Interactions of cells with the extracellular matrix (ECM) have important roles in various physiological and pathological processes, including tissue morphogenesis during embryonic development, wound healing and tumor invasion. Although most of the proteins involved in cell-ECM interactions have been identified, the underlying mechanisms and involved signaling pathways are incompletely understood. Here, atomic force microscope-based imaging and single-cell force measurements were used to characterize the interactions of different cell types with ECM proteins. The interplay between cells and ECM is complex. However, two interaction types, protein-protein and protein-carbohydrate, predominate. Integrins, adhesion receptors for ECM, mediate the former, galectins, a family of animal lectins, the latter. In the second chapter of this thesis, the contributions of both receptor families to the interactions of epithelial MDCK cells with ECM proteins are presented. It was found that galectins-3 and 9 are highly expressed in MDCK cells and required for optimal long-term adhesion (90 minutes) to ECM proteins collagen-I and laminin-111. Interestingly, early adhesion (< 2 minutes) to laminin-111, was integrin-independent and instead mediated by carbohydrate interactions and galectins. In contrast, early adhesion to collagen-I was exclusively mediated by integrins. Moreover, cells frequently entered an enhanced adhesion state, marked by a significant increase in the force required for cell detachment. Although adhesion was mediated by integrins, adhesion enhancement was especially observed in cells depleted for galectin-3. It was proposed that galectin-3 influences integrin-mediated adhesion complex formation by altering receptor clustering. To control their attachment to ECM proteins, cells regulate integrin receptors. One regulatory process is integrin crosstalk, where the binding of one type of integrin influences the activity of another type. In the third chapter, the implementation of a single-cell force spectroscopy assay to identify such crosstalks and gain insight into their mechanisms is described. In this assay the interactions of integrin receptors being specifically attached to one ligand are characterized in dependence of another ligand-bond receptor pair. With this assay a crosstalk between collagen-binding integrin α1β1 and fibronectin-binding integrin α5β1 was identified in HeLa cells. This crosstalk was directional from integrin α1β1 to integrin α5β1 and appeared to regulate integrin α5β1 by inducing its endocytosis. In the fourth and final chapter, mechanisms of matrix-induced cell alignment were studied by imaging cells on two-dimensional matrices assembled of highly aligned collagen fibrils. Integrin α2β1 was identified as the predominant receptor mediating cell polarization. Time-lapse AFM demonstrated that during alignment cells deform the matrix by reorienting individual collagen fibrils. Cells deformed the collagen matrix asymmetrically, revealing an anisotropy in matrix rigidity. When matrix rigidity was rendered uniform by chemical cross-linking or when the matrix was formed from collagen fibrils of reduced tensile strength, cell polarization did not occur. This suggested that both the high tensile strength and pliability of collagen fibrils contribute to the anisotropic rigidity of the matrix and lead to directional cellular traction and cell polarization. During alignment, cellular protrusions contacted the collagen matrix from below and above. This complex entanglement of cellular protrusions and collagen fibrils may further promote cell alignment by maximizing cellular traction. The work presented here adds to the understanding of cell-ECM interactions. Atomic force microscopy imaging allowed characterizing the behavior of cells on nanopatterned collagen matrices whereas single-cell force spectroscopy revealed insights into the regulation of cell adhesion by galectins. Furthermore, methodological advances in the single-cell force spectroscopy assay allowed the intracellular regulation of receptor molecules to be studied. The work demonstrates that atomic force microscopy is a versatile tool to study cell-ECM interactions.

During vertebrate development, gastrulation leads to the formation of three distinct germlayers. In zebrafish a central process is the delamination and the ingression of single cells from a common ancestor tissue - that will lead to the formation of the germlayers. Several molecules have been identified to regulate this process but the precise cellular mechanisms are poorly understood. Differential adhesiveness, a concept first introduced by Steinberg over 40 years ago, has been proposed to represent a key phenomena by which single hypoblast cells separate from the epiblast to form the mesendoderm at later stages. In this work it is shown that differential adhesion among the germlayer progenitor cells alone cannot predict germlayer formation. It is a combination of several mechanical properties such as cell cortex tension, cell adhesion and membrane mechanical properties that influence the migratory behavior of the constituent cells.

