We use time-lapse AFM to visualize collagen fibrils self-assembly. A solution of acid-solubilized collagen was injected into the AFM fluid cell and fibril formation was observed in vitro. Single fibrils continuously grew and fused with each other until the supporting surface was completely covered by a nanoscopically well-defined collagen matrix. Laterally, the fibrils grew in steps of ~4 nm suggesting a two-step mechanism. In a first step, collagen molecules associated together. In the second step, these molecules rearranged into a structure called a microfibril. High-resolution AFM topographs revealed substructural details of the D-band architecture. These substructures correlated well with those revealed from positively stained collagen fibers imaged by transmission electron microscopy. Secondly, a covalent assembly approach to prepare membrane protein for AFM imaging that avoids crystallization was proposed. High-resolution AFM topographs can reveal structural details of single membrane proteins but, as a prerequisite, the proteins must be adsorbed to atomically flat mica and densely packed in a membrane to restrict their lateral mobility. Atomically flat gold, engineered proteins, and chemically modified lipids were combined to rapidly assemble immobile and fully oriented samples. The resulting AFM topographs of single membrane proteins were used to create averaged structures with a resolution approaching that of 2D crystals. Finally, the contribution of specific amino acid residues to the stability of membrane proteins was studied. Two structurally similar proteins sharing only 30% sequence identity were compared. Single-molecule atomic force microscopy and spectroscopy was used to detect molecular interactions stabilizing halorhodopsin (HR) and bacteriorhodopsin (BR). Their unfolding pathways and polypeptide regions that established stable segments were compared. Both proteins unfolded exactly via the same intermediates. This 3 Molecular Assemblies observed by AFM observation implies that these stabilizing regions result from comprehensive contacts of all amino acids within them and that different amino acid compositions can establish structurally indistinguishable energetic barriers. However, one additional unfolding barrier located in a short segment of helix E was detected for HR. This barrier correlated with a Pi-bulk interaction, which locally disrupts helix E and divides into two stable segments.

Atomic force microscopy (AFM) is a powerful technique that enables to study biological macromolecules and dynamic biological processes at different scales. It is an excellent tool for imaging of biological objects under various conditions at a nanometer resolution. Force mode of AFM, so called single molecule force spectroscopy (SMFS), allows for investigation of the strength of molecular interactions of different origins established between and within biological molecules. In the present work, SMFS was used to detect and locate structurally and functionally important interactions of sodium/glycine betaine transporter BetP of Corynebacterium glutamicum, which serves as a model system for this class of proteins. Mechanical pulling of BetP molecules embedded into the lipid membranes resulted in a step-wise unfolding of the protein and revealed insights into its structural stability. Effect of the lipid environment, N- and C-terminal extensions on inramolecular interactions of BetP as well as protein activation and ligand binding were investigated in great detail. In another part of this work, I demonstrate an application of the AFM based technique that can record unfolding of a protein under force-clamp conditions. This method directly measures the kinetics of the protein unfolding, allowing for the use of simple methods to analyze the data. For the first time the force-clamp technique was used to describe in detail unfolding kinetics of the membrane protein, i. e. Na+/H+-antiporter NhaA from Escherichia coli. Performed here experiments on NhaA in its functionally active and inactive states demonstrated the advantages of examining unfolding kinetics at the single-molecule level. It was possible to observe unfolding events for pH-activated conformation of NhaA that due to the low frequency of occurrence were not represented in the ensemble average of the single-molecule measurements. As mechanical unfolding, similarly to bond rupture, is a force-dependent process, force-clamp technique can allow for a more direct way of probing protein unfolding and is anticipated to be also useful to examine the folding/unfolding kinetics of other membrane proteins.

No description available.

