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.

La bactérie Pseudomonas aeruginosa (PA) est un pathogène responsable de 20%-30% des infections nosocomiales en milieu hospitalier. Pour les individus sains, elle ne présente pas de réel danger, mais pour les personnes atteintes par la mucoviscidose et les patients immunodéprimés, elle est la cause principale de mortalité et des infections pulmonaires. PA a développé des souches multi-résistantes aux antibiotiques et des nouvelles approches thérapeutiques plus efficaces sont donc nécessaires. Elle se fixe à la surface des cellules-hôtes par une interaction entre des protéines (lectines) présentes sur sa membrane et des sucres présents sur la membrane cellulaire. L’interaction lectine-sucre joue un rôle important dans l’adhésion de la bactérie puis dans la fabrication d’un biofilm pathogène.Une nouvelle approche thérapeutique consiste à créer des molécules synthétiques (glycomimes) de plus grande affinité que les sucres présents sur les cellules. Pour cela, plus de 150 glycomimes ont été synthétisés et examinés afin de trouver le meilleur candidat pour empêche le processus d'infection de bactéries. Certains d'entre eux ont été choisis et étudiés par la Microscopie à Force Atomique (AFM). Cette thèse est consacrée à l’étude des interactions lectine-glycomime et aussi cellule-bactérie par AFM. L’imagerie combinée avec la modélisation permet de comprendre le rôle du glycomime sur la géométrie des complexes créés et la spectroscopie permet de mesurer les forces d’interaction présentes lors de l’adhésion, au niveau moléculaire et cellulaire. Une réduction de l’adhésion bactérienne a été observée après l’introduction du glycomime, confirmant son rôle d’inhibiteur et la validité de toute la démarche. L’objectif ultime est l’identification des meilleurs glycomimes à introduire afin de développer de nouveaux médicaments. / Pseudomonas aeruginosa (PA) is a human opportunistic pathogen responsible for 20% -30% of nosocomial infections in French hospitals. For healthy people, it presents no real danger, but for people with cystic fibrosis disease and immune-compromised patients, it is the leading cause of mortality and lung infections. PA has developed antibiotic multi-resistant strains and new and more effective therapeutic approaches are needed. It binds to the surface of the host cells by an interaction between proteins (lectins) present on the membrane and sugars of the host-cell membrane. The lectin-sugar interaction plays an important role in adherence of the bacteria and in the manufacture of a pathogenic biofilm.A new therapeutic approach is to create synthetic molecules (glycoclusters) of greater affinity than the natural sugars present on the cells. To this aim, more than 150 glycoclusters have been synthetized and screened to find the best candidate to inhibit the bacteria infection process. Some of them have been selected and studied by Atomic Force Microscopy (AFM). In particular, this thesis is devoted to study the lectin-glycocluster and cell-bacteria interactions by AFM. The combination of AFM imaging with molecular dynamic simulations let understanding the role of the geometry of the glycoclusters on the complex formation, while AFM spectroscopy accesses the lectin-glycocluster interaction forces at the molecular and cellular levels. The reduction of bacterial adhesion has been observed upon the addition of the glycocluster. This confirms the anti-adhesive properties of the glycocluster and validates the procedure. The ultimate goal is the identification of the best glycoclusters in order to develop new drugs.

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

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

The group 2 late embryogenesis abundant (LEA) proteins, also known as the dehydrins, are intrinsically disordered proteins that are expressed in plants experiencing extreme environmental conditions such as drought or low temperature. In this work, we study the potential roles that dehydrins may have in stabilizing membranes and actin microfilaments during cold stress. We have cloned and expressed in E. coli two dehydrins from Thellungiella salsuginea, denoted TsDHN-1 (acidic) and TsDHN-2 (basic). These proteins were expressed as SUMO-fusion proteins for in vitro phosphorylation by casein kinase II (CKII), and for structural analysis by CD and Fourier transform infrared (FTIR) spectroscopy. We show using transmission-FTIR spectroscopy that ordered secondary structure is induced and stabilized in these proteins by association with large unilamellar vesicles emulating the lipid compositions of plant plasma and organellar membranes. The increase in secondary structure by membrane association is further facilitated by the presence of Zn2+. Lipid composition and temperature have synergistic effects on the secondary structure. Our single molecule force spectroscopy studies also suggest tertiary folding of both TsDHN-1 and TsDHN-2 induced by association with lipids. From Langmuir-Blodgett monolayer compression studies, and from topographic studies using atomic force microscopy at variable temperature, we conclude that TsDHN-1 stabilizes the membrane at lower temperatures. Finally, we show that the conformations of TsDHN-1 and TsDHN-2 are affected by pH, interactions with cations and membranes, and phosphorylation. Actin assembly by these dehydrins was assessed by sedimentation assays, and viewed by transmission electron and atomic force microscopy. Phosphorylation enabled both dehydrins to polymerize actin filaments, a phenomenon that may occur in the cytosols of plant cells undergoing environmental stress. These results support the hypothesis that dehydrins stabilize plant organellar membranes and/or the cytoskeleton in conditions of stress, and further that phosphorylation may be an important feature of this stabilization. / NSERC