Due to their therapeutic applications such as radical scavenging, MRI contrast imaging, Photoluminescence imaging, drug delivery, etc., nanoparticles (NPs) have a significant importance in bio-nanotechnology. The reason that prevents the utilizing NPs for drug delivery in medical field is mostly due to their biocompatibility issues (incompatibility can lead to toxicity and cell death). Changes in the surface conditions of NPs often lead to NP cytotoxicity. Investigating the role of NP surface properties (surface charges and surface chemistry) on their interactions with biomolecules (Cells, protein and DNA) could enhance the current understanding of NP cytotoxicity. Hence, it is highly beneficial to the nanotechnology community to bring more attention towards the enhancement of surface properties of NPs to make them more biocompatible and less toxic to biological systems. Surface functionalization of NPs using specific ligand biomolecules have shown to enhance the protein adsorption and cellular uptake through more favorable interaction pathways. Cerium oxide NPs (CNPs also known as nanoceria) are potential antioxidants in cell culture models and understanding the nature of interaction between cerium oxide NPs and biological proteins and cells are important due to their therapeutic application (especially in site specific drug delivery systems). The surface charges and surface chemistry of CNPs play a major role in protein adsorption and cellular uptake. Hence, by tuning the surface charges and by selecting proper functional molecules on the surface, CNPs exhibiting strong adhesion to biological materials can be prepared. By probing the nanoscale interaction forces acting between CNPs and protein molecules using Atomic Force Microscopy (AFM) based force-distance (F-D) spectroscopy, the mechanism of CNP-protein adsorption and CNP cellular uptake can be understood more quantitatively. The work presented in this dissertation is based on the application of AFM in studying the interaction forces as well as the mechanical properties of nanobiomaterials. The research protocol employed in the earlier part of the dissertation is specifically aimed to understand the operation of F-D spectroscopy technique. The elastic properties of thin films of silicon dioxide NPs were investigated using F-D spectroscopy in the high force regime of few 100 nN to 1 µN. Here, sol-gel derived porous nanosilica thin films of varying surface morphology, particle size and porosity were prepared through acid and base catalyzed process. AFM nanoindentation experiments were conducted on these films using the F-D spectroscopy mode and the nanoscale elastic properties of these films were evaluated. The major contribution of this dissertation is a study exploring the interaction forces acting between CNPs and transferrin proteins in picoNewton scale regime using the force-distance spectroscopy technique. This study projects the importance of obtaining appropriate surface charges and surface chemistry so that the NP can exhibit enhanced protein adsorption and NP cellular uptake.

No description available.

Multivalente Wechselwirkungen sind in diversen biomolekularen und supramolekularen Systemen anzutreffen. Gewöhnlich werden sie durch ihre thermische Stabilität charakterisiert. Doch auch das mechanische Reißverhalten ist relevant: Ein System mit großer Reißlänge (Verformbarkeit) weist zwar eine geringere Reißkraft auf, kann aber besser auf äußere Einflüsse ohne Bindungsbruch reagieren. Daher besteht ein zunehmendes Interesse an Modellen zur Vorhersage der mechanischen Stabilität multivalenter Wechselwirkungen. Einzelmolekül-Kraftspektroskopie (SMFS) ist eine nützliche Methode, um den Reißprozess nichtkovalenter Wechselwirkungen zu studieren. Im Rahmen dieser Dissertation wurden mono- und bivalenten Pyridine, komplexiert und verbunden durch Cu(II) und Zn(II), entworfen und untersucht. Die drei bivalenten Pyridine wiesen unterschiedlich flexible Rückgratstrukturen auf (flexibel, teilflexibel, steif). Überraschenderweise wurde ein anderer Trend für die Verformbarkeiten gemessen (flexibel > steif > teilflexibel). Durch Vergleich von experimentellen Daten mit ab-initio Berechnungen konnten komplexe Reißmechanismen vorgeschlagen werden: Das Lösungsmittel war entscheidend und führte zu wasserverbrückten Zwischenprodukten, was die Verformbarkeit aller Systeme stark erhöhte. Im bivalente System mit teilflexiblem Rückgrat, koordiniert durch Cu(II), rissen beide Bindungen gleichzeitig bei vergleichsweise großen Kräften. Die beiden anderen Systeme mit Cu(II) wurden in zweistufigen Prozessen voneinander getrennt, was kleinere Reißkräfte zur Folge hatte. Insbesondere das flexible System war zwar thermisch stabiler, brach aber leichter als das monovalente System. Damit wurde zum ersten Mal der große Einfluss des Rückgrats, bei sonst gleicher Art von Wechselwirkung, auf die mechanische Stabilität bivalenter Wechselwirkungen gezeigt. Außerdem ist das entwickelte Modellsystem sehr nützlich für weiterführende Untersuchungen in biologisch relevanten wässrigen Lösungsmitteln. / Multivalent interactions are ubiquitous in biomolecular and supramolecular systems. They are commonly characterized by their thermal stability in terms of average bond lifetime or equilibration constant. However, also mechanical stabilities are relevant: A system with high rupture length (malleability) has a lower rupture force, but can more easily adopt to external constraints without rupture. Thus it is of ever-increasing interest to find appropriate models that allow predictions on the mechanical stability of multivalent interactions. Single-molecule force spectroscopy (SMFS) is a powerful tool to study the rupture process of non-covalent interactions. In the present thesis, a comprehensive study on the mechanical stability of bivalent pyridine coordination compounds with the metal ions Cu(II) and Zn(II) was performed. Surprisingly, three different backbone flexibilities (high, intermediate, low) did not correlate with the measured malleabilities (high > low > intermediate). Instead, comparison between experimental results and ab-initio calculations revealed more complex underlying rupture mechanisms: Due to the aqueous environment, hydrogen bound complexes were formed and important intermediate structures that strongly increased malleabilities. Both interactions of the intermediately flexible bivalent system with Cu(II) broke simultaneous, yielding comparatively large rupture forces. The bivalent interactions of high and low backbone flexibility with Cu(II) broke stepwise at smaller forces. Although being thermally more stable, the highly flexible system even broke at lower forces than the monovalent system. Thereby it was shown for the first time, that rupture forces of similar systems can be tuned over a broad range, just by changing the connecting backbone structure. Furthermore, the developed approach is a rich toolkit to study further the balanced interplay between rupture force and malleability in biologically relevant aqueous solvents.

