Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

Modelo cinético estocástico para a transcrição considerando colisões entre as moléculas de RNA polimerase

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo do coeficiente de difusão no enovelamento de proteína

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Analysis of modified bowtie nanoantennas in the excitation and emission regimes

In this work, we analyze modified bowtie nanoantennas with polynomial sides in the excitation and emission regimes. In the excitation regime, the antennas are illuminated by an incident plane wave, and in the emission regime, the excitation is fulfilled by infinitesimal electric dipole positioned in the gap of the nanoantennas. Several antennas with different sizes and polynomial order were numerically analyzed by method of moments. The results show that these novel antennas possess a controllable resonance by the polynomial order and good characteristics of near field enhancement and confinement for applications in enhancement of spontaneous emission of a single molecule.

Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Non-centrosymmetric crystals of new N-benzylideneaniline derivatives as potential materials for non-linear optics

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Transcrição cooperativa de genes ribossomais em Escherichia coli usando um modelo estocástico e dependente de sequência

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Síntese de polímeros supramoleculares derivados dos ácidos palmítico e mirístico com meglumina e suas caracterizações em meio aquoso

Pós-graduação em Química - IQ

Rotational diffusion membrane and fluorescence anisotropy.

Structural properties of model membranes, such as lipid vesicles, may be investigated through the addition of fluorescent probes. After incorporation, the fluorescent molecules are excited with linearly polarized light and the fluorescence emission is depolarized due to translational as well as rotational diffusion during the lifetime of the excited state. The monitoring of emitted light is undertaken through the technique of time-resolved fluorescence: the intensity of the emitted light informs on fluorescence decay times, and the decay of the components of the emitted light yield rotational correlation times which inform on the fluidity of the medium. The fluorescent molecule DPH, of uniaxial symmetry, is rather hydrophobic and has collinear transition and emission moments. It has been used frequently as a probe for the monitoring of the fluidity of the lipid bilayer along the phase transition of the chains. The interpretation of experimental data requires models for localization of fluorescent molecules as well as for possible restrictions on their movement. In this study, we develop calculations for two models for uniaxial diffusion of fluorescent molecules, such as DPH, suggested in several articles in the literature. A zeroth order test model consists of a free randomly rotating dipole in a homogeneous solution, and serves as the basis for the study of the diffusion of models in anisotropic media. In the second model, we consider random rotations of emitting dipoles distributed within cones with their axes perpendicular to the vesicle spherical geometry. In the third model, the dipole rotates in the plane of the of bilayer spherical geometry, within a movement that might occur between the monolayers forming the bilayer. For each of the models analysed, two methods are used by us in order to analyse the rotational diffusion: (I) solution of the corresponding rotational diffusion equation for a single molecule, taking into account the boundary conditions imposed by the models, for the probability of the fluorescent molecule to be found with a given configuration at time t. Considering the distribution of molecules in the geometry proposed, we obtain the analytical expression for the fluorescence anisotropy, except for the cone geometry, for which the solution is obtained numerically; (II) numerical simulations of a restricted rotational random walk in the two geometries corresponding to the two models. The latter method may be very useful in the cases of low-symmetry geometries or of composed geometries.

Design and synthesis of novel non peptidomimtic beta-secretase inhibitors in the treatment of Alzheimer's disease

