Myosin II is the molecular motor responsible for muscle contraction. It transforms the chemical energy in ATP into mechanical work while interacting with actin filaments in so called cross-bridge cycles. Myosin II or its proteolytic fragments e.g., heavy meromyosin (HMM) can be adsorbed to moderately hydrophobic surfaces in vitro, while maintaining their ability to translocate actin filaments. This enables observation of myosin-induced actin filament sliding in a microscope. This “in vitro motility assay” (IVMA) is readily used in fundamental studies of actomyosin, including studies of muscle contraction. The degree of correlation of the myosin II function in the IVMA with its function in muscle depends on how the myosin molecules are arranged on the surface. Therefore a multi-technique approach, including total internal reflection spectroscopy, fluorescence interference contrast microscopy and quartz crystal microbalance with dissipation, was applied to characterize the HMM surface configurations. Several configurations with varying distributions were identified depending on the surface property. The most favorable HMM configurations for actin binding were observed on moderately hydrophobic surfaces.   The effects on actomyosin function of different cargo sizes and amount of cargo loaded on an actin filament were also investigated. No difference in sliding velocities could be observed, independent of cargo size indicating that diffusional processive runs of myosin II along an actin filament are not crucial for actomyosin function in muscle. Furthermore, a tool for accurate velocity measurements appropriate for IVMAs at low [MgATP] was developed by utilizing the actin filament capping protein CapZ. These improvements allowed an investigation of the [MgATP]-velocity relationship to study possible processivity in fast skeletal muscle myosin II.  It is shown that the [MgATP]–velocity relationship is well described by a Michaelis-Menten hyperbola.  In addition, statistical cross-bridge modeling showed that the experimental results are in good agreement with recent findings of actomyosin cross-bridge properties, e.g., non-linear cross-bridge elasticity. However, no effect of inter-head cooperativity could be observed.   In conclusion, the described results have contributed to in-depth understanding of the actomyosin cross-bridge cycle in muscle contraction.

The auditory brainstem is comprised of a number of synapses specialized for the transmission of high-fidelity synaptic signals. Within the first three postnatal weeks, these pathways acquire the ability to process high-frequency signals without compromising timing information. However, little is known regarding developmental adaptations which confer this ability. Situated in the sound localization pathway, the calyx of Held-medial nucleus of the trapezoid body synapse provides an ideal model for investigating such adaptations as both the pre- and postsynaptic neurons are accessible to electrophysiological experimentation. Using this synapse, we have shown herein that the spatial coupling between voltage-gated calcium channels (VGCCs) and synaptic vesicles (SVs) tightens during development. Immature synapses use a loosely-coupled arrangement of many N- and P/Q-type VGCCs (“microdomain” modality) while mature synapses use a tightly-coupled arrangement of fewer P/Q-type VGCCs, to release SVs (“nanodomain” modality). As a consequence of this tightening, synaptic delay (SD) shortens. By fluorescence- and electron microscopy of SVs near active zones, we further identified the filamentous protein septin 5 as a molecular substrate, differentiating the two release modalities, which may act as a spatial barrier separating VGCCs and SVs in immature synapses. Finally, we have demonstrated that changes in release modality affect the nature of short-term plasticity observed at this synapse. Using trains of action potentials as presynaptic voltage-commands, we showed that, downstream of calcium influx, the microdomain modality promotes short-term facilitation in excitatory postsynaptic currents (IEPSC), and calcium-dependent decreases in SD, with these being absent in synapses employing the nanodomain modality. In contrast, we found that as a result of depletion of SVs, short-term depression of IEPSC dominates in synapses using the nanodomain modality, and correlates with calcium-dependent increases in SD. These findings imply that the type of release modality has a significant impact on the strength and timing of synaptic responses. The microdomain modality imparts greater dynamic range in timing and strength, but does so at the cost of efficiency and fidelity, while the nanodomain modality is a key accomplishment consolidating the high-fidelity abilities of this synapse.