Beta-barrel outer membrane proteins (OMPs) present on the outer membrane of Gram-negative bacteria are vital to cell survival. Their biogenesis is a challenging process which is tightly regulated by protein-chaperone interactions at various stages. Upon secretion from the inner membrane, OMPs are solubilized by periplasmic chaperones seventeen kilodalton protein (Skp) and survival factor A (SurA) and maintained in a folding competent state until they reach the outer membrane. As periplasm has an energy deficient environment, thermodynamics plays an important role in fine tuning these chaperone-OMP interactions. Thus, a complete understanding of such associations necessitates an investigation into both structural and thermodynamic aspects of the underlying intercommunication. Yet, they have been difficult to discern because of the conformational heterogeneity of the bound substrates, fast chain dynamics and the aggregation prone nature of OMPs. This demands for use of single molecule spectroscopy techniques, specifically, single molecule Förster resonance energy transfer (smFRET). In this thesis, upon leveraging the conformational and temporal resolution offered by smFRET, an exciting insight is obtained into the mechanistic and functional features of unfolded and Skp/SurA - bound states of two differently sized OMPs: OmpX (8 β-strands) and outer membrane phospholipase A (OmpLA – 12 β-strands). First, it was elucidated that the unfolded states of both the proteins exhibit slow interconversion within their sub-populations. Remarkably, upon complexing with chaperones, irrespective of the chosen OMP, the bound substrates expanded with localised chain reconfiguration on a sub-millisecond timescale. Yet, due to the different interaction mechanisms employed by Skp (encapsulation) and SurA (multivalent binding), their clients were found to be characterised by distinct conformational ensembles. Importantly, the extracted thermodynamic parameters of change in enthalpy and entropy exemplified the mechanistically dissimilar functionalities of the two chaperones. Furthermore, both Skp and SurA were found to be capable of disintegrating aggregated OMPs rather cooperatively, highlighting their multifaceted chaperone activity. This work is of significant fundamental value towards understanding the ubiquitous chaperone-protein interactions and opens up the possibility to design drugs targeting the chaperone-OMP complex itself, one step ahead of the OMP assembly on the outer membrane.

Host cell binding is an essential step in colonization by many bacterial pathogens, and the Lyme disease agent, Borrelia burgdorferi, which colonizes multiple tissues, is capable of attachment to diverse cell types. Glycosaminoglycans (GAGs) are ubiquitously expressed on mammalian cells and are recognized by multiple B. burgdorferi surface proteins. We previously showed that B. burgdorferi strains differ in the particular spectrum of GAGs that they recognize, leading to differences in the cultured mammalian cell types that they efficiently bind. The molecular basis of these binding specificities remains undefined, due to the difficulty of analyzing multiple, potentially redundant cell attachment pathways and to the paucity of genetic tools for this pathogen. Complementation of a high-passage non-adherent B. burgdorferi strain reveals that the expression of DbpA, DbpB, or BBK32, is sufficient to confer efficient spirochete attachment to 293 epithelial cells. Epithelial cell attachment by DbpA and B was mediated by dermatan sulfate, while BBK32 recognized dermatan and heparan sulfate. The GAG binding properties of bacteria expressing DbpB or DbpA were distinguishable in that DbpB, but not DbpA, promoted spirochetal attachment to C6 glial cells. Furthermore, DbpA alleles from diverse Lyme disease spirochetes exhibit allelic variation with respect to binding decorin, dermatan sulfate, and epithelial cells. Targeted disruption of bbk32 resulted in decreased spirochete binding to fibronectin, GAGs, and mammalian cells. Thus, DbpA, DbpB, and BBK32 may play central but distinct roles in cell type-specific binding by Lyme disease spirochetes. This study illustrates that transformation of high-passage B. burgdorferi strains and targeted gene disruption provide a comprehensive genetic approach to analyze virulence-associated phenotypes conferred by multiple bacterial factors.

