6H, ¡µC336-C6H, ¡µC337-C6H, C3H and C6H (His6 tagged at the C-teminus of wild-type capsid protein)¡Awere expressed and VLPs formation ability were examined. Wild-type and N-terminal recombination (N6H, His6 tagged at the N-teminus of wild-type capsid protein) were also used for comparison. These His-tagged VLPs can be further purified by Ni-NTA agarose, and their thermal stability of mutant VLPs were analyzed by Circular Dichroism. The Western blotting and ELISA assay were utilized to analyzed N-teminus or C-terminus was located at the surface of virus icosahedron. Once the four amino acids at the C-terminus of capsid protein were truncated (¡µC334-C6H), the mutated cpasid protein cannot assemble into VLPs. The same phenomenon was also observed in C6H. The related productions of wild-type, ¡µC335-C6H, ¡µC336-C6H, ¡µC337-C6H, C3H VLPs were about 100%, 56%, 116%, 141%, and 193%, respectively. Using Circular Dichroism to observe the thermal stability of mutant VLPs, the results revealed that the Tm of mutant VLPs were about 3oC lower than wild-type VLPs (61oC). The results of Western blotting and ELISA assay suggest that the C-termius of DGNNV capisid protein was exposed to the surface of virus structure.