The auditory brainstem is comprised of a number of synapses specialized for the transmission of high-fidelity synaptic signals. Within the first three postnatal weeks, these pathways acquire the ability to process high-frequency signals without compromising timing information. However, little is known regarding developmental adaptations which confer this ability. Situated in the sound localization pathway, the calyx of Held-medial nucleus of the trapezoid body synapse provides an ideal model for investigating such adaptations as both the pre- and postsynaptic neurons are accessible to electrophysiological experimentation. Using this synapse, we have shown herein that the spatial coupling between voltage-gated calcium channels (VGCCs) and synaptic vesicles (SVs) tightens during development. Immature synapses use a loosely-coupled arrangement of many N- and P/Q-type VGCCs (“microdomain” modality) while mature synapses use a tightly-coupled arrangement of fewer P/Q-type VGCCs, to release SVs (“nanodomain” modality). As a consequence of this tightening, synaptic delay (SD) shortens. By fluorescence- and electron microscopy of SVs near active zones, we further identified the filamentous protein septin 5 as a molecular substrate, differentiating the two release modalities, which may act as a spatial barrier separating VGCCs and SVs in immature synapses. Finally, we have demonstrated that changes in release modality affect the nature of short-term plasticity observed at this synapse. Using trains of action potentials as presynaptic voltage-commands, we showed that, downstream of calcium influx, the microdomain modality promotes short-term facilitation in excitatory postsynaptic currents (IEPSC), and calcium-dependent decreases in SD, with these being absent in synapses employing the nanodomain modality. In contrast, we found that as a result of depletion of SVs, short-term depression of IEPSC dominates in synapses using the nanodomain modality, and correlates with calcium-dependent increases in SD. These findings imply that the type of release modality has a significant impact on the strength and timing of synaptic responses. The microdomain modality imparts greater dynamic range in timing and strength, but does so at the cost of efficiency and fidelity, while the nanodomain modality is a key accomplishment consolidating the high-fidelity abilities of this synapse.

This dissertation is divided into three major sections (one on dendrimers, one on tripodal metal ligands and one on a research oriented chemistry curricula) with a primary focus on different types of multicomponent assemblies. In the first chapter, a system is described that used a multicomponent assembly of AT-PAMAM dendrimers and an indicator, carboxyfluorescein, to detect and identify various polyanions at a low micromolar concentration. The system was able to successfully differentiate twelve anions, many of biological interest, including three tricarboxylates. The tricarboxylates were differentiated based primarily on the regiochemistry of the anionic groups. In the second chapter, further studies with AT-PAMAM dendrimers were carried out to provide some understanding of the thermodynamic origins of binding. Utilizing isothermal titration calorimetry, the binding of the dendrimers to large polyanionic dendrons with increasing numbers of charges was studied. Through these studies, the thermodynamic values of the binding events were obtained allowing us to explore the properties of the dendrimers. The cooperativity of the system was measured, and primarily negative cooperativity determined by the entropic contributions was uncovered. As the dendrimers increased in size, the thermodynamic origins of binding were determined to a greater extent by the entropy of binding. In the third chapter, a novel dynamic ligand system for metal binding is described. In the presence of a metal salt, a heterocyclic aldehyde and a secondary amine with two heterocyclic arms reversibly condense to form a hemiaminal with a tripodal metal binding site. This chapter describes studies on the metal binding ability, the variety of metals that will lead to this formation, the effects of anions and the range of aldehydes that can be used are described. Furthermore, the system’s reversibility was explored. Finally, the use of a bistriazole secondary amine was explored. The modular nature of triazole formation could lead to the introduction of additional functionalities. The fourth chapter discusses how the novel ligand system could be used to study the enantiomeric excess (ee) of chiral thiols. Based upon the system’s ability to form a stable hemiaminal thioether, a CD signal could be generated that is proportional to the amount of a particular enantiomer in solution. Using this system, a calibration curve relating CD signal and ee can be generated giving the ee of an unknown solution. In the final chapter, a look at the Freshman Research Initiative will be carried out with a focus on the ability to teach basic skills in an introductory laboratory through research. Four different skills or techniques will be explored through three different FRI streams,x and how they teach the four skills. Finally, analysis of the success of the program, particularly students’ success in the next laboratory course in the sequence, is discussed, and a model for adopting this type of teaching at other universities is given. / text

T cell activation and thymic selection are thought to be determined by the binding propensity (avidity or affinity) of the T cell receptor (TCR) to its ligands. However, binding propensity quantified by previous 3D TCR–pMHC kinetics such as using tetramer staining or surface plasmon resonance (SPR) under estimate TCR–pMHC interaction due to neglecting physiological conditions. Recent studies considering membrane contribution in TCR–pMHC interaction reported 2D kinetics and force regulated bond dissociation kinetics have better prediction to biological responses in CD8+ T cells. In this study, we further tested the findings in CD4+ T cells and CD4+ CD8+ (double-positive, DP) thymocytes. We analyzed TCR–pMHC interaction for a well-characterized panel of altered peptide ligands (APLs) on multiple transgenic mouse TCR systems. Using ultrasensitive 2D mechanical assays, in situ 2D kinetic measurements show better sensitivity than the SPR 3D kinetic measurements in gauging the ligand potency and thymic selection. Furthermore, force-regulated bond lifetime of TCR–pMHC interaction amplifies the discrimination in recognition of APLs and thymic selection. When force was applied to TCR–pMHC–CD4/8 bonds, two distinct patterns emerged: agonist/negative selecting ligands formed CD4/8-dependent catch-slip bonds where lifetime first increased, reached a maximum, then decreased with increasing force, whereas antagonist/positive selecting ligands formed slip-only bonds where lifetime monotonically decreases with increasing force. Our results highlight an important role of mechanical force in ligand discrimination and suggest a new mechanism for T cell activation and thymic selection that is distinct from previous models based on 3D measurements.

