A major challenge in biology is to understand and predict the effect of mutations on protein structure, stability and function. Chapter 1 provides a general introduction on protein sequence-structure relationships and use of the CcdAB toxin-antitoxin system as a model to study molecular determinants of mutant phenotypes. In Chapter 2, we describe the use of saturation mutagenesis combined with deep sequencing to determine phenotypes for 1664 single-site mutants of the E. coli cytotoxin, CcdB. We examined multiple expression levels, effects of multiple chaperones and proteases and employed extensive in vitro characterization to understand how mutations affect these phenotypes. While general substitution preferences are known, eg polar residues preferred at exposed positions and non-polar ones at buried positions, we show that depth from the surface is important and that there are distinctly different energetic penalties for each specific polar, charged and aromatic amino acid introduced at buried positions. We also show that over-expression of ATP independent chaperones can rescue mutant phenotypes. Other studies have primarily looked at effects of ATP dependent chaperone expression on phenotype, where it is not possible to say whether mutational effects on folding kinetics or thermodynamic stability are the primary determinant of altered phenotypes, since there is energy input with these chaperones. The data suggest that mutational effects on folding rather than stability determine the in vivo phenotype of CcdB mutants. This has important implications for efforts to predict phenotypic effects of mutations and in protein design. While looking at the mutational landscape of a given gene from an evolutionary perspective, it is important to establish the genotype-phenotype relationships under physiologically relevant conditions. At the molecular level, the relationship between gene sequence and fitness has implications for understanding both evolutionary processes and functional constraints on the encoded proteins. Chapter 3 describes a methodology to test the fitness of individual CcdB mutants in E.coli over several generations by monitoring the rate of plasmid loss. We also propose a methodology for high throughput analysis of a pool of CcdB mutants using deep sequencing to quantitate the relative population of each mutant in a population of E.coli cells, grown for several generations and build the fitness landscape. While the F-plasmid based CcdAB system is known to be involved in plasmid maintenance through post-segregational killing, recent identification of ccdAB homologs on the chromosome, including in pathogenic strains of E.coli and other bacteria, has led to speculations on their functional role on the chromosome. In Chapter 4, we show that both the native ccd operon of the E.coli O157 strain as well as the ccd operon from the F- plasmid when inserted on the E.coli chromosome lead to protection from cell death under multiple antibiotic stress conditions through formation of persisters. Both the ccdF and ccdO157 operons may share common mechanisms for activation under stress conditions and also display weak cross activation. The chromosomal toxin shows weaker activity as compared to the plasmidic counterpart and is therefore less efficient in causing cell death. This has important implications in generation of potential therapeutics that target these TA systems. Chapter 5 describes the use of site-saturation mutagenesis coupled with deep sequencing to infer mutational sensitivity for the intrinsically disordered antitoxin, CcdA. The data allows us to make comparisons between overall as well as residue specific mutational sensitivity patterns with that of globular proteins, like CcdB (described in Chapter 2) and study toxin- antitoxin interaction and regulation through saturation suppressor mutagenesis. Interestingly, we found several examples of synonymous point mutations in CcdA that lead to loss of its activity. In Chapter 6 we attempt to explore the molecular bases for some of these synonymous mutations. In most cases the mutated codon has a similar overall codon preference to the WT one. Initial findings suggest a change in mRNA structure leading to change in CcdB: CcdA ratio, thereby causing cell death. These observations have important implications, because TA systems are ubiquitous, highly regulated and are known to be involved in multiple functions including drug tolerance. However a role for RNA structure in their regulation has not been shown previously. Appendix–I lists the mutational sensitivity scores for the CcdB mutants. Phenotypes for CcdA mutants obtained through deep sequencing have been tabulated in Appendix-II. Overall, we provide extensive datasets for mutational sensitivities of a globular (CcdB) and an intrinsically disordered protein (CcdA). Exploration of the molecular determinants of these mutant phenotypes not only provides interesting insights into CcdAB operon function but is also useful in understanding various aspects of protein stability, folding and activity as well as regulation of gene expression in bacteria.

