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Energy landscape of defects in body-centered cubic metals. / Exploration du paysage énergétique de défauts dans les métaux cubiques centrés.Alexander, Rebecca 04 November 2016 (has links)
Les matériaux composants les réacteurs nucléaires subissent des conditions d’irradiationsévères, donnant lieu à des modifications de leurs propriétés mécaniques. Le vieillissement de cesmatériaux soulève des questions aussi importantes que celles liées à la sécurité des centrales existantes etaux futurs réacteurs à fission et à fusion. Dans plusieurs situations les matériaux de structure cristallinecubique centrée CC sont utilisés ayant pour base le fer, le tungstène, le vanadium et le tantale. Lescollisions entre les particules irradiantes et les atomes constituants les matériaux engendrent des défautsponctuels dont la migration mène à la formation d’amas responsables du vieillissement. Dans cette thèsenous avons étudié les propriétés énergétiques des défauts ponctuels dans les métaux CC citésprécédemment à l’échelle atomique. La modélisation des défauts ponctuels à l’échelle atomique peut êtreréalisée avec différentes méthodes se différenciant uniquement par la qualité de la description del’interaction entre atomes. Les études utilisant des interactions atomiques exactes, type ab initio,nécessitent des calculs lourds rendant impossible l’étude directe des amas de grandes tailles. Avec lamodélisation des interactions atomiques via les potentiels semi-empiriques on réduit la fiabilité et lecaractère prédictif du calcul. Ceux-ci permettent toutefois de réaliser une étude des amas en fonction deleur taille. Dans cette thèse nous avons développé un modèle énergétique original pour les boucles dedislocation ainsi que pour les amas interstitiels tridimensionnels de type C15. Le modèle obtenu est sanslimite de taille et peut être paramétré entièrement par les calculs ab initio. Afin de tester sa robustessepour les grandes tailles d’amas nous avons également paramétré ce modèle par rapport à des calculs enpotentiels semi-empiriques et comparé les prédictions du modèle aux simulations atomiques. Grâce ànotre développement nous avons pu déterminer : (i) la stabilité relative des boucles de dislocationd’interstitiels d’après leur vecteur de Burgers. (ii) La stabilité des amas C15 par rapport aux amas de typeboucle. Nous avons montré que les amas de type C15 étaient plus stables lorsqu’ils impliquent moins de41 interstitiels dans le fer. (iii) Dans le Ta nous avons pu mettre en évidence la même stabilité jusqu’à 20interstitiels. Les expériences dans le fer irradié montrent qu’en fonction de la température d’irradiation, ilse forme des boucles de dislocation très mobiles de vecteur de Burgers ½<111> ou immobiles ayant unvecteur de Burgers <100>. Les mécanismes de formation sous irradiation en fonction de la température,des amas de type <100> étaient une question restée sans explication théorique depuis 50 ans. Dans cettethèse, grâce à la précision de notre modèle énergétique, nous avons pu tester plusieurs théories.Notamment nous avons montré que les amas C15 constituent un catalyseur dans la formation des boucles<100>. Les clusters C15 peuvent se former, par germination, directement dans le processus d’irradiation.Ces clusters sont immobiles et peuvent croitre. A partir d’une certaine taille les amas C15 se dissocienten boucles ½ <111> ou <100>. Nous avons étendu notre modèle au calcul d’énergie libre de formationdes défauts permettant ainsi des prédictions à température finie que nous avons comparées auxsimulations atomiques. Les lois établies dans cette thèse en utilisant notre modéle pour calculer l’énergielibre de formation en fonctions de la taille des amas, ont été ensuite utilisées dans une simulation dedynamique d’amas. Nous avons ainsi pu prédire avec un très bon accord expérience-théorie laconcentration des amas d’interstitiels en fonction de leurs tailles au cours du murissement d’Oswald postirradiationdans un échantillon de Fer sous atmosphère d’Hélium. Le succès d’une telle approche nouspermet d’espérer étendre ce type d’étude à des matériaux plus complexes. / The structural materials in nuclear reactors are subjected to severe irradiation conditions,leading to changes in their mechanical properties. The aging of these materials raises important issuessuch as those related to the safety of existing plants