Single-molecule force spectroscopy (SMFS) with atomic force microscope (AFM) has advanced our knowledge of the mechanical aspects of biological processes, and helped us take big strides in the hitherto unexplored areas of protein (un)folding. One such virgin land is that of membrane proteins, where the advent of AFM has not only helped to visualize the difficult to crystallize membrane proteins at the single-molecule level, but also given a new perspective in the understanding of the interplay of molecular interactions involved in the construction of these molecules. My PhD work was tightly focused on exploiting this sensitive technique to decipher the intra- and intermolecular interactions in membrane proteins, using bacteriorhodopsin and bovine rhodopsin as model systems. Using single-molecule unfolding measurements on different bacteriorhodopsin oligomeric assemblies - trimeric, dimeric and monomeric - it was possible to elucidate the contribution of intra- and interhelical interactions in single bacteriorhodopsin molecules. Besides, intriguing insights were obtained into the organization of bacteriorhodopsin as trimers, as deduced from the unfolding pathways of the proteins from different assemblies. Though the unfolding pathways of bacteriorhodopsin from all the assemblies remained the same, the different occurrence probability of these pathways suggested a kinetic stabilization of bacteriorhodopsin from a trimer compared to that existing as a monomer. Unraveling the knot of a complex G-protein coupled receptor, rhodopsin, showed the existence of two structural states, a native, functional state, and a non-native, non-functional state, corresponding to the presence or absence of a highly conserved disulfide bridge, respectively. The molecular interactions in absence of the native disulfide bridge mapped onto the three-dimensional structure of native rhodopsin gave insights into the molecular origin of the neurodegenerative disease retinitis pigmentosa. This presents a novel technique to decipher molecular interactions of a different conformational state of the same molecule in the absence of a high-resolution X-ray crystal structure. Interestingly, the presence of ZnCl2 maintained the integrity of the disulfide bridge and the nature of unfolding intermediates. Moreover, the increased mechanical and thermodynamic stability of rhodopsin with bound zinc ions suggested a plausible role for the bivalent ion in rhodopsin dimerization and consequently signal transduction. Last but not the least, I decided to dig into the mysteries of the real mechanisms of mechanical unfolding with the help of well-chosen single point mutations in bacteriorhodopsin. The monumental work has helped me to solve some key questions regarding the nature of mechanical barriers that constitute the intermediates in the unfolding process. Of particular interest is the determination of altered occurrence probabilities of unfolding pathways in an energy landscape and their correlation to the intramolecular interactions with the help of bioinformatics tools. The kind of work presented here, in my opinion, will not only help us to understand the basic principles of membrane protein (un)folding, but also to manipulate and tune energy landscapes with the help of small molecules, proteins, or mutations, thus opening up new vistas in medicine and pharmacology. It is just a matter of a lot of hard work, some time, and a little bit of luck till we understand the key elements of membrane protein (un)folding and use it to our advantage.