É conhecido que a força iônica do meio desempenha um papel fundamental na estrutura de vesículas aniônicas de DMPG (dimiristoil fosfatidilglicerol) em dispersões aquosas. A baixa força iônica (~ 6 mM), as dispersões de DMPG exibem várias características anômalas, que foram interpretadas como a abertura de poros na bicamada ao longo da larga região de transição de fase gel-fluida (de ~ 18°C a 30°C). Aqui, revisitamos o sistema de DMPG em tampão a baixa força iônica, mas com dispersões obtidas após a extrusão por filtros de 100 nm, portanto menos polidispersas. Para enfatizar as interações eletrostáticas entre as cabeças polares dos lipídios, que não estarão blindadas pela presença de sais na solução, estudamos dispersões de DMPG em água pura, de modo a monitorar os agregados presentes na dispersão, e suas interações. As dispersões em água foram caracterizadas antes e depois da extrusão. Para tal, utilizamos diversas técnicas experimentais, em diferentes temperaturas: espalhamento de luz estático (SLS) e dinâmico (DLS), calorimetria diferencial de varredura (DSC), Ressonância Paramagnética Eletrônica (RPE) de marcadores de spin incorporados aos agregados, espalhamento de raios-X a altos e baixos ângulos (WAXS e SAXS), e medidas de viscosidade, turbidez, mobilidade eletroforética e condutividade elétrica. Resultados das várias técnicas com dispersões extrusadas de DMPG em tampão mostraram que o comportamento anômalo é observado de forma similar ao de dispersões não extrusadas. Entretanto, o pico de SAXS em muito baixo ângulo é visto de 5 a 45°C, e não apenas na região de transição de fase, portanto não deve ser modelado como a distância entre poros na bicamada lipídica que se abririam nesta região. A distância de repetição relacionada a este pico diminui na região de transição de fase, e com o aumento da concentração lipídica. Medidas de DSC indicaram que, em água, a região de transição de fase da vesícula de DMPG é ainda mais ampla, começando em torno de 10°C, mas ainda terminando em ~ 30oC. No entanto, a alta condutividade elétrica, viscosidade, mobilidade eletroforética, raio efetivo, e a baixa turbidez, vistas apenas na região de transição de fase do DMPG em tampão, são encontradas até altas temperaturas em água, quando a bicamada lipídica já se encontra na fase fluida. Medidas de RPE e WAXS mostraram a transição da membrana de uma fase mais rígida/imóvel/organizada para uma fase mais frouxa/móvel. Dados de espalhamento de luz, RPE e SAXS mostram que, similar ao DMPG em tampão, em água, o DMPG organiza-se como vesículas esféricas, unilamelares, mas possivelmente menores e mais carregadas, exibindo fortes interações vesícula-vesícula. Nas medidas de SAXS, o pico de Bragg na região de muito baixo ângulo foi visto em todas as temperaturas (de 5 a 60°C), sendo que a distância de repetição diminui para temperaturas maiores do que 10oC. Os resultados obtidos para dispersões em água, reforçam o comportamento anômalo observado anteriormente para dispersões em tampão em baixa força iônica. De acordo com eles, propomos a existência de vesículas altamente deformadas e ionizadas a partir de uma certa temperatura, T1 para o DMPG em água e Tmon em tampão baixa força iônica, sendo que em água a forte repulsão eletrostática PG--PG- levaria a fortes deformações e interações vesícula-vesícula, em uma ampla extensão de temperaturas. / It is known that the ionic strength plays a fundamental role in the structure of DMPG (dimyristoyl phosphatidylglycerol) anionic vesicles in water medium. At low ionic strength (~ 6 mM), DMPG dispersions display several anomalous characteristics, which were interpreted as the opening of bilayer pores along the wide bilayer gel-fluid transition region (from ~ 18°C to 30°C). Here, we revisit DMPG in buffer at low ionic strength, but with dispersions obtained after the extrusion by 100 nm filters, thus less polydisperse. To emphasize electrostatic interactions between the polar head-groups, which will not be shielded by ions in solution, we studied DMPG dispersions in pure water to monitor the aggregates in the dispersion and their interactions. Water dispersions were characterized before and after extrusion. For such, we used several experimental techniques, at different temperatures: light scattering, both static (SLS) and dynamic (DLS); differential scanning calorimetry (DSC); electron spin resonance (ESR) of spin labels incorporated into the aggregates, Small and Wide Angle X-Ray Scattering (SAXS and WAXS); and viscosity, turbidity, electrophoretic mobility and electrical conductivity measurements. Several techniques with extruded dispersions of DMPG in buffer showed that the anomalous behavior is also observed. However, the SAXS