and future reactors. In many cases, materials withbody-centered cubic bcc crystal structure are used with iron, tungsten, vanadium and tantalum as basemetal. Collisions between irradiating particles and atoms constituting materials generate point defectswhose migration leads to the formation of clusters responsible for aging. In this thesis, we studied theenergetic properties of point defects in the bcc metals mentioned above at the atomic scale. Modelingpoint defects at the atomic scale can be achieved with different methods that differ only in the quality ofthe description of the interaction between atoms. Studies using accurate atomic interactions such ab initiocalculations are computationally costly making it impossible to directly study clusters of large sizes. Themodeling of atomic interactions using semi-empirical potentials reduces the reliability of predictivecalculations but allow calculations for large-sized clusters. In this thesis we have developed a uniqueenergy model for dislocation loops as well as for three-dimensional interstitial cluster of type C15. Theresulting model has no size limit and can be set entirely by ab initio calculations. To test its robustness forlarge sizes of clusters we also set this model with semi-empirical potentials calculations and comparedthe predictions of the model to atomic simulations. With our development we have determined: (i) Therelative stability of interstitial dislocation loops according to their Burgers vectors. (ii) The stability of theclusters C15 compared to the type of cluster loop. We showed that the C15 type clusters are more stablewhen they involve less than 41 interstitials in iron. (iii) In Ta we were able to show the same stability till20 interstitials. The experiments involving iron show that depending on the irradiation temperature,highly mobile dislocation loops of Burgers vector ½ <111> or loops with Burgers vector <100> areformed. Considering formation mechanisms under irradiation as a function of temperature, formation ofthe <100>-type clusters lacked an acceptable theoretical explanation for about 50 years. In this thesis, theaccuracy of our energy model enabled validation of several theories proposed in the last 50 years. Inparticular we have shown that the formation of loops <100> at high temperatures can be formed fromC15 clusters which may be created directly in the irradiation process. These clusters are immobile andcan grow. Beyond a certain size, the C15 clusters dissociate into loops ½ <111> or <100>. We haveextended our model to free energy calculation of defect formation allowing for finite temperaturepredictions which is further compared to atomic simulations. The laws established in this thesis using ourmodel to calculate the free energy of formation of the cluster size functions were then used in a clusterdynamics simulation. On comparison with experiments involving post-irradiation Oswald ripening in asample of iron exposed to an atmosphere of helium, our energy model showed significant improvementsover older energy laws, such as the capillary law widely-used in multiscale computation cluster dynamicsor Monte Carlo kinetics. We conclude that the new laws established from our calculations are essential topredict the concentration of dislocation loop under irradiation, depending on their sizes. The success ofsuch an approach encourages extension of a similar study in more complex materials.
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Struktur der Energielandschaft und Relaxation von +/- J Spinglas-ModellenKrawczyk, Jaroslaw 28 April 2003 (has links)
Die komplizierte Struktur der Energielandschaft wurde am Beispiel des +/- J Spinglas-Modells untersucht. Sie ist in glasartigen Systemen der Schlüssel zum Verständnis einer verlangsamten Dynamik. Es wurde ein enger Zusammenhang zwischen der Dynamik und der Energielandschaft nachgewiesen. Die Energielandschaft wird in +/- J Spinglas Modellsystemen durch Cluster charakterisiert, die infolge ihrer Konnektivität größere Objekte (z.B. Täler) bilden. Einzelne Cluster, aber auch ganze Täler, sind miteinander durch sogenannten Sattelcluster verknüpft. Die physikalischen Eigenschaften werden durch die Strukturen der Verknüpfungen und durch die innere Struktur der Cluster geprägt. Zur Beschreibung der Energielandschaften wurde die genaue Kenntnis der Zustände benutzt. Auf der Grundlage des &quot;branch-and-bound&quot; Verfahrens