We applied single-molecule fluorescence (SMF) methods to probe the properties of individual fluorescent probes, and to characterize the proteins of interest to which these probes were attached. One remarkable advantage of SMF spectroscopy is the ability to investigate heterogeneous subpopulations of the ensemble, which are buried in ensemble averaging in other measurements. Other advantages include the ability to probe the entire dynamic sequences of a single molecule transitioning between different conformational states. For the purpose of having an extended observation of single molecules, while maintaining the native nanoscale surroundings, we developed an improved vesicle preparation method for encapsulating scarce biological samples. SMF investigations revealed that molecules trapped in vesicles exhibit nearly ideal single-emitter behavior, which therefore recommends the vesicle encapsulation for reproducible and reliable SMF studies. Hyperactive Signal-Transducer-and-Activator-of-Transcription 3 (STAT3) protein contributes significantly to human cancers, such as leukemia and lymphoma. We have proposed a novel therapeutic strategy by designing a cholesterol-based protein membrane anchor (PMA), to tether STAT3 to the cell membrane and thus inhibit unwanted transcription at the cell nucleus. We designed in vitro proof-of-concept experiments by encapsulating STAT3 and PMAs in phospholipid vesicles. The efficiency and the stability of STAT3 anchoring in the lipid membrane were interrogated via quantitative fluorescence imaging and multiparameter SMF spectroscopy. Our in vitro data paved the way for the in vivo demonstration of STAT3 inhibition in live cells, thus demonstrating that PMA-induced protein localization is a conceptually viable therapeutic strategy. The recent discovery of intrinsically disordered proteins (IDPs) highlights important exceptions to the traditional structure-function paradigm. SMF methods are very suited for probing the properties of such highly heterogeneous systems. We studied in detail the effects of electrostatics on the conformational disorder of an IDP protein, Sic1 from yeast, and found that the electrostatic repulsion is a major factor controlling the dimensions of Sic1. Based on our data we also conclude that a rod-like shape seems a better candidate than a random Gaussian chain to describe and predict the behavior of Sic1.

Eukaryotic initiation factor-4E (eIF4E) controls the rate of cap-dependent translation initiation and is in turn exquisitely regulated by 4E-BPs. 4E-BP2 binds eIF4E with the highest affinity and is implicated in cancer, and metabolic and neurological disorders. Herein we use NMR, ITC and fluorescence to characterize 4E-BP2 structural and binding properties. Isolated 4E-BP2 is intrinsically disordered, but possesses some transient secondary structural propensities. eIF4E, however, is folded but has a disordered N-terminus. The eIF4E:4E-BP2 interaction is tight (Kd = 10-9 nM) and involves 4E-BP2 C-terminal and canonical binding regions, and the disordered eIF4E N-terminus. 4E-BP2 remains largely disordered upon binding to eIF4E. Noteworthy, high affinity interactions are not necessarily mediated by static structures, and 4E-BP2 binding is not the simple “disorder-to-order” transition observed in many interactions involving disordered proteins. This study offers molecular insights into 4E-BP2 functionality, and lays a foundation for development of novel therapies for cancer and neurological disorders.

Eukaryotic initiation factor-4E (eIF4E) controls the rate of cap-dependent translation initiation and is in turn exquisitely regulated by 4E-BPs. 4E-BP2 binds eIF4E with the highest affinity and is implicated in cancer, and metabolic and neurological disorders. Herein we use NMR, ITC and fluorescence to characterize 4E-BP2 structural and binding properties. Isolated 4E-BP2 is intrinsically disordered, but possesses some transient secondary structural propensities. eIF4E, however, is folded but has a disordered N-terminus. The eIF4E:4E-BP2 interaction is tight (Kd = 10-9 nM) and involves 4E-BP2 C-terminal and canonical binding regions, and the disordered eIF4E N-terminus. 4E-BP2 remains largely disordered upon binding to eIF4E. Noteworthy, high affinity interactions are not necessarily mediated by static structures, and 4E-BP2 binding is not the simple “disorder-to-order” transition observed in many interactions involving disordered proteins. This study offers molecular insights into 4E-BP2 functionality, and lays a foundation for development of novel therapies for cancer and neurological disorders.