peak at very low angles is seen from 5 to 45°C, and not only in the phase transition region, therefore it should not be modeled as the distance of correlated pores in the lipid bilayer that would open in this region. The repeating distance related to this peak decreases in the phase transition region, and with increasing lipid concentration. DSC indicates that, in water, the bilayer gel-fluid transition is even wider, starting around 10oC but still ending ~ 30oC. However, high electric conductivity, viscosity, electrophoretic mobility, effective radius and low turbidity found only in the gel-fluid transition region for DMPG in buffer, are found at higher temperatures in water, when lipid bilayers are already in the fluid state. ESR and WAXS measurements evidenced the transition of the membrane from a more rigid/immobile/organized phase to a more soft/mobile phase. Light scattering, ESR and SAXS data showed that, similar to DMPG in buffer, in water, DMPG is organized as spherical unillamelar vesicles, but possibly smaller, highly charged, displaying strong vesicle-vesicle interactions. With SAXS the Bragg peak at very low angles was seen at all temperatures (from 5 to 60°C) with the repetition distance decreasing at temperatures higher than 10 ° C. The results obtained for water dispersions reinforce the anomalous behavior previously observed for buffer at low ionic strength dispersions. According to them, we propose the existence of highly deformed and ionized vesicles from a certain temperature, T1 for DMPG in water and Tmon in buffer at low ionic strength. In water the strong PG- - PG- electrostatic repulsion would lead to strong deformations and vesicle-vesicle interactions, over a wide range of temperatures.

Realizamos estudos, por espectroscopia de fluorescência de estado estacionário e resolvida no tempo, de dinâmica conformacional de três famílias de peptídeos: o terminal carboxílico do peptídeo neuroendócrino (7B2CT); o peptídeo estimulador do melanócito (alfa-MSH); e os peptídeos derivados da seqüência consensual de peptídeos que se ligam a heparina (peptídeo Cardin). Utilizamos os métodos de fluorescência baseados na supressão da emissão do fluoróforo presente no peptídeo, tanto por interação colisional com um supressor como por transferência de energia para um grupo aceitador presente no peptídeo. No segundo caso, dentro da hipótese de que diferentes conformações do peptídeo estão presentes durante o decaimento da fluorescência, supusemos que o decaimento da intensidade era modulado por uma função de distribuição de distâncias doador-aceitador, f(r). Foi desenvolvido um procedimento computacional usando o programa CONTIN, para recuperar, a partir dos dados de fluorescência resolvida no tempo, a distribuição de distância entre o doador e o aceitador presentes nos peptídeos. A metodologia se mostrou útil para obter informações quantitativas sobre a dinâmica conformacional dos peptídeos, sua dependência com o solvente e sua interação com outras moléculas presentes no meio. O peptídeo 7B2CT e seus análogos A12 e A18 foram estudados pela fluorescência da tirosina, presente na posição cinco na seqüência de aminoácidos. Não houve diferenças significativas no decaimento da intensidade, no decaimento da anisotropia e na supressão por iodeto entre os três peptídeos, que pudessem ser correlacionados com as diferenças observadas na inibição da pro-hormone convertase 2 (PC2). O peptídeo alfa-MSH e seu análogo mais potente [Nle(4),0-Phe(7)] alfa-MSH (NDP-alfa-MSH), que contém o resíduo fluorescente triptofano, foram modificados no seu terminal amino com o grupo ácido amino benzóico (Abz), e foram estudados por métodos de fluorescência. Observamos transferência de energia entre o resíduo triptofano, atuando como doador, e o aceitador o-Abz. Verificamos a uma ampla distribuição de distâncias Trp-o-Abz para o alfa-MSH em água, enquanto três populações de distâncias foram observadas para o análogo modificado NDP-alfa-MSH em água, indicando estados com conformações distintas para o petídeo sintético, comparado com o hormônio nativo. Medidas em trifluoroetanol resultaram em duas populações de distâncias, tanto para o hormônio nativo como para o hormônio análogo, refletindo a diminuição, induzida pelo solvente, das conformações disponíveis para os peptídeos. Os peptídeos Cardin foram estudados na presença de heprarina, de micelas de SDS e na mistura TFE/água. O grupo fluorescente Abz foi incorporado no terminal amino e o grupo aceitador etilenodiamina-N-[2,4- dinitrofenil] (Eddnp) foi incorporado ao terminal carboxílico dos peptídeos. A distribuição de distâncias entre as extremidades, recuperadas dos dados de fluorescência resolvida no tempo, indicaram