Le repliement des protéines est principalement gouverné par les interactions spécifiques des structures secondaires. 1, 2 Toutefois, il existe expérimentalement peu d’informations sur les propriétés mécaniques fondamentales des hélices α et des feuillets β isolées. Les recherches antérieures sur l'étude du déploiement des hélices sont peu concluantes 3-5 et à notre connaissance l'étude des propriétés mécaniques d'un feuillet β isolé, intramoléculaire est sans précédent. Les copolymères PEG114-b-poly(L-lysine)134-(2-pyridyl disulfure),PEG114-b-poly(L-lysine)-b-PEG114 et poly(L-acide glutamique)85-b-(2-pyridyldisulfure) été synthétisés et utilisés comme systèmes modèles pour tester les propriétés mécaniques des motifs secondaires de type hélice α et feuillet β. Les résultats obtenus se sont révélés être en bon accord avec les résultats théoriques obtenus en utilisant un modèle statistique basé sur AGAGIR 6. La différence de force de déroulement comparant les hélices de poly(L-Lysine) ≈ 30 pN et de poly(L-acide glutamique) ≈ 20 pN des copolymères diblocs a été attribuée à l'hydrophobicité différente des chaînes latérales. La plus grande hydrophobie dumotif lysine conduit à de plus grandes interactions entre les chaînes latérales qui empêchent les fluctuations aléatoires au sein de l’hélice, et conduisent à une stabilité supérieure de l'hélice α. Lorsque les expériences ont été conduites dans des conditions favorisant la solubilité des chaînes latérales de lysine, les interactions ont diminué à une force de ≈ 20 pN, similaire à la force des interactions observées pour le poly(L-acide glutamique). Nous supposons qu'un minimum de ≈ 20 pN est nécessaire pour rompre la liaison hydrogène en maintenant l'hélice α, car cette force a été obtenue dans des conditions où les interactions de la chaîne latérale étaient minimisées. La présence de plateaux de force constants et d'inflexions correspondantes démontre une force de dépliement indépendante de la longueur, qui supporte un mécanisme de déroulement tour-par-tour pour l'hélice. De plus, la plus grande hydrophobie des chaînes latérales a été suggérée non seulement pour stabiliser la structure en hélice, mais également pour inhiber la formation d'une structure de type β-turn métastable intermédiaire lorsque les forces entropiques dominent. Des études préliminaires ont été effectuées sur le système de PEG114-bpoly(L-Lysine)134-(2-pyridyl disulfure) après induction d’une transition - β par un traitement thermique dans des conditions basiques. Une inflexion à une force≈ 70 pN a été obtenue, ce qui suggère la formation d'une interaction de type feuillet β. Une stratégie bottom-up a ainsi été proposée avec succès, démontrant le potentiel d'utilisation de tels systèmes artificiels pour simplifier et modéliser des systèmes biologiques réels. La compréhension de ces modèles isolés plus simples aidera sans doute la compréhension de systèmes plus complexes. / Proteins fold by the initial, preferential folding of secondarystructures 1, 2, however surprisingly little is known about the basic mechanicalproperties of isolated α-helices and β-sheets from an experimental standpoint.Previous investigations into studying the generic unfolding behaviour of α-heliceshave proved inconclusive 3-5, and to our knowledge the study of an isolated,intramolecular β-sheet is unprecedented.Bioinspired PEG114-b-poly(L-glutamic acid)85-(2-pyridyl disulphide),PEG114-b-poly(L-lysine)134-(2-pyridyl disulphide) and PEG114-b-poly(Llysine)134–b-PEG114 were designed, synthesized and utilized as model systems toprobe the mechanical properties of α-helix and β-sheet secondary motifs. Theobtained results were shown to be in good agreement with theoretical resultsobtained by utilizing a AGAGIR-based statistical mechanical model 6. Thedifference in unravelling force comparing the helices of poly(L-Lysine) ≈30 pNand poly(L-glutamic acid) ≈20 pN diblock copolymers was attributed to thediffering hydrophobicity of the side chains. The greater hydrophobicity of thelysine allowed greater interactions between the side chains and sterically hinderedrandom helix-coil fluctuations, which lead to a superior α-helix stability. Whenexperiments were conducted in conditions promoting the solubility of the lysineside chains, the interactions decreased to a force of ≈20 pN, similar to the force ofinteractions observed for the poly(L-glutamic acid). We infer that a minimum of≈20 pN is needed to rupture the hydrogen bonding maintaining the α-helix as thisforce was obtained in conditions where the side chain interactions wereminimized.The presence of constant force plateaus and corresponding inflectionsdemonstrates a length independent unfolding force, which supports a turn-by-turnunfolding mechanism for the α-helix.In addition, the greater hydrophobicity of the side chains was suggestedto not only stabilize the α-helix structure, but also to inhibit the formation of anintermediate metastable β-hairpin-like structure when entropic forces dominate.Preliminary studies were also conducted on the PEG114-b-poly(LLysine)134-(2-pyridyl disulphide) system after a α-β transition had been inducedby heat in basic conditions, where an inflection at a much higher force of ≈ 70 pNwas obtained suggesting the formation of a β-sheet interaction.A bottom-up, investigative strategy has thus been successfully proposeddemonstrating the potential of utilizing such artificial systems to simplify andexemplify real biological systems. The comprehension of these simpler isolatedmodels will no doubt aid the understanding of more complex systems.