The aspartic protease BACE1 (β-amyloid precursor protein cleaving enzyme, β-secretase) is recognized as one of the most promising targets in the treatment of Alzheimer's disease (AD). The accumulation of β-amyloid peptide (Aβ) in the brain is a major factor in the pathogenesis of AD. Aβ is formed by initial cleavage of β-amyloid precursor protein (APP) by β-secretase, therefore BACE1 inhibition represents one of the therapeutic approaches to control progression of AD, by preventing the abnormal generation of Aβ. For this reason, in the last decade, many research efforts have focused at the identification of new BACE1 inhibitors as drug candidates. Generally, BACE1 inhibitors are grouped into two families: substrate-based inhibitors, designed as peptidomimetic inhibitors, and non-peptidomimetic ones. The research on non-peptidomimetic small molecules BACE1 inhibitors remains the most interesting approach, since these compounds hold an improved bioavailability after systemic administration, due to a good blood-brain barrier permeability in comparison to peptidomimetic inhibitors. Very recently, our research group discovered a new promising lead compound for the treatment of AD, named lipocrine, a hybrid derivative between lipoic acid and the AChE inhibitor (AChEI) tacrine, characterized by a tetrahydroacridinic moiety. Lipocrine is one of the first compounds able to inhibit the catalytic activity of AChE and AChE-induced amyloid-β aggregation and to protect against reactive oxygen species. Due to this interesting profile, lipocrine was also evaluated for BACE1 inhibitory activity, resulting in a potent lead compound for BACE1 inhibition. Starting from this interesting profile, a series of tetrahydroacridine analogues were synthesised varying the chain length between the two fragments. Moreover, following the approach of combining in a single molecule two different pharmacophores, we designed and synthesised different compounds bearing the moieties of known AChEIs (rivastigmine and caproctamine) coupled with lipoic acid, since it was shown that dithiolane group is an important structural feature of lipocrine for the optimal inhibition of BACE1. All the tetrahydroacridines, rivastigmine and caproctamine-based compounds, were evaluated for BACE1 inhibitory activity in a FRET (fluorescence resonance energy transfer) enzymatic assay (test A). With the aim to enhancing the biological activity of the lead compound, we applied the molecular simplification approach to design and synthesize novel heterocyclic compounds related to lipocrine, in which the tetrahydroacridine moiety was replaced by 4-amino-quinoline or 4-amino-quinazoline rings. All the synthesized compounds were also evaluated in a modified FRET enzymatic assay (test B), changing the fluorescent substrate for enzymatic BACE1 cleavage. This test method guided deep structure-activity relationships for BACE1 inhibition on the most promising quinazoline-based derivatives. By varying the substituent on the 2-position of the quinazoline ring and by replacing the lipoic acid residue in lateral chain with different moieties (i.e. trans-ferulic acid, a known antioxidant molecule), a series of quinazoline derivatives were obtained. In order to confirm inhibitory activity of the most active compounds, they were evaluated with a third FRET assay (test C) which, surprisingly, did not confirm the previous good activity profiles. An evaluation study of kinetic parameters of the three assays revealed that method C is endowed with the best specificity and enzymatic efficiency. Biological evaluation of the modified 2,4-diamino-quinazoline derivatives measured through the method C, allow to obtain a new lead compound bearing the trans-ferulic acid residue coupled to 2,4-diamino-quinazoline core endowed with a good BACE1 inhibitory activity (IC50 = 0.8 mM). We reported on the variability of the results in the three different FRET assays that are known to have some disadvantages in term of interference rates that are strongly dependent on compound properties. The observed results variability could be also ascribed to different enzyme origin, varied substrate and different fluorescent groups. The inhibitors should be tested on a parallel screening in order to have a more reliable data prior to be tested into cellular assay. With this aim, preliminary cellular BACE1 inhibition assay carried out on lipocrine confirmed a good cellular activity profile (EC50 = 3.7 mM) strengthening the idea to find a small molecule non-peptidomimetic compound as BACE1 inhibitor. In conclusion, the present study allowed to identify a new lead compound endowed with BACE1 inhibitory activity in submicromolar range. Further lead optimization to the obtained derivative is needed in order to obtain a more potent and a selective BACE1 inhibitor based on 2,4-diamino-quinazoline scaffold. A side project related to the synthesis of novel enzymatic inhibitors of BACE1 in order to explore the pseudopeptidic transition-state isosteres chemistry was carried out during research stage at Università de Montrèal (Canada) in Hanessian's group. The aim of this work has been the synthesis of the δ-aminocyclohexane carboxylic acid motif with stereochemically defined substitution to incorporating such a constrained core in potential BACE1 inhibitors. This fragment, endowed with reduced peptidic character, is not known in the context of peptidomimetic design. In particular, we envisioned an alternative route based on an organocatalytic asymmetric conjugate addition of nitroalkanes to cyclohexenone in presence of D-proline and trans-2,5-dimethylpiperazine. The enantioenriched obtained 3-(α-nitroalkyl)-cyclohexanones were further functionalized to give the corresponding δ-nitroalkyl cyclohexane carboxylic acids. These intermediates were elaborated to the target structures 3-(α-aminoalkyl)-1-cyclohexane carboxylic acids in a new readily accessible way.