The transition between the closed and open conformations of the Sec61 complex permits nascent protein insertion into the translocation channel. A critical event in this structural transition is the opening of the lateral translocon gate that is formed by four transmembrane (TM) spans (TM2, TM3, TM7 and TM8 in Sec61p) to expose the signal sequence-binding (SSB) site. To gain mechanistic insight into lateral gate opening, mutations were introduced into a lumenal loop (L7) that connects TM7 and TM8. The sec61 L7 mutants were found to have defects in both the posttranslational and cotranslational translocation pathways due to a kinetic delay in channel gating. The translocation defect caused by L7 mutations could be suppressed by the prl class of sec61 alleles that reduce the fidelity of signal sequence recognition. The prl mutants are proposed to act by destabilizing the closed conformation of the translocation channel. Our results indicate that the equilibrium between the open and closed conformations of the protein translocation channel maintains a balance between translocation activity and signal sequence recognition fidelity. In the opening of the translocation channel, both the lateral and lumenal gate must open in a coordinated fashion for efficient protein translocation to occur. The lumenal gate is composed of a short helix of the loop preceding the second TM span, referred to as the plug helix, and six hydrophobic pore ring residues which form the constriction ring in the center of the channel. We identified three lateral gate polar residues and three hydrophobic residues from the plug domain that affect channel gating. Mutagenesis of the lateral gate polar cluster residues yields either a gain of function (prl phenotype) or a loss of function (translocation defect) phenotype. The combination of polar cluster mutations with each other or with plug domain mutations which cause a prl phenotype resulted in the mutually suppressive or additive phenotypes in double mutant strains. Cooperation between these residues is made possible through a structural link which connects the two translocation channel gates at their interface. The structural link provides a mechanism for the channel to coordinate the movement of multiple domains in the channel gating conformational change. Translocation assays demonstrated that this mechanism of gating regulation is particularly important for efficient protein translocation of substrates using the posttranslational translocation pathway. Our results indicate that residues from the plug and lateral gate domain form a regulatory cluster of residues responsible for efficient translocation channel gating.

Poldip2 est une protéine ubiquitaire initialement identifiée comme étant un partenaire de la sous unité p50 de la polymerase δ intervenant dans la réplication et la réparation de l’ADN. Depuis sa découverte en 2003, beaucoup d’autres partenaires et fonctions lui ont été attribués. Elle joue, entre autre, un rôle régulateur de l’isoforme NADPH oxydase NOX4. A ce jour, le mode d’action de cette régulation n’a pas encore été identifié. Seul fait connu est que Poldip2 augmente l’activité de NOX4 en s’associant au partenaire membranaire de NOX4, la protéine p22phox. L’association de p22phox à d’autres isoformes de NADPH Oxydase (NOX1, NOX2 ou NOX3) suggère une interaction possible entre ces derniers et Poldip2. Par ailleurs la co-localisation de NOX4 et NOX2 dans plusieurs types cellulaires, tels que les cellules du muscle lisse et l’endothélium mais également la coexpression de Poldip2 et NOX2 dans les artérioles rénale font de NOX2 un bon candidat pour l’étude de l’effet régulateur possible de Poldip2 de cet isoforme. Dans cette perspective, la protéine recombinante Poldip2 (rat) a été produite de manière hétérologue dans un système d’expression de levure P. pastoris. Grace à un vecteur d’expression spécifique de cette levure, Poldip2 est sécrété dans le milieu extracellulaire. La protéine a été purifiée à partir du milieu de culture. L’analyse de la séquence par spectrométrie de masse a permis de confirmer l’identité du Poldip2 recombinant produit par la levure. Après avoir caractérisé structuralement Poldip2 et confirmé sa capacité à augmenter l’activité de NOX4, nous avons étudié son effet sur NOX2 des phagocytes. De manière surprenante, nos études en système cell-free ont montré des propriétés inhibitrices de Poldip2 sur NOX2 avec des interactions privilégiées avec certaines des composantes du complexe oxydase. Nos résultats suggèrent que l’interaction de Poldip2 avec le complexe pourrait constituer une nouvelle voie de régulation de NOX2 en perturbant l’assemblage du complexe NADPH oxydase. / Poldip2 is an ubiquitous protein initially identified as a partner for polymerase δ p50 subunit and is involved in DNA replication and repairing. Since its discovery in 2003, many partners and functions has been assigned to it. Poldip2 is also involved in NADPH Oxidase NOX4 isoform regulation. The enhancement of NOX4 activity was attributed to Poldip2 interaction with the membrane partner p22phox. However the mechanism by which it regulates NOX4 has not been identified yet. The association of p22phox with other Nox isoform (NOX1, NOX2 or NOX3) questions the possible interaction of Poldip2 with NOX2. Furthermore the colocalization of NOX4 and NOX2 in several cell types as the smouth muscle cells and endothelium cells but also Poldip2 and NOX2 coexpression in renal arterioles, makes NOX2 a good candidate for studying the possible regulatory effect of Poldip2 on the NOX2 isoform. On this purpose the recombinant protein Poldip2 (rat) was produced in the yeast P. pastoris. Using a specific expression vector Poldip2 was secreted in the extracellular media. The protein was purified from culture media. Sequence analysis by mass spectrometry allowed to confirm the recombinant protein identity produced in yeast. After the structural characterization of poldip2 and the confirmation of its functionality on NOX4, the protein was used to study its effect on NOX2 phagocyte. Surprisingly our study on cell free assay shows that Poldip2 has inhibiting properties regarding NOX2 and interacts in a privileged manner with certain components of the NADPH Oxidase complex. Our result suggest that the interaction of Poldip2 and the complex might constitute a new regulation for NOX2 by disturbing the NADPH Oxidase assembly.