war es möglich, für kleine Systeme alle Zustände bis zu der dritten Anregung zu bestimmen. Danach wurden die Konfigurationen so sortiert, dass die Beziehungen zwischen ihnen, wie z.B. Nachbarschaften und Clusterzugehörigkeiten, einfach zu finden waren. Es gelang, die exakte Landschaft für Systeme bis L=6 aufzubauen. Für größere Systeme ist es zur Zeit unmöglich, alle niederenergetischen Zustände zu finden. Eine alternative Möglichkeit, die Struktur zu beschreiben, erhält man durch Untersuchung der Verteilung der Overlap. An der Gestalt der Verteilung erkennt man, ob die niederenergetische Struktur kompliziert oder einfach ist. Bei genaueren Untersuchungen ist es sogar möglich, die Anzahl der existierenden Täler abzuschätzen. Die Untersuchungen der Overlap bei 8555 3D Systemen (L=4) weisen darauf hin, dass bei kleineren Grundzustandsenergien die Struktur durch zwei spiegelsymmetrische Täler geprägt ist. Mit wachsender Grundzustandsenergie wird die Struktur der Systeme immer komplizierter. Eine weitere wichtige Komponente der Energielandschaft ist die innere Struktur der Sattelcluster. Ein Sattelcluster besteht aus wenigstens drei Gruppen von Konfigurationen. Zwei Gruppen enthalten Konfigurationen, die mit den Grundzustandsclustern verbunden sind, und die dritte Gruppe verbindet die beiden. Es passiert oft, dass die Konfigurationsgruppen, die verschiedene Grundzustandscluster verbinden, weit voneinander entfernt liegen. Dies wurde als ein wichtiger Aspekt erkannt, der zu einer Verlangsamung dynamischer Prozesse führt. Der andere Aspekt der Energielandschaft ist ihr Zusammenhang mit dem Realraumbild. Das Realraumbild ist als die Lage der Spins auf dem Gitter zu verstehen. Spins kann man zu verschiedenen Spindomänen zusammenfassen, die dann auf natürliche Weise die Struktur der Energielandschaft generieren. Für die Größe der einzelnen Cluster sind die freien Spins verantwortlich. Es wurde bestätigt, dass die Existenz einzelner Täler durch Spindomänen erklärt werden kann. Dabei wird durch das kollektive Umdrehen aller Spins in einer solcher Domäne ein anderer Cluster in einem anderen Tal erzeugt. Neben dem Zusammenhang von Spindomänen und Energielandschaft konnte der Einfluss von bestimmten zusammenhängenden Strukturen freier Spins genauer aufgeklärt werden. Hier ergeben sich Ansatzpunkte für weitergehende Untersuchungen.
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Unveiling the double-well energy landscape in a ferroelectric layerHoffmann, Michael, Fengler, Franz P. G., Herzig, Melanie, Mittmann, Terence, Max, Benjamin, Schroeder, Uwe, Negrea, Raluca, Lucian, Pinitilie, Slesazeck, Stefan, Mikolajick, Thomas 17 October 2022 (has links)
The properties of ferroelectric materials, which were discovered almost a century ago¹ , have led to a huge range of applications, such as digital information storage² , pyroelectric energy conversion³ and neuromorphic computing⁴⁻⁵ . Recently, it was shown that ferroelectrics can have negative capacitance⁶⁻¹¹, which could improve the energy efficiency of conventional electronics beyond fundamental limits¹²⁻¹⁴. In Landau–Ginzburg–Devonshire theory¹⁵⁻¹⁷, this negative capacitance is directly related to the doublewell shape of the ferroelectric polarization–energy landscape, which was thought for more than 70 years to be inaccessible to experiments¹⁸. Here we report electrical measurements of the intrinsic double-well energy landscape in a thin layer of ferroelectric Hf₀.₅Zr₀.₅O₂. To achieve this, we integrated the ferroelectric into a heterostructure capacitor with a second dielectric layer to prevent immediate screening of polarization charges during switching. These results show that negative capacitance has its origin in the energy barrier in a double-well landscape. Furthermore, we demonstrate that ferroelectric negative capacitance can be fast and hysteresis-free, which is important for prospective applications¹⁹. In addition, the Hf₀.₅Zr₀.₅O₂ used in this work is currently the most industry-relevant ferroelectric material, because both HfO₂ and ZrO₂ thin films are already used in everyday electronics²⁰. This could lead to fast adoption of negative capacitance effects in future products with markedly improved energy efficiency.
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Magnetic Actuation of Biological SystemsLauback, Stephanie Diane 23 October 2017 (has links)
No description available.