The atomic force microscope (AFM) provides a powerful instrument for investigating and manipulating biological samples down to the subnanometer scale. In contrast to other microscopy methods, AFM does not require labeling, staining, nor fixation of samples and allows the specimen to be fully hydrated in buffer solution during the experiments. Moreover, AFM clearly compares in resolution to other techniques. In general, the AFM can be operated in an imaging or a force spectroscopy mode. In the present work, advantage was taken of this versatility to investigate single biomolecules and biomolecular assemblies. A novel approach to investigate the visco-elastic behavior of biomolecules under force was established, using dextran as an example. While a molecule tethered between a solid support and the cantilever tip was stretched at a constant velocity, the thermally driven oscillation of the cantilever was recorded. Analysis of the cantilever Brownian noise provided information about the visco-elastic properties of dextran that corresponded well to parameters obtained by alternative methods. However, the approach presented here was easier to implement and less time-consuming than previously used methods. A computer controlled force-clamp system was set up, circumventing the need for custom built analogue electronics. A commercial PicoForce AFM was extended by two computers which hosted data acquisition hardware. While the first computer recorded data, the second computer drove the AFM bypassing the manufacturer's microscope control software. To do so, a software-based proportional-integral-differential (PID) controller was implemented on the second computer. It allowed the force applied to a molecule to be held constant over time. After tuning of the PID controller, response times obtained using that force-clamp setup were comparable to those of the recently reported analogue systems. The performance of the setup was demonstrated by force-clamp unfolding of a pentameric Ig25 construct and the membrane protein NhaA. In the latter case, short-lived unfolding intermediates that were populated for less than 10 ms, could be revealed. Conventional single-molecule dynamic force spectroscopy was used to unfold the serine:threonine antiporter SteT from Bacillus subtilis, an integral membrane protein. Unfolding force patterns revealed the unfolding barriers stabilizing structural segments of SteT. Ligand binding did not induce new unfolding barriers suggesting that weak interactions with multiple structural segments were involved. In contrast, ligand binding caused changes in the energy landscape of all structural segments, thus turning the protein from a brittle, rigid into a more stable, structurally flexible conformation. Functionally, rigidity in the ligand-free state was thought to facilitate specific ligand binding, while flexibility and increased stability were required for conformational changes associated with substrate translocation. These results support the working model for transmembrane transport proteins that provide alternate access of the binding site to either face of the membrane. Finally, high-resolution imaging was exploited to visualize the extracellular surface of Cx26 gap junction hemichannels (connexons). AFM topographs reveal pH-dependent structural changes of the extracellular connexon surface in presence of HEPES, an aminosulfonate compound. At low pH (< 6.5), connexons showed a narrow and shallow channel entrance, which represented the closed pore. Increasing pH values resulted in a gradual opening of the pore, which was reflected by increasing channel entrance widths and depths. At pH > 7.6 the pore was fully opened and the pore diameter and depth did not increase further. Importantly, coinciding with pore gating a slight rotation of the subunits was observed. In the absence of aminosulfonate compounds, such as HEPES, acidification did not affect pore diameters and depths, retaining the open state. Thus, the intracellular concentration of taurine, a naturally abundant aminosulfonate compound, might be used to tune gap junction sensitivity at low pH.

Interactions of cells with their environment regulate important cellular functions and are required for the organization of cells into tissues and complex organisms. These interactions involve different types of adhesion receptors. Interactions with extracellular matrix (ECM) proteins are mainly mediated by the integrin family of adhesion molecules. Situations in which integrin-ECM interactions are deregulated cause diseases and play a crucial role in cancer cell invasion. Thus, the mechanisms underlying integrin-binding and regulation are of high interest, particularly at the molecular level. How can cell-ECM interactions be studied? While there are several methods to analyze cell adhesion, few provide quantitative data on adhesion forces. One group, single-cell force spectroscopy (SCFS), quantifies adhesion at the single-cell level and can therefore differentiate the adhesive properties of individual cells. One implementation of SCFS is based on atomic force microscopy (AFM); this