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Les protéines accomplissent leur fonction dans la cellule grâce à leur faculté de changer de forme. Chaque classe de protéines peut se caractériser par une structure spécia- lisée partagée par ses membres avec un certain degré de variabilité. Tel est le cas des protéines à motifs mains-EF, qui se transforment en liant et déliant l ’ion calcium. Ce motif permet à la Troponin C de s’ouvrir et se refermer afin de moduler le mécanisme de contraction des fibres musculaires. Un mécanisme similaire permet à la Calmoduline de gérer l’activité de divers canaux cellulaires. Les techniques de simulations numériques peuvent aider à comprendre les trajectoires de ces transformations. Le projet principal de cette thèse consistait à développer une méthode informatique multi-échelle permettant de simuler des mouvements complexes à l’intérieur d ’une protéine. La représentation multi-échelle développée peut changer et s’adapter en cours de simulation. La méthode, ART holographique, explore l’espace en générant des basculements d’ensembles atomiques, selon des champs de force atomistiques non biaisés indiquant à tout moment comment les ensembles doivent pivoter. La méthode réduit le calcul des fluctuations locales mais conserve une représentation spatiale complète. La représentation multi-échelle est combinée à une technique de recherche de passages de transition énergétiquement favorables, ART nouveau, qui conduit la trajectoire moléculaire d ’étape en étape. Appliquée à plusieurs protéines, dont la Calmodulin et la Troponin C, ART holographique génère des trajectoires de transformation entre des conformations distantes de celles-ci, déjà connues grâce aux techniques de RMN ou de cristallographie. L’usage d ’une représentation spatiale complète tout au long de la simulation favorise le discernement de certains détails des mécanismes. Le rôle, l’ordre d ’intervention, ainsi que la coopérativité de certains résidus et structures impliqués dans le mécanisme des paires main-EF ont été explorés plus en détail et un état intermédiaire est proposé. / Proteins accomplish their function inside cells by means of conformational changes. Each protein class may be characterized by a specialized structure shared by its members with some variability. EF-hands proteins present a special motif which transforms itself while binding or unbinding the calcium ion. This structure allows Troponin C domains to open and close as it modulates the muscular fibers contraction. A similar mechanism allow Calmodulin to manage the activity of a diversity of protein channels. Computational techniques may help discover how these transformations occur. The main project of this thesis was the development of a multi-scale computational method for the simulation of complex motions inside a protein. The multi-scale approach is designed to adapt and change all along the simulation. The method, holographic ART, explore conformational space by generating swiveling and rotation of atomic ensembles, leaded by non biased atomistic forcefields. This determines at each step the overall motion, keeping a complete spatial representation, but with minimal local fluctuations computation. The multi-scale representation is combined with a unbiased open ended algorithm for identifying transitions states, ART nouveau, which guides the molecular trajectory from state to state. Applied to several proteins, the method was able to generate transforma- tion trajectories between distant conformations known from NMR and crystallography techniques. The use of a complete spatial representation throughout the simulation allows the method to capture atomistic details of each event. The purpose, the intervention order, as well as cooperativity between some residues and sub-structures involved in the EF-hand pair mechanism have been explored more in detail and an intermediate state is proposed. / Les films de simulations qui accompagnent le document ont été réalisés avec Pymol.