New Synthetic Polyamines as Multi-Target-Directed Ligands for the Treatment of Alzheimer's Disease and Cancer: Design, Synthesis and Biological Evaluation

Alzheimer's disease (AD) and cancer represent two of the main causes of death worldwide. They are complex multifactorial diseases and several biochemical targets have been recognized to play a fundamental role in their development. Basing on their complex nature, a promising therapeutical approach could be represented by the so-called "Multi-Target-Directed Ligand" approach. This new strategy is based on the assumption that a single molecule could hit several targets responsible for the onset and/or progression of the pathology. In particular in AD, most currently prescribed drugs aim to increase the level of acetylcholine in the brain by inhibiting the enzyme acetylcholinesterase (AChE). However, clinical experience shows that AChE inhibition is a palliative treatment, and the simple modulation of a single target does not address AD aetiology. Research into newer and more potent anti-AD agents is thus focused on compounds whose properties go beyond AChE inhibition (such as inhibition of the enzyme β-secretase and inhibition of the aggregation of beta-amyloid). Therefore, the MTDL strategy seems a more appropriate approach for addressing the complexity of AD and may provide new drugs for tackling its multifactorial nature. In this thesis, it is described the design of new MTDLs able to tackle the multifactorial nature of AD. Such new MTDLs designed are less flexible analogues of Caproctamine, one of the first MTDL owing biological properties useful for the AD treatment. These new compounds are able to inhibit the enzymes AChE, beta-secretase and to inhibit both AChE-induced and self-induced beta-amyloid aggregation. In particular, the most potent compound of the series is able to inhibit AChE in subnanomolar range, to inhibit β-secretase in micromolar concentration and to inhibit both AChE-induced and self-induced beta-amyloid aggregation in micromolar concentration. Cancer, as AD, is a very complex pathology and many different therapeutical approaches are currently use for the treatment of such pathology. However, due to its multifactorial nature the MTDL approach could be, in principle, apply also to this pathology. Aim of this thesis has been the development of new molecules owing different structural motifs able to simultaneously interact with some of the multitude of targets responsible for the pathology. The designed compounds displayed cytotoxic activity in different cancer cell lines. In particular, the most potent compounds of the series have been further evaluated and they were able to bind DNA resulting 100-fold more potent than the reference compound Mitonafide. Furthermore, these compounds were able to trigger apoptosis through caspases activation and to inhibit PIN1 (preliminary result). This last protein is a very promising target because it is overexpressed in many human cancers, it functions as critical catalyst for multiple oncogenic pathways and in several cancer cell lines depletion of PIN1 determines arrest of mitosis followed by apoptosis induction. In conclusion, this study may represent a promising starting pint for the development of new MTDLs hopefully useful for cancer and AD treatment.

Biomimetisches Modell eines Photosystems aus dem pflanzlichen Photosyntheseapparat