technique has been employed in the presented work. Advantageously AFM-SCFS combines high temporal and spatial cell manipulation, the ability to measure a large range of adhesion forces and sufficiently high-force resolution to allow the study of single-molecule binding events in the context of a living cell. Since individual adhesion receptors can be analyzed within their physiological environment, AFM-SCFS is a powerful tool to study the mechanisms underlying integrin-regulation. The presented work is split into six chapters. Chapter one gives background information about cell-ECM interactions. In chapter two, different adhesion assays are compared and contrasted. The theoretical Bell-Evans model which is used to interpret integrin-mediated cell adhesion is discussed in chapter three. Thereafter, the three projects that form the core of the thesis are detailed in chapters four through six. In the first project (chapter 4), α2β1-integrin mediated cell adhesion to collagen type I, the most abundant structural protein in vertebrates, was quantified using CHO cells. Firstly, α2β1-collagen interactions were investigated at the single-molecule level. Dynamic force spectroscopy permitted calculation of bond specific parameters, such as the bond dissociation rate koff (1.3 ± 1.3 sec-1) and the barrier width xu (2.3 ± 0.3 Å). Next, α2β1-integrin mediated cell adhesion to collagen type I was monitored over contact times between 0 and 600 sec. Thereby the kinetics of α2β1-integrin mediated interactions was explored and insights into the underlying binding mechanisms were gained. In the second project (chapter five), effects of cryptic integrin binding sites within collagen type I exerted on pre-osteoblasts were investigated. Collagen type I matrices were thermally denatured which lead to exposure of cryptic RGD (Arg-Gly-Asp)-motifs. As a consequence pre-osteoblasts enhanced their adhesion to denatured collagen. Compared to native collagen type I, adhesion to denatured collagen was mediated by a different set of integrins, including αv- and α5β1-integrins. Cells grown on denatured collagen showed enhanced spreading and motility, which correlated with increased focal adhesion kinase phosphorylation levels. Moreover, osteogenic differentiation kinetics and differentiation potential were increased on denatured collagen. The findings of this project open new perspectives for optimization of tissue engineering substrates. In the third part (chapter six), the effect of the fusion protein BCR/ABL, a hallmark of chronic myeloid leukemia, on adhesion of myeloid progenitor cells was studied. Adhesion between BCR/ABL transformed progenitor cells to bone marrow derived stromal cells and to different ECM proteins was quantitatively compared to that of control cells. The tyrosine kinase activity of BCR/ABL enhanced cell adhesion, which was blocked by imatinib mesylate, a drug interfering with BCR/ABL activity. BCR/ABL-enhanced adhesion correlated with increased β1-integrin cell surface concentrations. Since adhesion of leukemic cells to the bone marrow compartment is critical for the development of drug resistance, the reported results may provide a basis for optimized target therapies. In the three described projects AFM-based SCFS was applied to investigate early steps of integrin-mediated adhesion at the molecular level. Taken together, the results demonstrate that AFM-SCFS is a versatile tool that permits monitoring of cell adhesion from single-molecule interactions to the formation of more complex adhesion sites at the force level. / Interaktionen zwischen Zellen und ihrer Umgebung sind maßgeblich an der Regulierung zellulärer Funktionen beteiligt und daher notwendig für die Organisation von Zellen in Geweben und komplexen Organismen. Zellinteraktionen mit der extrazellulären Matrix (EZM) werden hauptsächlich durch Integrine vermittelt. Situationen, in denen Integrin- EZM Interaktionen verändert sind, können Krankheiten verursachen und spielen zudem eine wichtige Rolle bei der Invasion von Krebszellen. Daher besteht ein großes Interesse darin, die molekularen Mechanismen, die Integrin-EZM Interaktionen regulieren, besser zu verstehen. Wie können Zell-EZM Interaktionen untersucht werden? Obwohl es mehrere Methoden gibt, mit denen Zelladhäsion untersucht werden kann, sind die wenigsten dazu geeignet, Zelladhäsionskräfte zu quantifizieren. Einzelzellspektroskopie erfasst die Adhäsionskräfte einzelner Zellen quantitativ und ermöglicht dadurch eine differenzierte Betrachtung der Adhäsion individueller Zellen. Eine Variante der Einzelzellspektroskopie basiert auf der Rasterkraftmikroskopie (AFM); diese Technik wurde in der vorliegenden Arbeit verwendet. Ein Vorteil von AFM- Einzelzellspektroskopie besteht darin, dass Zellen mit hoher zeitlicher und räumlicher Präzision manipuliert werden können. Zelladhäsionskräfte können zudem über einen großen Kraftbereich hinweg untersucht werden. Dabei ermöglicht es die hohe Kraftauflösung, einzelne Integrin-Ligandenbindungen in lebenden Zellen zu untersuchen. Die vorliegende Arbeit gliedert sich in sechs Kapitel. Kapitel eins gibt