À la différence des liquides simples, les solides amorphes, une vaste catégorie de matériaux allant des verres métalliques aux émulsions concentrées, ne se mettent à s'écouler qu'au-delà d'une contrainte finie. Notre thèse a pour objet la modélisation de cet écoulement, dans un cadre général et avec un accent mis sur les hétérogénéités. En premier lieu, notre travail a porté sur l'inclusion d'inhomogénéités dans le cadre de la théorie de couplage de modes appliquée à la rhéologie et nous avons notamment obtenu une équation générale d'évolution des inhomogénéités de densité. À basse température, l'écoulement est en effet fortement hétérogène : des phases de déformation élastique sont entrecoupées de réarrangements de particules, brusques et localisés, qui interagissent par le biais des déformations élastiques qu'ils génèrent. En second lieu, nous avons donc considéré un modèle calqué sur ce scénario et affiné ses éléments constitutifs pour rendre compte de la compétition entre cisaillement appliqué et réarrangements locaux, à l'origine de la courbe d'écoulement des matériaux athermiques. Cette dernière a été reproduite de manière satisfaisante. Pour ce qui est des corrélations spatiales dans l'écoulement, nous avons montré qu'il n'existe pas de loi d'échelle universelle dans les modèles élasto-plastiques, malgré la présence d'une classe de longueurs de corrélation décroissant comme dot{gamma}^{ icefrac{-1}{d}} en d dimensions, dans le régime dominé par le cisaillement. Par ailleurs, dans diverses variantes du modèle, le cisaillement se trouve localisé dans une région du matériau. Ce phénomène apparaît dès lors que les blocs élasto-plastiques sont durablement fragilisés à la suite d'un événement plastique. Enfin, les prédictions du modèle ont été directement mises en regard avec des expériences sur l'écoulement en microcanal d'émulsions concentrées et des simulations de dynamique moléculaire à température nulle. Les écarts observés nous ont poussé à développer et implémenter un code plus flexible, qui s'appuie sur une routine simplifiée d'Éléments Finis et rend mieux compte du désordre structurel et des effets inertiels. / Contrary to the case of simple fluids, a finite stress is required to initiate the flow of amorphous solids, a broad class of materials ranging from bulk metallic glasses to dense emulsions. The objective of this thesis is to model the flow of these materials in a general framework, with an emphasis on heterogeneities. In a first approach, using the liquid regime as a starting point, I have investigated to what extent inhomogeneities can be accommodated in the framework of the mode-coupling theory of rheology. A generic equation for the evolution of density inhomogeneities has been derived. At low temperatures, the flow is indeed quite heterogeneous: it consists of periods of elastic deformation interspersed with swift localised rearrangements of particles, that induce long-range elastic deformations and can thereby spark off new rearrangements. In a second approach, a model rooted in this scenario has been refined so as to reflect the interplay between the external drive and the localised rearrangements, which is at the origin of the flow curve of athermal solids. The latter has been reproduced satisfactorily. Turning to spatial correlations in the flow, we have shown that there exists no universal scaling for these correlations in elastoplastic models, although a broad class of correlation lengths scale with dot{gamma}^{ icefrac{-1}{d}} in the shear-dominated regime in d dimensions. Besides, shear localisation has been observed in diverse variants of the model, whenever blocks are durably weakened following a plastic event. Finally, we have directly compared model predictions to experimental results on the flow of dense emulsions through microchannels and to athermal molecular dynamics simulations. Spurred on by the observation of some discrepancies, we have developed and implemented a more flexible code, based on a simplified Finite Element routine, which notably provides a better account of structural disorder and inertial effects.