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Investigation of biological macromolecules using atomic force microscope-based techniquesBippes, Christian Alexander 19 August 2009 (has links) (PDF)
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 (&lt; 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 &gt; 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.
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Paper del nucli hidrofòbic principal de la RNasa A en el plegament i desplegament induïts per pressió i temperaturaFont i Sadurní, Josep 02 June 2006 (has links)
Utilitzant temperatura i pressió com a agents desnaturalitzants s'ha explorat la contribució a l'estabilitat de diferents residus del principal nucli hidrofòbic de la RNasa A. Aquests resutats suggereixen que el principal nucli hidrofòbic d'aquest enzim, està fortament empaquetat i ha revelat l'existència de reordenacions en l'interior de la proteïna.El mètode dels valors , han permès estudiar el paper de les interaccions hidrofòbiques establertes pels residus del principal nucli hidrofòbic de la RNasa A en el seu estat de transició induït per pressió. En conjunt, aquests resultats suggereixen que l'estat de transició de la RNasa A, s'assemblaria a un glòbul col·lapsat amb una cadena estructurada però amb un debilitat nucli hidrofòbic.S'ha explorat també, el paisatge energètic del plegament/desplegament proteic de la variant Y115W de la RNasa A. L'estat de transició sembla interaccionar fortament amb la capa d'hidratació d'aquest estat, tal i com indiquen els resultats en presència de glicerol. / Using temperature and pressure as denaturants we have explored the contributions to stability of the hydrophobic core residues of RNase A. These results are consistent with an exquisite tight core packing and the existence of rearrangements in the protein interior.The role of hydrophobic interactions established by the residues of the main hydrophobic core of RNase A in its pressure-folding transition state, was investigated using the -value method. Altogether the results suggest that the pressure-folding transition state of RNase A, looks like a collapsed globule with some secondary structure and a weakened hydrophobic core. Pressure-jump induced relaxation kinetics was used to explore the energy landscape of protein folding/unfolding of Y115W variant of RNase A. The transition state appears to interact strongly with the hydration shell, as indicated by results in the presence of glycerol.
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Evolution des propriétés diélectriques, ferroélectriques et électromécaniques dans le système pseudo-binaire (1-x)BaTi0.8Zr0.2O3- xBa0.7Ca0.3TiO3 / Corrélations structures et propriétés / Evolution of the dielectric, ferroelectric and electromechanical properties in the pseudo-binary system (1-x)-BaTi0.8Zr0.2O3 xBa0.7Ca0.3TiO3 / structure-property correlationsBenabdallah, Feres 20 May 2013 (has links)
Ce travail de thèse a pour objectif la caractérisation des propriétés physico-chimiques descéramiques de composition (1-x) BaTi0.8Zr0.2O3-x Ba0.7Ca0.3TiO3 préparées par frittage conventionnelet frittage flash (SPS). Les études structurales réalisées au voisinage du point triple (x≈ 0.32) à l’aidede la diffraction des RX de haute résolution (synchrotron) sur poudre ont introduit des modificationsmajeures sur le diagramme de phase température-composition déjà proposé. La réponseélectromécanique géante mesurée est alors corrélée à la dégénérescence du profil de l’énergie libreinduite par les instabilités structurales. De plus, la flexibilité de la polarisation sous contraintesthermique et électrique est couplée à un assouplissement de la maille cristalline. Ces deuxcaractéristiques contribuent ensemble à une réponse électromécanique colossale via une forteactivité des murs de domaine. La dégradation des propriétés diélectriques, ferroélectriques etpiézoélectriques pour les céramiques BCTZ (x=0.32 et 0.5) élaborées par frittage flash estessentiellement attribuée aux fluctuations importantes de composition et à la stabilisation de laconfiguration des murs de domaines avec la diminution de la taille des grains. / The aim of this work is to make a full characterization of the structural, microstructural, dielectric,ferroelectric and piezoelectric properties of the perovskite-structured oxides (1-x) BaTi0.8Zr0.2O3-xBa0.7Ca0.3TiO3 prepared by a conventional solid-state reaction method (conventional sintering) andSPS fabrication technique. Using high-resolution synchrotron x-ray powder diffraction, the structuralinvestigations carried out close to the triple point (x≈ 0.32) have introduced significant corrections tothe previously published composition-temperature phase diagram. The colossal electromechanicalresponse was then correlated to a strongly degenerate free energy landscape caused by structuralinstabilities. Furthermore, the coupling between the high polarization flexibility under electric andthermal stresses and the ‘lattice softening’ gives rise to a giant electromechanical response due tohigh domain wall activities. The decrease of the dielectric, ferroelectric and piezoelectric propertiesof BCTZ ceramics (x=0.32 and 0.5) processed by SPS was essentially attributed to the largecompositional fluctuations and stable domain wall configurations as the grain size decreased.