Hintergrundinformationen über Zell-EZM Wechselwirkungen. In Kapitel zwei werden verschiedene Adhäsionsassays einander gegenüber gestellt. Das theoretische Bell-Evans Modell, mit dessen Hilfe die gewonnenen Daten interpretiert wurden, wird in Kapitel drei diskutiert. Im Anschluss werden drei Projekte, welche das Herzstück dieser Doktorarbeit bilden, in Kapiteln vier bis sechs näher ausgeführt. Im ersten Projekt (Kapitel vier) wurde die Adhäsion von α2β1-Integrin exprimierenden CHO Zellen zu Kollagen I, dem häufigsten strukturellen Protein in Wirbeltieren, quantitativ untersucht. Zunächst wurden α2β1-Kollagen-Interaktionen auf Einzelmolekülebene analysiert. Mithilfe der dynamischen Kraftspektroskopie wurden für diese Bindung Dissoziationsrate koff (1.3 ± 1.3 sec-1) und Potentialbarrierenbreite xu (2.3 ± 0.3 Å) bestimmt. Daraufhin wurde die α2β1-vermittelte Adhäsion über einen Zeitraum von zehn Minuten untersucht. Dadurch konnten Einblicke in die Kinetik von α2β1-integrin vermittelter Zelladhäsion sowie in die zugrunde liegenden Regulationsmechanismen gewonnen werden. Im zweiten Projekt (Kapitel fünf) wurde die Rolle von kryptischen Integrin-Bindungsstellen in Kollagen I untersucht. Die zuvor verwendeten Kollagenoberflächen wurden thermisch denaturiert, wodurch versteckte RGD (Arg-Gly-Asp)-Sequenzen freigelegt wurden. Die partielle Denaturierung hatte- verglichen mit nativem Kollagen I- eine erhöhte Adhäsion von Präosteoblasten (MC3T3-E1) zur Folge, was auf das Binden zusätzlicher Integrine zurückgeführt wurde. Im Unterschied zu nativem Kollagen wurde die Zelladhäsion zu denaturiertem Kollagen I u.a. durch αv- and α5β1-Integrine vermittelt. Präosteoblasten zeigten verstärktes Zellspreiten sowie höhere Motilität auf denaturiertem Kollagen I; zudem wurde ein erhöhtes Differenzierungpotential der Präosteoblasten festgestellt. Die in diesem Projekt erhaltenen Einblicke bilden eine hilfreiche Basis für die Entwicklung optimierter Oberflächen für diverse Zell- und Gewebekulturanwendungen. Im dritten Projekt (Kapitel sechs) wurde der Einfluss des Fusionproteins BCR/ABL, charakteristisch für chronische myeloische Leukämie, auf die Adhäsion von myeloischen Vorläuferzellen untersucht. Dazu wurde die Adhäsion von BCR/ABL transformierten Vorläuferzellen (32D Zellen) bzw. Kontrollzellen zu Stromazellen (M2-10B4) sowie verschiedenen EZM Proteinen untersucht. BCR/ABL erhöhte die Zelladhäsion der myeloischen Vorläuferzellen signifikant. Dieser Effekt wurde durch die Zugabe von Imatinib, welches die Tyrosinkinaseaktivität von BCR/ABL inhibiert, aufgehoben. Die BCR/ABL-verstärkte Zelladhäsion korrelierte mit erhöhten β1-Integrin-konzentrationen. Da die Adhäsion von Leukämiezellen im Knockenmark bekanntermaßen kritisch für die Entwicklung von Resistenzen gegenüber verschiedenen Wirkstoffen ist, könnten die Ergebnisse dieser Studie eine Grundlage für die Entwicklung optimierter Target-Therapien sein. In den drei beschriebenen Projekten wurde AFM Einzelzellspektroskopie verwendet, um Integrin- vermittelte Adhäsion auf molekularer Ebene zu untersuchen. Die Ergebnisse zeigen, dass AFM-Einzelzellspektroskopie ein vielseitiges Werkzeug darstellt, das überaus geeignet dazu ist, Zelladhäsion- ausgehend von Einzelmolekülinteraktionen bis hin zur Entstehung komplexerer Adhäsionsstellen- auf der Kraftebene zu verfolgen.

Orientador: Mônica Alonso Cotta / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin / Made available in DSpace on 2018-08-17T12:15:05Z (GMT). No. of bitstreams: 1 Moreau_AlbertoLuisDario_D.pdf: 4972430 bytes, checksum: 23390541e98ea8174b689428392b8457 (MD5) Previous issue date: 2011 / Resumo: Na primeira parte deste trabalho, nós investigamos o processo de crescimento de um biofilme de bactérias (Xylella fastidiosa) inoculadas sobre lamínulas de vidro. O tamanho e a distância entre os biofilmes foram estudados por imagens de microscopia óptica; e uma análise fractal foi realizada usando conceitos de escala e imagens de AFM. Observamos que biofilmes diferentes mostram características fractais semelhantes, embora as variações na morfologia possam ser identificadas para diferentes estádios de crescimento do biofilme. Dois tipos de padrões estruturais são identificados através da dimensão fractal (Df) sugerindo que o crescimento do biofilme pode ser entendido como o modelo de Eden nos estágios de formação e no final, enquanto para o estágio de maturação aparecem evidências do modelo DLA (diffusion-limited aggregation). Estes resultados foram correlacionados à formação da matriz do biofilme que pode dificultar a difusão dos nutrientes e por isso criar condições para um crescimento DLA. Ainda com o AFM, fizemos medidas de espectroscopia de força para estudar a interação específica entre antígeno-anticorpo relacionados ao vírus CTV (citrus tristeza virus). Para tanto foi realizado o estudo da imobilização deste material biológico nas superfícies da ponta do AFM, e nos substratos planos de Si e InP. Usamos para isto imagens topográficas de AFM, imagens de microscopia eletrônica e ensaios imunoquímicos de ELISA; com isso pudemos confirmar que tanto o antígeno quanto o