a presença de conformações estendidas em solução aquosa e a ocorrência de conformações compactas na interação com heparina e SDS ou em soluções com TFE. As distâncias entre as extremidades recuperadas foram maiores que aquelas esperadas para osI peptídeos na conformação hélice alfa, sugerindo a ocorrência de estruturas dobradas além da hélice alfa. A metodologia da transferência de energia se mostrou útil para os estudos de dinâmica de peptídeos em solução. / Steady state and time-resolved fluorescence spectroscopy were used to study the conformational dynamics of three families of peptides: the carboxyl terminal of the neuroendocrine peptide (782Cl), the alpha melanocytestimulating hormone (alpha-MSH) and heparin-binding consensus sequence peptides (Cardin motif peptides). The fluorescence methods were based on quenching of the emission of a fluorophore present in the peptide, either by collisional interaction with a quencher, as by energy transfer to an acceptor group. In the second case, within the hypothesis that different peptide conformations are in equilibrium during the fluorescence decay, we supposed that the intensity decay was modulated by an acceptor-donor distance distribution function, f(r). A computational procedure was developed using the CONTIN program, to recover, from the time-resolved fluorescence data, the distance distribution between donor and acceptor groups attached to the peptides. The methodology proved to be useful to provide quantitative information about conformational dynamics of peptides, its dependency on the solvent and its interaction with other molecules present in the medium. The peptide 782CT and its analogs A12 and A18 were studied by examination of fluorescence from the tyrosine residue present in the position five of the amino acid sequence. There were no appreciable differences in the intensity decay, anisotropy decay and iodide quenching between the three peptides, that could be correlated to observed differences in the inhibition of the pro-hormane convertase 2 (PC2). The peptide hormone alpha-MSH and its more potent analog [Nle(4),0- Phe(7)]alpha-MSH (NDP-alpha-MSH), containing the fluorescent residue tryptophan, were labeled at the amino terminal with the amino benzoic acid (Abz) group, and were also examined by fluorescence methods. We observed energy transfer between the tryptophan residue acting as donor and Abz as acceptor, and verified a broad Trp-o-Abz distance distribution for alpha-MSH in aqueous medium, while three different distance populations could be identified for the labeled analog NDP-alpha-MSH in water, indicating distinct conformational states for the synthetic peptide, compared with the native hormone. Measurements in trifluoroethanol resulted in the recovery of two Abzlrp distance populations, both for the native and the analog hormones, reflecting the decrease, induced by the solvent, of the conformational states available to the peptides. The Cardin motif peptides were examined in the presence of heparin, SDS micelles and in TFE/water mixtures. The fluorescent group Abz was attached to the amino terminal and the acceptor group N-(2,4 dinitrophenyl)ethylenediamine (Eddnp) was bound to the carboxyl terminal of the peptides. The end-to-end distance distribution recovered from time-resolved fluorescence data indicated extend conformation in aqueous medium and the occurrence of compact conformations under interaction with heparin and SDS or in the medium containing TFE. The end-to-end distances recovered were lower than those expected for the peptides in alpha helix conformation, suggesting the occurrence of turned structures beyond the alpha helix. The energy transfer methodology shows to be useful to study conformational dynamics of peptides in solution.

Low intensity and low frequency ultrasound has been shown to modulate ion channel currents, membrane capacitive currents, and as a result, neuronal activity. Ultrasound has been used as a non-invasive way to modulate neuronal activity in vivo using mice as well as human subjects. Ultrasound with acoustic frequency as low as 0.35 MHz can be focussed on a region as small as 2 mm with reversible effects and no increase in temperature. In this study, two ultrasound transducers with different resonant frequency have been used to excite neuronal cultures. The resulting changes in the network properties such as synchronised network burst frequency, density, clustering and path length have been analysed. The study shows that ultrasound stimulation at acoustic frequency 450 kHz (ISPPA =11.3 mW/cm2) significantly modulates the above mentioned parameters and causes deviations from small world network properties of the control network.