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The Voronoi liquid : a new model to probe the glass transition / Le liquide de Voronoï : un nouveau modèle pour l'étude de la transition vitreuseRuscher, Céline 05 October 2017 (has links)
Comprendre l’origine microscopique du ralentissement de la dynamique au voisinage de la transition vitreuse reste l’un des problèmes fondamentaux de la physique de la matière condensée. Au cours de ce travail, nous introduisons un nouveau modèle de liquide, appelé liquide de Voronoï, et dont les interactions sont directement reliées aux propriétés géométriques des tessellations de Voronoï. Pour cette classe de liquides, les interactions sont à plusieurs corps et agissent de telle sorte que le système est toujours sous tension tout en restant stable. Le but de ce travail est d’étudier un mélange binaire du liquide de Voronoï et de voir de quelles façons ces interactions exotiques affectent le scénario habituel de la transition vitreuse. Tout au long de ce travail, nous caractérisons le liquide de Voronoï bidisperse théoriquement et par le biais des simulations numériques. Nous proposons également des comparaisons avec des liquides de Lennard-Jones surfondus bien décrit dans la littérature. / Understanding the origin of the important slowing down of the dynamics near glass transition is still one of the remaining fundamental problems of condensed matter physics. During this work we introduced a brand-new model of liquids named Voronoi liquid, whose interactions are directly related to the geometrical properties of Voronoi tessellations. For these class of liquids interactions are intrinsically manybody and act in such a way that the liquid is always under tension but remains stable. The aim of this work is to use a binary mixture of the Voronoi liquid to see to what extend these exotic interactions may affect the classical scenario of glass transition. Throughout this work we characterize theoretically and by mean of numerical simulation the bidisperse Voronoi liquid. Comparisons with well-known Lennard-Jones glass formers are systematically performed.
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Tailoring the magnetic order in mesoscopic spin systemsStopfel, Henry January 2017 (has links)
Mesoscopic spin systems can be designed and fabricated using modern nano-fabrication techniques. These systems can contain large numbers of patterned ferromagnetic elements, for which the shape will generally determine their effective mesospin dimensionality. The lateral arrangement of these mesospins can be further used to tune the interactions between them. With an appropriate choice of material, it is possible to define a temperature range where thermal fluctuations of these mesospins are experimentally accessible. To actively define this range, we use δ-doped Palladium, a three-layer system of Palladium—Iron—Palladium, for which the Curie-temperature scales with the Iron layer thickness. The patterned mesoscopic elements used in this work have a stadium-like shape that promotes a single magnetic domain state, thus making these islands behave as one-dimensional Ising-like mesospins that can be observed using magnetic imaging techniques. We investigate the impact on the magnetic order resulting from modifications of the square spin ice geometry. By adding, removing and merging elements in the square artificial spin ice architecture, energy-landscape variations can be realized. Firstly, an added interaction modifier is used to equilibrate the interactions between the mesospins at the vertex level, which can restore the degenerate ground state of the square spin ice model. Secondly, the removal of elements can lead to topologically frustrated spin systems, as not all building blocks can simultaneously be in their lowest energy state. Furthermore, the merging results in multiple element sizes in the mesospin system. As the magnetization reversal barrier is dependent on the element size, these mesospin systems have different energy barriers. The thermal ordering process in such a system differs from a single-size element system with its unique energy barrier. Using reciprocal space analysis tools like the magnetic spin structure factor we show that systems with multiple element sizes achieve a higher short-range order then their single-size element references. The magnetic order in mesoscopic spin systems could successfully be tailored by modifications of the lattice geometry.
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Downhill folders in slow motion:Mukhortava, Ann 23 October 2017 (has links) (PDF)
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.
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