anticorpo foram imobilizados e que eles continuavam em seus estados nativos. Com as medidas de espectroscopia de força, detectamos que a diferença de força entre as interações específicas (antígeno-anticorpo) e não-específicas (antígeno-antígeno) foi de aproximadamente 60%. Utilizamos a mesma rotina de preparação em substrato de InP para o desenvolvimento de um biossensor baseado no funcionamento de um transistor FET (field-effect transistor). Os anticorpos foram imobilizados na superfície do semicondutor, enquanto doses de antígenos livres eram adicionadas a uma célula líquida que mantinha contato com esta superfície. Com curvas de corrente vs tensão em regiões lineares do dispositivo, estudamos a resposta, a sensibilidade e a especificidade do sensor, obtendo resultados promissores indicando viabilidade no desenvolvimento e no uso do mesmo. Por fim, estudamos a durabilidade de pontas de AFM com CNT (carbon nanotube) encapsulados com carbono amorfo numa amostra padrão semicondutora de pontos quânticos, além de estudar a sua estabilidade em meio líquido. Duas pontas foram estudadas, uma fabricada pelo nosso grupo e outra comercial, fornecida pela empresa americana CDI (Carbon Design Inovation). Utilizamos ferramenta de FT (fourier transform) para o estudo da resolução das pontas em imagens topográficas de AFM, e verificamos que ambas as pontas duraram mais de 400 imagens tendo uma perda da resolução de ~ 7% no ar e de ~ 5% ¿ em relação às medidas a seco ¿ em meio líquido, mostrando a viabilidade de seu uso no estudo de amostras biológicas / Abstract: We have investigated the growth process of Xylella fastidiosa biofilms inoculated on glass. The size and the distance between biofilms were analyzed by optical microscopy images; a fractal analysis was carried out using scaling concepts and Atomic Force Microscopy (AFM) images. We observed that different biofilms show similar fractal characteristics, although morphological variations can be identified for the different biofilm stages. Two types of structural patterns are suggested from the observed fractal dimensions Df: and suggest that the biofilm growth can be understood as an Eden model in the initial and final stages, while diffusion-limited aggregation (DLA) seems to dominate the maturation stage. Changes in the correlation length parallel to the surface were also observed; these results were correlated to the biofilm matrix formation which can hinder nutrient diffusion and thus create conditions to drive DLA growth. Atomic force spectroscopy was used as a method to investigate the specific antibody-antigen binding using proteins of the CTV (citrus tristeza virus). Subsequently, the chemical processes of covalent immobilization of the used biomolecules to different solid supports ¿ Si3N4 AFM Tips, Si and InP plane substrates ¿ was developed and characterized. The verification of the chemical binding process by different methods like AFM topography experiments, electron microscopy and ELISA immunochemical assays showed a successful immobilization of the biomolecules and that they were still in their native state. The analysis of the spectroscopic force data showed a significant difference in binding force between the specific antibody-antigen complexes and the non-specific controls (approximately 60%). The same chemical immobilization process was used to bind biomolecules to solid InP supports to develop a biosensor based on the field-effect transistor (FET) principle. The same antibodies, as used in atomic force experiments, were immobilized covalently to the semiconductor surface. The antibody-antigen complexation by adding the specific antigens to the functionalized surface was detected through changes in the current vs tension curves of semiconductor sample. The characterization of the electrochemical response, the molecular sensibility and the specificity of this biosensor showed a suitable method to detect specific molecular binding events. Further, the durability and stability of AFM tips with bonded carbon nanotubes with encapsulated amorphous carbon was studied on a standard semiconductor sample with quantum dots in air and liquid environment. Two different CNT AFM-tips were studied within this study in acoustic mode. One was assembled in our group and the other tip was provided by the american CDI (Carbon Design Innovation) company. The topographic AFM images were analyzed via FT (Fourier Transform) to study the spatial resolution of these tips. In air, both types of CNT tips showed a minor resolution decrease of approximately 6% after 400 topographic scans. In liquid environment an overall 10% lower spatial resolution of the tips was observed compared to the resolution in air which nevertheless makes these CNT AFM-tips suitable for experiments with native biological samples / Doutorado / Biofísica / Doutor em Ciências