The Tumor Necrosis Factor derived-TIP peptide is a small 17 amino acids cyclic peptide with lectin-like activity, that possesses several therapeutically relevant biological activities, among which is activation of alveolar liquid clearance in both healthy and injured lungs in vivo. Accumulation of fluid in the lungs? alveoli and interstitial spaces is a life-threatening condition called pulmonary edema. The mortality rate due permeability pulmonary edema, accompanied by a dysfunction of the alveolar/capillary barrier, is high because no effective treatment lacking side effects exists nowadays. It is known that the TIP peptide is able to activate vectorial Na+ transport ? which mediates lung liquid clearance. However, the mechanism of action of remains elusive. The aim of this thesis was to investigate the initial steps of interaction between the TIP peptide and airway epithelial cells. Numerous novel methods and single-molecule techniques were used to unravel: (i) how the TIP peptide interacts with the molecules on the apical side of the lung epithelial cells; (ii) whether the TIP peptide need to be internalized inside of the cells to trigger its effects; (iii) the nature of the interaction between the TIP peptide and its putative receptor(s); (iv) the putative receptor(s) for the TIP peptide on the apical surface of the lung epithelial cells.

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.:I Theoretical background 1 1 Introduction 3 2 Protein folding: the downhill scenario 5 2.1 Protein folding as a diffusion on a multidimensional energy landscape 5 2.2 Downhill folding proteins 7 2.2.1 Thermodynamic description of downhill folders 7 2.2.2 Identification criteria for downhill folders 8 2.3 Lambda repressor as a model system for studying downhill folding 9 2.3.1 Wild-type lambda repressor fragment λ{6-85} 10 2.3.2 Acceleration of λ{6-85} folding by specifific point mutations 11 2.3.3 The incipient-downhill λYA and downhill λHA variants 14 2.4 Single-molecule techniques as a promising tool for probing downhill folding dynamics 17 3 Single-molecule protein folding with optical tweezers 19 3.1 Optical tweezers 19 3.1.1 Working principle of optical tweezers 19 3.1.2 The optical tweezers setup 21 3.2 The dumbbell assay 22 3.3 Measurement protocols 23 3.3.1 Constant-velocity experiments 23 3.3.2 Constant-trap-distance experiments (equilibrium experiments) 24 4 Theory and analysis of single-molecule trajectories 27 4.1 Polymer elasticity models 27 4.2 Equilibrium free energies of protein folding in optical tweezers 28 4.3 Signal-pair correlation analysis 29 4.4 Force dependence of transition rate constants 29 4.4.1 Zero-load extrapolation of rates: the Berkemeier-Schlierf model 30 4.4.2 Detailed balance for unfolding and refolding data 31 4.5 Direct measurement of the energy landscape via deconvolution 32 II Results 33 5 Efficient strategy for protein-DNA hybrid formation 35 5.1 Currently available strategies for protein-DNA hybrid formation 35 5.2 Novel assembly of protein-DNA hybrids based on copper-free click chemistry 37 5.3 Click-chemistry based assembly preserves the native protein structure 40 5.4 Summary 42 6 Non-equilibrium mechanical unfolding and refolding of lambda repressor variants 45 6.1 Non-equilibrium unfolding and refolding of lambda repressor λWT 45 6.2 Non-equilibrium unfolding and refolding of incipient-downhill λYA and downhill λHA variants of lambda repressor 48 6.3 Summary 52 7 Equilibrium unfolding and refolding of lambda