Ces dix dernières années ont vu émerger des avancées technologiques majeures, nous permettant capturer une image instantanée des processus physique. L'amélioration systématique de la résolution temporelle de ces instants, grâce aux lasers (de différente sorte) aux impulsions ultracourtes, a joué un rôle important dans l'exploration des transitions de phases photo-induites dans différents matériaux, et leur potentiel applicatif. Néanmoins, ce progrès technologique incontestable a poussé à ses limites notre capacité de décrire les phénomènes hors-équilibre très complexes qui pilotent les transitions. Ils sont intrinsèquement multi-échelles dans le temps et dans l'espace, s'étalant de la femtoseconde aux plusieurs jours, et de la dimension atomique jusqu'à celle d'un cristal macroscopique. Les expériences résolues en temps permettent de séparer temporellement différents dégrées de liberté et les phénomènes pilotés par ceux-ci, au lieu d'observer seulement leur moyenne statistique. La première étape (processus photo-induit) de cette séquence temporelle est liée à l'absorption d'un photon, la deuxième (élastique) est pilotée par la dilation du volume macroscopique du matériau, et la troisième étape (thermique) est due aux effets de chaleur. Cette approche séquentielle offre de nouvelles possibilités pour mieux comprendre comment impacter les matériaux de façon contrôlée et efficace. Les lasers opérant dans le moyen infrarouge (mid IR) permettent de suivre le déroulement d'une transition de phase par le changement de vibrations des molécules/liaisons ciblées. Cette spécificité au site moléculaire combinée avec la résolution en temps ultracourte devrait ouvrir une nouvelle fenêtre d'observation des phénomènes qui échappaient aux études scientifique. Ce travail de thèse a commencé exactement dans cet esprit. L'effort majeur a été dédié à l'application de la spectroscopie mid IR ultrarapide aux matériaux présentant une conversion de l'état de spin, [Fe(3-MeO-SalEen)]2PF6 en particulier. La principale difficulté de ce travail consistait à décrypter le contenu spectral des molécules hors-équilibre. Nous avons découvert que l'approche utilisé dans les spectroscopies résolues en temps de plus haute énergie (UV/VIS) ne suffit pas pour étudier la problématique posé dans le cadre de cette thèse. Une nouvelle approche a été pensée pour modéliser les spectres résolus en temps, et celle-ci consistait à séparer la réponse spectrale en deux contributions : le transfert de poids spectral, et un décalage spectral. J'ai pu démontrer que ces deux contributions suivent sensiblement le changement d'état de spin, et la pression (dilatation du volume). L'analyse de données basée sur ce modèle, corrobore les résultats obtenus jusqu'alors avec d'autres techniques. Sur l'échelle de temps ultracourts, plus difficile à modéliser, nous avons pu néanmoins résoudre très clairement le refroidissement vibrationnelle (VC) de l'état électronique haut spin -chaud. A ma connaissance, ce phénomène dans un système solide présentant crossover de spin n'a jamais été observé directement. / The past few decades have seen great advancements in technology that allow us to capture the picture of a physical process, as the adage “seeing is believing” implies how people understand the world. The increasing temporal resolution of lasers played an important role in the study of materials, among which materials exhibiting photo-induced phase transition are of great importance thanks to their potential for future applications. However, as we proceed further and further in the investigation of the mechanism of phase transition, we found ourselves confronted with the very complex nature of phase transition dynamics. It is intrinsically multi-scale in time and space, from femtosecond to days and from atomic dimensions to macroscopic distances. Time resolved experiments disentangle different degrees of freedom and different phenomena in a step-like manner, rather than providing a statistical average. The first step is photo induced due to absorption of photons, the second step (elastic step) is pressure induced due to volume dilation, and the third step is temperature induced due to dissipation of heat. This step-like approach offers an opportunity to understand the mechanism, so that we could effectively impact the materials and possibly control phase transition. Mid IR lasers have a unique advantage of monitoring phase transition through vibrational modes on specific molecular sites. Implementing ultrafast mid IR spectroscopy in phase transition materials should be therefore very insightful in discovering new phenomena and revealing hidden mechanism. This PhD project, focusing on mid IR technique, started exactly in this context. The main effort is dedicated to the application of ultrafast mid IR spectroscopy to the spin crossover solids, [Fe(3-MeO-SalEen)]2PF6. The major challenge in this work was to comprehend the shape of transient mid IR spectra. We found out that this is conceptually different from the experiences accumulated in UV/VIS spectroscopy. A suitable model had to be developed, separating the transient IR spectra into two contributions: spectral weight transfer and spectral shift. I demonstrated that these two components are sensitive to the spin change and pressure effect (volume dilation), respectively. Data analysis based on the new model shows consistency with previously published results. On the ultrafast timescale, more difficult to fit our model to, vibrational cooling (VC) of electronically hot HS state has been very well resolved. To the best of my knowledge, direct observation of VC in solid state SCO compound by IR spectroscopy has not been reported earlier.

No description available.