No description available.

Lipid bilayers and lipid-associated proteins play crucial roles in biology. As in vivo studies and manipulation are inherently difficult, membrane-mimetic systems are useful for the investigation of lipidic phases, lipid–protein interactions, membrane protein function and membrane structure in vitro. This dissertation describes a route to leverage the programmability of DNA nanotechnology to create DNA-encircled bilayers (DEBs), a novel nano-scaled membrane-mimetic system. DEBs are made of multiple copies of an alkylated oligonucleotide hybridized to a single-stranded minicircle, in which up to two alkyl chains per helical turn point to the inside of the toroidal DNA ring. When phospholipids are added, a bilayer is observed to self-assemble within the ring such that the alkyl chains of the oligonucleotides stabilize the hydrophobic rim of the bilayer to prevent formation of vesicles and support thermotropic lipid phase transitions. This straight-forward and robust route enables the rational design of DEBs so that their size, shape or functionalization can be adapted to the specific needs of biophysical investigations of lipidic phases and the properties of membrane proteins. Next, we optimized the DEB system to provide proper anchoring of a large variety of lipids by creating an improved DNA scaffold. This scaffold, called DNA double-decker, consists of two interconnected DNA minicircles stacked on top of each other. In comparison to the DNA minicircle in DEB system, this scaffold is two times thicker and contains two times more hydrophobic strands, which should increase the stability of the lipid bilayer rim. Finally, we explored the option of using DEBs in studies of GPCRs using CCR5 as a model protein. The CCR5 was labeled with DNA strands, purified and characterized. The strands on CCR5 are complementary to the protruding strands on the DNA minicircle in DEBs. This can allow the reconstitution of GPCRs inside DEBs with controlled orientation of the receptor.

Although cytoplasmic lipid droplets (LDs) are the major reserves for energy-dense neutral lipids in plants, the cellular mechanisms for packaging neutral lipids into LDs remain poorly understood. To gain insights into the cellular processes of neutral lipid accumulation and compartmentalization, a necessary step forward would be to characterize functional roles of lipogenic proteins that participate in the compartmentalization of neutral lipids in plant cells. In this study, the lipogenic proteins, Arabidopsis thaliana SEIPIN homologues and mouse (Mus Musculus) fat storage-inducing transmembrane protein 2 (FIT2), were characterized for their functional roles in the biogenesis of cytoplasmic LDs in various plant tissues. Both Arabidopsis SEIPINs and mouse FIT2 supported the accumulation of neutral lipids and cytoplasmic LDs in plants. The three Arabidopsis SEIPIN isoforms play distinct roles in compartmentalizing neutral lipids by enhancing the numbers and sizes of LDs in various plant tissues and developmental stages. Further, the potential applications of Arabidopsis SEIPINs and mouse FIT2 in engineering neutral lipids and terpenes in plant vegetative tissues were evaluated by co-expressing these and other lipogenic proteins in Nicotiana benthamiana leaves. Arabidopsis SEIPINs and mouse FIT2 represent effective tools that may complement ongoing strategies to enhance the accumulation of desired neutral lipids and terpenes in plant vegetative tissues. Collectively, our findings in this study expand our knowledge of the broader cellular mechanisms of LD biogenesis that are partially conserved in eukaryotes and distinct in plants and suggest novel targets that can be introduced into plants to collaborate with other factors in lipid metabolism and elevate oil content in plant tissues.