repressor variants 53 7.1 Importance of the trap stiffness to resolve low-force nanometer transitions 54 7.2 Signal pair-correlation analysis to achieve millisecond transitions 56 7.3 Force-dependent equilibrium kinetics of λWT 59 7.4 Equilibrium folding of incipient-downhill λYA and downhill λHA variants of lambda repressor 61 7.5 Summary 65 8 Model-free energy landscape reconstruction for λWT, incipient-downhill λYA and downhill λHA variants 69 8.1 Direct observation of the effect of a single mutation on the conformational heterogeneity and protein stability 71 8.2 Artifacts of barrier-height determination during deconvolution 75 8.3 Summary 76 9 Conclusions and Outlook 79 / 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.:I Theoretical background 1 1 Introduction 3 2 Protein folding: the downhill scenario 5 2.1 Protein folding as a diffusion on a multidimensional energy landscape 5 2.2 Downhill folding proteins 7 2.2.1 Thermodynamic description of downhill folders 7 2.2.2 Identification criteria for downhill folders 8 2.3 Lambda repressor as a model system for studying downhill folding 9 2.3.1 Wild-type lambda repressor fragment λ{6-85} 10 2.3.2 Acceleration of λ{6-85} folding by specifific point mutations 11 2.3.3 The incipient-downhill λYA and downhill λHA variants 14 2.4 Single-molecule techniques as a promising tool for probing downhill folding dynamics 17 3 Single-molecule protein folding with optical tweezers 19 3.1 Optical tweezers 19 3.1.1 Working principle of optical tweezers 19 3.1.2 The optical tweezers setup 21 3.2 The dumbbell assay 22 3.3 Measurement protocols 23 3.3.1 Constant-velocity experiments 23 3.3.2 Constant-trap-distance experiments (equilibrium experiments) 24 4 Theory and analysis of single-molecule trajectories 27 4.1 Polymer elasticity models 27 4.2 Equilibrium free energies of protein folding in optical tweezers 28 4.3 Signal-pair correlation analysis 29 4.4 Force dependence of transition rate constants 29 4.4.1 Zero-load extrapolation of rates: the Berkemeier-Schlierf model 30 4.4.2 Detailed balance for unfolding and refolding data 31 4.5 Direct measurement of the energy landscape via deconvolution 32 II Results 33 5 Efficient strategy for protein-DNA hybrid formation 35 5.1 Currently available strategies for protein-DNA hybrid formation 35 5.2 Novel assembly of protein-DNA hybrids based on copper-free click chemistry 37 5.3 Click-chemistry based assembly preserves the native protein structure 40 5.4 Summary 42 6 Non-equilibrium mechanical unfolding and refolding of lambda repressor variants 45 6.1 Non-equilibrium unfolding and refolding of lambda repressor λWT 45 6.2 Non-equilibrium unfolding and refolding of incipient-downhill λYA and downhill λHA variants of lambda repressor 48 6.3 Summary 52 7 Equilibrium unfolding and refolding of lambda repressor variants 53 7.1 Importance of the trap stiffness to resolve low-force nanometer transitions 54 7.2 Signal pair-correlation analysis to achieve millisecond transitions 56 7.3 Force-dependent equilibrium kinetics of λWT 59 7.4 Equilibrium folding of incipient-downhill λYA and downhill λHA variants of lambda repressor 61 7.5 Summary 65 8 Model-free energy landscape reconstruction for λWT, incipient-downhill λYA and downhill λHA variants 69 8.1 Direct observation of the effect of a single mutation on the conformational heterogeneity and protein stability 71 8.2 Artifacts of barrier-height determination during deconvolution 75 8.3 Summary 76 9 Conclusions and Outlook 79