The proton dependent oligopeptide transporters (POT family) are members of the Major Facilitator Superfamily of secondary active transporter proteins. They use the transmembrane proton gradient to drive the uptake of di- and tripeptides into the cytoplasm. Members of the family are highly conserved in pro- and eukaryotic genomes, and in humans they are responsible for the oral absorption of many drug families, including -lactam antibiotics. Recently, the crystal structures of PepTSo and PepTSt, two prokaryotic homologues of the human proteins PepT1 and PepT2, captured the proteins in two distinct conformations, providing insight into the structural aspects of the transport mechanism. A protocol was designed for functional liposome reconstitution of POT proteins, and transport assays were conducted to characterise their substrate specificity, pH dependence and kinetic properties. Using site-directed mutagenesis, we identified binding site residues involved in peptide recognition and proton translocation, and distinguished between the two roles by comparing protein activity in proton- and peptide-driven conditions. We also investigated the roles of key residues in the conformational transitions that accompany the transport cycle, using data from biochemical assays, molecular dynamics simulations and modeling, as well as electron paramagnetic resonance measurements. In addition, several bacterial POT members were screened for crystallisation, in order to assess their stability and crystal diffraction quality in different detergents. Further work was performed with bacterial POT homologues YdgR and GkPOT, including binding studies using NMR spectroscopy and assaying drug transport in vivo and in vitro. Together, the data establish bacterial POTs as model systems for studying the mammalian oligopeptide transporters, and a mechanistic model for peptide transport is proposed.

Correct functioning of the brain relies upon the precise connectivity between the billions of neurons that make up this crucial organ. Aberrations in the formation of these elaborate neural networks lead to neurodegenerative and neuropsychiatric disorders. A synapse-spanning molecular triad, involving members of the Neurexin, Cbln and ionotropic glutamate receptor delta families of proteins, is crucial for the accurate formation and proper function of synapses in the cerebellum. This trans-synaptic complex has been implicated in the molecular mechanisms behind motor control and motor learning, and furthermore individual members have been linked to diseases such as Alzheimer’s, autism spectrum disorders and schizophrenia. The major findings presented in this thesis include: crystal structures of the amino-terminal domains (ATD) of the two members of the ionotropic glutamate receptor delta (iGluR-Delta) family, functional characterisation of the effects of disrupting the ATD interface in one member of the iGluR-Delta family, a crystal structure of the C1q domain of Cbln1, biophysical analysis of the molecular interactions within the Neurexin-Cbln1-GluD2 trans-synaptic complex, as well as evidence for the domain arrangement of the ecto-domain of the iGluR-Delta proteins. Together, these data enhance our knowledge of the molecular details of this macro-molecular complex and provide evidence to support models for the mechanisms of their involvement in synapse formation and function, thereby making a contribution to the vast and medically relevant field of molecular neurobiology.

This thesis investigates the mechanisms behind natural silk spinning by integrating rheology, spectroscopy and small angle scattering to better understand this process and to guide our efforts towards mimicking Nature’s ways of producing high performance fibres. As a result of natural selection, arthropods such as spiders and moths have evolved the ability to excrete silk proteins in a highly controlled manner. Spun from liquid feedstocks, silk fibres are used ex vivo to build structures with mechanical properties currently unmatched by industrial filaments. As yet, relatively little attention has been directed to the investigation of spinning under biologically relevant conditions. To better understand how and why silk is spun, this thesis bridges the gap between liquid silk flow properties and structure development. To directly connect the two, I have developed and deployed novel experimental platforms that combine infrared spectroscopy and small angle scattering with rheology. This approach has clarified long-standing ambiguities on the structural root of silk’s apparently complex flow properties. Small angle scattering revealed the length scales involved in the flow induced solidification under a range of spinning conditions. Mo reover, infrared spectroscopy offered a unique perspective into silk’s formation process immediately after excretion. In a similar manner to the post-extrusion tuning of the properties of partly solidified spider silk filaments, this thesis has revealed that silkworm silk fibres are far from completely formed once excreted. One might describe the filaments of mulberry silkworm as seeded molten polymers that form its hydrogen bonding network and crystallises slowly on site. Consequently, it enlightens that post-spinning conditions are equally paramount for silkworm silk, giving an explanation for the relatively poorer mechanical properties. The comparison of silks from a range of species, allowed this hypothesis to be extended to wild silkworm silk. My insights into spinning had the fortuitous repercussion of facilitating silk fibre solubilisation leading to the development of better artificial silk feedstocks flowing like native silks. With these findings, I believe we are now in an improved position to conceive artificial fibres with properties rivalling those of Nature.