In dieser Arbeit wurde ein biomimetisches Modell für ein pflanzliches Photosystem bestehend aus dem rekombinanten Hauptlichtsammlerkomplex (LHCII) als Absorptions- und Energietransfereinheit und einem N-terminal an das Protein gebundenen Farbstoff als Energieakzeptor hergestellt. Mehrere LHCII-Farbstoff-Konstrukte wurden getestet, die höchste Energietransfereffizienz von komplexgebundenem Chlorophyll-a zum Energieakzeptor konnte an einem LHCII-Benzoylterrylendicarboximid-Konstrukt gemessen werden. Bei Raumtemperatur wurde hier 70% der Chlorophyll-a-Anregungsenergie auf den Farbstoff übertragen, bei 77 K sogar 85%. LHCII-Farbstoffkonstrukte können helfen, strukturelle und funktionelle Eigenschaften des LHCII näher zu beleuchten. So konnte bereits in dieser Arbeit gezeigt werden, daß der N-Terminus des Komplexes im zeitlichen Mittel in eine größere Annäherung zum pigmentierten Teil des LHCII kommen muß, sonst sind Energietransfereffizienzen obiger Größenordnung nicht möglich. Weitere Erkenntnisse werden von einzelmolekülspektroskopischen Untersuchungen erwartet. Voraussetzung hierfür ist jedoch eine orientierte Immobilisierung des LHCII auf einer Glasoberfläche. Es gelang, den Komplex über eine auf molekularer Ebene eingeführte Aminosäuresequenz aus sechs Histidinen an die Nickelchelatgruppe einer auf Glas immobilisierten Meerrettich-Peroxidase zu binden. Einzelmolekülspektroskopisch konnte eine LHCII-Immobilisation senkrecht zur Proteinsymmetrieachse nachgewiesen werden. Mittelfristig wird angestrebt, LHCII-Farbstoffkonstrukte auch für photovoltaische Anwendungen nutzbar zu machen. Ein erster Meilenstein wurde in dieser Arbeit erreicht, indem es gelang, LHCII an Titandioxid, Halbleiter der sog. Grätzelzelle, zu binden.

Zwei-Photonen-Fluoreszenzmikroskopie und -Spektroskopie von Sauerstofftransportproteinen

In dieser Arbeit wurde die intrinsische Tryptophanfluoreszenz von Proteinen nach Zwei-Photonen-Anregung untersucht. Als interessantes Modellsystem wurde das Sauerstofftransportprotein der Vogelspinne Eurypelma californicum gewählt. Zum einen besitzt das Protein 148 Tryptophan-Seitenketten, so daß deren geringer Absorptionsquerschnitt kompensiert werden kann und eventuell einzelne Proteine aufgrund ihrer Tryptophanfluoreszenz detektiert werden können. Zum anderen signalisiert diese Fluoreszenz die Sauerstoffbeladung, so daß die kooperative Sauerstoffbindung auf Einzelmolekülebene untersucht werden könnte. Als limitierender Faktor hat sich die Photostabilität der Tryptophane nach Zwei-Photonen-Anregung herausgestellt. Im Mittel können von einem Hämocyanin-Molekül drei Photonen detektiert werden, bevor alle 148 Tryptophan-Seitenketten geblichen sind. Dies ist ein für Einzelmolekülspektroskopie äußerst niedriger Wert. Trotz dieser geringen Photostabilität ist es zum erstem Mal gelungen, die Diffusion einzelner Proteine mit Hilfe ihrer intrinsischen Tryptophanfluoreszenz zu beobachten. Wenn in einer geeigneten Umgebung die Photostabilität der Tryptophane höher ist, so reicht die Zahl der detektierten Photonen aus, um einzelne Teilchen abzubilden. Überraschend hat sich ergeben, daß es möglich ist, durch Lichteinstrahlung von außen in das Sauerstoffbindungsgleichgewicht einzugreifen und die Reaktion des Proteins auf die Auslenkung aus dem Gleichgewichtszustand zu beobachten. Das intensitätsabhängige Sauerstoffbindungsverhalten wurde modelliert und an die Messungen angepaßt. Die lichtinduzierte Sauerstoffabgabe führt anscheinend nicht zu einem Konformationswechsel.