Die Proteinfaltung ist ein Prozess der molekularen Selbstorganisation, bei dem sich eine lineare Kette von Aminosäuren zu einer definierten, funktionellen dreidimensionalen Struktur zusammensetzt. Der Prozess der Faltung ist ein thermisch getriebener diffusiver Prozess durch eine Gibbs-Energie-Landschaft im Konformationsraum für die Struktur der minimalen Energie. Während dieses Prozesses zeigt die freie Enthalpie des Systems nicht immer eine monotone Abnahme; stattdessen führt eine suboptimale Kompensation der Enthalpie- und der Entropieänderung während jedes Faltungsschrittes zur Bildung von Freien-Enthalpie-Faltungsbarrieren. Diese Barrieren und damit verbundenen hochenergetischen Übergangszustände, die wichtige Informationen über Mechanismen der Proteinfaltung enthalten, sind jedoch kinetisch unzugänglich. Um den Prozess der Barrierebildung und die strukturellen Merkmale von Übergangszuständen aufzudecken, werden Proteine genutzt, die über barrierefreie Pfade falten – so genannte “downhill folder“. Aufgrund der geringen Faltungsbarrieren werden wichtige Interaktionen der Faltung zugänglich und erlauben Einblicke in die ratenbegrenzenden Faltungsvorgänge. In dieser Arbeit vergleichen wir die Faltungsdynamiken von drei verschiedenen Varianten eines Lambda-Repressor-Fragments, bestehend aus den Aminosäuren 6 bis 85: ein Zwei-Zustands-Falter λWT (Y22W) und zwei downhill-folder-artige Varianten, λYA (Y22W/Q33Y/ G46,48A) und λHA (Y22W/Q33H/G46,48A). Um auf die Kinetik und die strukturelle Dynamik zu greifen zu können, werden Einzelmolekülkraftspektroskopische Experimente mit optische Pinzetten mit Submillisekunden- und Nanometer-Auflösung verwendet. Ich fand, dass die niedrige denaturierende Kraft die Mikrosekunden Faltungskinetik von downhill foldern auf eine Millisekunden-Zeitskala verlangsamt, sodass das System für Einzelmolekülstudien gut zugänglich ist. Interessanterweise zeigten sich unter Krafteinwirkung die downhill-folder-artigen Varianten des Lambda-Repressors als kooperative Zwei-Zustands-Falter mit deutlich unterschiedlicher Faltungskinetik und Kraftabhängigkeit. Drei Varianten des Proteins zeigten ein hoch konformes Verhalten unter Last. Die modellfreie Rekonstruktion von Freien-Enthalpie-Landschaften ermöglichte es uns, die feinen Details der Transformation des Zwei-Zustands-Faltungspfad direkt in einen downhill-artigen Pfad aufzulösen. Die Auswirkungen von einzelnen Mutationen auf die Proteinstabilität, Bildung der Übergangszustände und die konformationelle Heterogenität der Faltungs- und Entfaltungszustände konnten beobachtet werden. Interessanterweise zeigen unsere Ergebnisse, dass sich die untersuchten Varianten trotz der ultraschnellen Faltungszeit im Bereich von 2 μs in einem kooperativen Prozess über verbleibende Energiebarrieren falten und entfalten, was darauf hindeutet, dass wesentlich schnellere Faltungsraten notwendig sind um ein downhill Limit vollständig zu erreichen. / Protein folding is a process of molecular self-assembly in which a linear chain of amino acids assembles into a defined, functional three-dimensional structure. The process of folding is a thermally driven diffusive search on a free-energy landscape in the conformational space for the minimal-energy structure. During that process, the free energy of the system does not always show a monotonic decrease; instead, sub-optimal compensation of enthalpy and entropy change during each folding step leads to formation of folding free-energy barriers. However, these barriers, and associated high-energy transition states, that contain key information about mechanisms of protein folding, are kinetically inaccessible. To reveal the barrier-formation process and structural characteristics of transition states, proteins are employed that fold via barrierless paths – so-called downhill folders. Due to the low folding barriers, the key folding interactions become accessible, yielding insights about the rate-limiting folding events. Here, I compared the folding dynamics of three different variants of a lambda repressor fragment, containing amino acids 6 to 85: a two-state folder λWT (Y22W) and two downhill-like folding variants, λYA (Y22W/Q33Y/G46,48A) and λHA (Y22W/Q33H/G46,48A). To access the kinetics and structural dynamics, single-molecule optical tweezers with submillisecond and nanometer resolution are used. I found that force perturbation slowed down the microsecond kinetics of downhill folders to a millisecond time-scale, making it accessible to single-molecule studies. Interestingly, under load, the downhill-like variants of lambda repressor appeared as cooperative two-state folders with significantly different folding kinetics and force dependence. The three protein variants displayed a highly compliant behaviour under load. Model-free reconstruction of free-energy landscapes allowed us to directly resolve the fine details of the transformation of the two-state folding path into a downhill-like path. The effect of single mutations on protein stability, transition state formation and conformational heterogeneity of folding and unfolding states was observed. Noteworthy, our results demonstrate, that despite the ultrafast folding time in a range of 2 µs, the studied variants fold and unfold in a cooperative process via residual barriers, suggesting that much faster folding rate constants are required to reach the full-downhill limit.