RNA-dependent RNA polymerases (RdRps) play a vital role in the life cycle of RNA viruses, being responsible for genome replication and mRNA transcription. In this thesis viral RdRps (vRdRps) of dsRNA bacteriophage phi6 (phi6 RdRp) and Severe Acute Respiratory Syndrome (SARS) coronavirus [non structural protein 12 (NSP-12)] are studied. For SARS polymerase NSP-12, a library-based screening method known as ESPRIT (Expression of Soluble Protein by Random Incremental Truncation) was employed in an attempt to isolate domains of NSP-12 that express solubly in Escherichia coli (E. coli) and are thereby suitable for structural studies. This experiment identified for the first time in a systematic fashion, conditions under which the SARS polymerase could be solubly expressed at small scale and allowed mapping of domain boundaries. Further experiments explored different approaches for increasing expression levels of tractable fragments at large scale. Bacteriophage phi6 RdRp is one of the best studied vRdRps. It initiates RNA synthesis using a de novo mechanism without the need for a primer. Although formation of the de novo initiation complex has been well studied, little is known about the mechanism for the transition from initiation to elongation (i.e. extension of an initiated dinucleotide daughter strand). In the phi6 RdRp initiation complex the C-terminal domain (CTD) blocks the exit path of the newly synthesised dsRNA which must be displaced for the addition of the third nucleotide. The crystal structure of a C-terminally truncated phi6 RdRp (P2T1) reveals the strong non-covalent interactions between the CTD and the main body of the polymerase that must be overcome for the elongation reaction to proceed. Comparing new crystal structures of complexes of both wild-type (WT) and a mutant RdRp (E634 to Q, which removes a salt-bridge between the CTD and main body of the polymerase) with various oligonucleotides (linear and hairpin), nucleoside triphosphates (NTPs) and divalent cations, alongside their biophysical and biochemical properties, provides an insight into the precise molecular details of the transition reaction. Thermal denaturation experiments reveal that Mn2+ acquired from the cell and bound at the phi6 RdRp non-catalytic ion site sufficiently weakens the polymerase structure to facilitate the displacement of the CTD. Our crystallographic and biochemical data also indicate that Mn2+ is released during this displacement and must be replaced for the elongation to proceed. Our data explain the role of the non-catalytic divalent cation in vRdRps and pinpoint the Mn2+-dependent step in viral replication. In addition, by inserting a dysfunctional Mg2+ at the non-catalytic ion site for both WT and E634Q RdRps we captured structures with two NTPs bound within the active site in the absence of Watson-Crick base pairing with template and could map movements of divalent cations during preinitiation through to initiation. Oligonucleotides present on the surface of phi6 RdRp allowed mapping of key residues involved in template entry and unwinding of dsRNA; these preinitiation stages have not been observed previously. Considering the high structural homology of phi6 RdRp with other vRdRps, particularly from (+)ssRNA hepatitis C virus (HCV), insights into the mechanistic and structural details of phi6 RdRp are thought to be relevant to the general understanding of vRdRps.