Einzelmolekülspektroskopische Studien an Farbstoff-markierten Chlorophyll-a/b-Lichtsammlerkomplexen und Untersuchungen zur Integration der Komplexe in elektrochemische Solarzellen

Die zentrale Funktion des Hauptlichtsammlerkomplexes des Photosystems II, LHCII, besteht in der Absorption von Sonnenlicht und der Bereitstellung von Energie für die photosynthetische Ladungstrennung im Reaktionszentrum des Photosystems. Auch in der Regulation der Photosynthese spielt der LHCII eine wichtige Rolle, da die Energieverteilung zwischen Photosystem I und Photosystem II im Rahmen des sog. „State Transition“-Prozesses über die Verteilung der Lichtsammlerkomplexe zwischen den beiden Photosystemen gesteuert wird. Im Blickfeld des ersten Teils dieser Arbeit stand die konformative Dynamik der N-terminalen Domäne des LHCII, die wahrscheinlich in die Regulation der Lichtsammlung involviert ist. Gemeinsam mit Mitarbeitern des 3. Physikalischen Instituts der Universität Stuttgart wurde an der Etablierung einer Methode zur einzelmolekülspektroskopischen Untersuchung der Dynamik des N-Terminus gearbeitet. Als Messgröße diente der Energietransfer zwischen einem Fluoreszenzfarbstoff, der an die N-terminale Domäne gekoppelt war, und den Chlorophyllen des Komplexes. Die Funktion des LHCII als effiziente Lichtantenne bildete die Grundlage für den zweiten Teil dieser Arbeit. Hier wurde untersucht, in wie weit LHCII als Lichtsammler in eine elektrochemische Solarzelle integriert werden kann. In der potentiellen Solarzelle sollte die Anregungsenergie des LHCII auf Akzeptorfarbstoffe übertragen werden, die in der Folge Elektronen in das Leitungsband einer aus Titandioxid oder Zinndioxid bestehenden porösen Halbleiterelektrode injizierten, auf der Komplexe und Farbstoffe immobilisiert waren.

Statistical mechanics of protein complexed and condensed DNA

In this thesis I treat various biophysical questions arising in the context of complexed / ”protein-packed” DNA and DNA in confined geometries (like in viruses or toroidal DNA condensates). Using diverse theoretical methods I consider the statistical mechanics as well as the dynamics of DNA under these conditions. In the first part of the thesis (chapter 2) I derive for the first time the single molecule ”equation of state”, i.e. the force-extension relation of a looped DNA (Eq. 2.94) by using the path integral formalism. Generalizing these results I show that the presence of elastic substructures like loops or deflections caused by anchoring boundary conditions (e.g. at the AFM tip or the mica substrate) gives rise to a significant renormalization of the apparent persistence length as extracted from single molecule experiments (Eqs. 2.39 and 2.98). As I show the experimentally observed apparent persistence length reduction by a factor of 10 or more is naturally explained by this theory. In chapter 3 I theoretically consider the thermal motion of nucleosomes along a DNA template. After an extensive analysis of available experimental data and theoretical modelling of two possible mechanisms I conclude that the ”corkscrew-motion” mechanism most consistently explains this biologically important process. In chapter 4 I demonstrate that DNA-spools (architectures in which DNA circumferentially winds on a cylindrical surface, or onto itself) show a remarkable ”kinetic inertness” that protects them from tension-induced disruption on experimentally and biologically relevant timescales (cf. Fig. 4.1 and Eq. 4.18). I show that the underlying model establishes a connection between the seemingly unrelated and previously unexplained force peaks in single molecule nucleosome and DNA-toroid stretching experiments. Finally in chapter 5 I show that toroidally confined DNA (found in viruses, DNAcondensates or sperm chromatin) undergoes a transition to a twisted, highly entangled state provided that the aspect ratio of the underlying torus crosses a certain critical value (cf. Eq. 5.6 and the phase diagram in Fig. 5.4). The presented mechanism could rationalize several experimental mysteries, ranging from entangled and supercoiled toroids released from virus capsids to the unexpectedly short cholesteric pitch in the (toroidaly wound) sperm chromatin. I propose that the ”topological encapsulation” resulting from our model may have some practical implications for the gene-therapeutic DNA delivery process.