Fundamental to cell adhesion and migration, integrins are large heterodimeric membrane proteins that link the extracellular matrix to the actin cytoskeleton. Uniquely, these adhesion receptors mediate inside-out signal transduction, whereby extracellular adhesion is activated from within the cell by talin, a large cytoskeletal protein that binds to the cytoplasmic tail of the β integrin subunit via its PTB-like F3 domain. Features of the interface between talin1 and small β3 fragments only have been described previously. Through NMR studies of full-length integrin β tails, we have found that β tails differ widely in their interactions with different talin isoforms. The muscle-specific β1D/talin2 complex exhibited particularly high affinity, leading to the X-ray crystal structure of the β1D tail/talin2 F2-F3 complex. Further NMR and biological experiments demonstrated that integrin activation is induced by a concerted series of interactions between the talin F3 domain and the β tail and between the talin F2 domain and the cell membrane. Additional studies revealed the structural determinants of tight talin2/β1D binding and the basis of more general differences between β1 and β3 talin binding. NMR studies were also performed on tyrosine-phosphorylated integrin tails binding to the PTB domains of talin1 and Dok1, an inhibitor of integrin activation; these revealed that phosphorylation can inhibit integrin activation by increasing the affinity of the β tail for talin competitors. Key residues governing this switch were identified, and proteins were engineered with reversed affinities, offering potentially useful biological tools. Taken together, these results reveal the remarkable complexity of structural features that enable talin and its competitors to mediate this important form of transmembrane signalling.

Precise regulation of cell cycle events by the Cdk-control network is essential for cell proliferation and the perpetuation of life. The unidirectionality of cell cycle progression is governed by several critical irreversible transitions: the G1-to-S transition, the G2-to-M transition, and the M-to-G1 transition. Recent experimental and theoretical evidence has pulled into question the consensus view that irreversible protein degradation causes the irreversibility of those transitions. A new view has started to emerge, which explains the irreversibility of cell cycle transitions as a consequence of systems-level feedback rather than of proteolysis. This thesis applies mathematical modelling approaches to test this proposal for the Mto- G1 transition, which consists of two consecutive irreversible substeps: the metaphase-to-anaphase transition, and mitotic exit. The main objectives of the present work were: (i) to develop deterministic models to identify the essential molecular feedback loops and to examine their roles in the irreversibility of the M-to-G1 transition; (ii) to present a straightforward and reliable workflow to translate deterministic models of reaction networks into stochastic models; (iii) to explore the effects of noise on the cell cycle transitions using stochastic models, and to compare the deterministic and the stochastic approaches. In the first part of this thesis, I constructed a simplified deterministic model of the metaphase-to-anaphase transition, which is mainly regulated by the spindle assembly checkpoint (the SAC). Based on the essential feedback loops causing the bistability of the transition, this deterministic model provides explanations for three open questions regarding the SAC: Why is the SAC not reactivated when the kinetochore tension decreases to zero at anaphase onset? How can a single unattached kinetochore keep the SAC active? How is the synchronized and abrupt destruction of cohesin triggered? This deterministic model was then translated into a stochastic model of the SAC by treating the kinetochore microtubule attachment at prometaphase as a noisy process. The stochastic model was analyzed and simulation results were compared to the experimental data, with the aim of explaining the mitotic timing regulation by the SAC. Our model works remarkably well in qualitatively explaining experimental key findings and also makes testable predictions for different cell lines with very different number of chromosomes. The noise generated from the chemical interactions was found to only perturb the transit timing of the mitotic events, but not their ultimate outcomes: all cells eventually undergo anaphase, however, the time required to satisfy the SAC differs between cells due to stochastic effects. In the second part of the thesis, stochastic models of mitotic exit were created for two model organisms, budding yeast and mammalian cells. I analyzed the role of noise in mitotic exit at both the single-cell and the population level. Stochastic time series simulations of the models are able to explain the phenomenon of reversible mitotic exit, which is observed under specific experimental conditions in both model organisms. In spite of the fact that the detailed molecular networks of mitotic exit are very different in budding yeast and mammalian cells, their dynamic properties are similar. Importantly, bistability of the transitions is successfully captured also in the stochastic models. This work strongly supports the hypothesis that uni-directional cell cycle progression is a consequence of systems-level feedback in the cell cycle control system. Systems-level feedback creates alternative steady states, which allows cells to accomplish irreversible transitions, such as the M-to-G1 transition studied here. We demonstrate that stochastic models can serve as powerful tools to capture and study the heterogeneity of dynamical features among individual cells. In this way, stochastic simulations not only complement the deterministic approach, but also help to obtain a better understanding of mechanistic aspects. We argue that the effects of noise and the potential needs for stochastic simulations should not be overlooked in studying dynamic features of biological systems.