Decades have passed since the realisation that a protein’s amino acid sequence can contain all the information required to form a complex three-dimensional fold. Until recently, these encoded structures were thought to be crucial determinants of protein function. Much effort was directed to fully understand the mechanisms behind how and why proteins fold, with natively unfolded proteins thought to be experimental artefacts. Today, the field of natively unfolded – or so-called intrinsically disordered – proteins, is rapidly developing. Protein disorder content has been positively correlated with organismal complexity, with over thirty percent of eukaryotic proteins predicted to contain disordered regions. However, the biophysical consequences of disorder are yet to be fully determined. With the aim of addressing some of the outstanding questions, the work described in this thesis focuses on the relevance of structure within disordered proteins. Whilst populating a variety of conformations in isolation, a subset of disordered proteins can fold upon binding to a partner macromolecule. This folded state may be present within the ensemble of conformations sampled by the unbound protein, opening the question of what comes first: folding or binding? Protein engineering techniques were employed to alter the level of residual ‘bound-like’ structure within the free conformational ensemble, and the consequences on coupled folding and binding reactions were investigated. Resultant changes in the rate of association are easily imaginable; yet, this work demonstrates that the majority of the observed changes in binding affinity were due to alterations in the rate of dissociation, thus altering the lifetime of the bound complex. Promiscuous binding is a touted advantage of being disordered. If many disordered proteins, each with their own conformational ensemble, can bind and fold to the same partner, then where is the folding component encoded? Does the partner protein template the folding reaction? Or, is the folding information contained within the disordered protein sequence? Utilising phi-value analysis on the BCL-2 family of proteins, residues in the disordered sequence were probed to ascertain which form contacts at the transition state of the reaction. Comparison with phi-value analyses of alternative pairs – sharing either the ordered or disordered protein – provides insight into the encoding of these interactions. In the context of a bimolecular reaction, the amino acid sequence of the disordered protein was shown to determine the interactions within the transition state. Thus, analogous to the discovery from decades’ past, it is the sequence of the protein that folds which encodes its pathway, even when binding is a prerequisite.

abstract: This work presents the integration of user intent detection and control in the development of the fluid-driven, wearable, and continuum, Soft Poly-Limb (SPL). The SPL utilizes the numerous traits of soft robotics to enable a novel approach to provide safe and compliant mobile manipulation assistance to healthy and impaired users. This wearable system equips the user with an additional limb made of soft materials that can be controlled to produce complex three-dimensional motion in space, like its biological counterparts with hydrostatic muscles. Similar to the elephant trunk, the SPL is able to manipulate objects using various end effectors, such as suction adhesion or a soft grasper, and can also wrap its entire length around objects for manipulation. User control of the limb is demonstrated using multiple user intent detection modalities. Further, the performance of the SPL studied by testing its capability to interact safely and closely around a user through a spatial mobility test. Finally, the limb’s ability to assist the user is explored through multitasking scenarios and pick and place tests with varying mounting locations of the arm around the user’s body. The results of these assessments demonstrate the SPL’s ability to safely interact with the user while exhibiting promising performance in assisting the user with a wide variety of tasks, in both work and general living scenarios. / Dissertation/Thesis / Masters Thesis Biomedical Engineering 2018

Orientador: Jorg Kobarg / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-14T01:48:42Z (GMT). No. of bitstreams: 1 Lanza_DanielCarlosFerreira_D.pdf: 39179290 bytes, checksum: cbd84a5b7ba74e985bc1fc48595debd6 (MD5) Previous issue date: 2009 / Resumo: A proteína FEZ1 foi caracterizada inicialmente como um ortólogo da proteína UNC76 de C. elegans, responsável pelo desenvolvimento e fasciculação neuronal nesse verme. Estudos subsequentes demonstraram sua atuação em processos de desenvolvimento neuronal, polarização celular, mecanismos de transporte associado à kinesinas e transporte de vesículas e mitocôndrias. Outros trabalhos demonstraram que a superexpressão de FEZ1 interfere no ciclo de vida de alguns tipos de vírus como HIV e JCV. FEZ1 é capaz de interagir com mais de 51 proteínas diferentes, e participa em muitos processos celulares. Observamos que FEZ1 apresenta ausência de estrutura molecular rígida, sendo pertencente à classe das natively unfolded proteins, e é capaz de formar dímeros em solução. Essa observação condiz com sua extrema capacidade de interagir com muitas proteínas diferentes. A capacidade de FEZ1 interagir com outras proteínas é influenciada pela fosforilação da sua região C-terminal por diferentes isoformas de PKC. FEZ1 interage e colocaliza com NEK1 e com CLASP2 em células de mamífero, em uma região candidata ao centrossomo. Essas interações são dependentes da região coiled-coil presente na parte C-terminal de FEZ1, e ocorrem em regiões coiled-coil de CLASP2 e NEK1. A interação com CLASP2 é rompida quando FEZ1 é fosforilada por PKC. A superexpressão de FEZ1 causa o fenótipo flower like observado em células de alguns tipos de leucemia. Nós observamos que FEZ1 interage e colocaliza com a e ?-tubulinas e que a formação desse fenótipo em células HEK293 ocorre devido a uma alteração na organização dos microtúbulos causada pelo excesso de FEZ1. A formação do fenótipo flower like é influenciada por ativação das vias de PKC e PI3K. Os dados obtidos durante o nosso trabalho indicam que FEZ1 é uma proteína intrinsecamente desenovelada, que atua em processos celulares associados ao citoesqueleto e centrossomo em conjunto com NEK1 e CLASP2, e que defeitos em sua regulação, possivelmente pelas vias de PKC ou PI3K, causam alteração da organização dos microtúbulos originando núcleos flower like. / Abstract: FEZ1 was identified first as a orthologue of C elegans UNC-76 protein, that plays functions related to neuronal development in this worm. Subsequent studies, shows FEZ1 functions in neuronal development process, cell polarization, transport mechanisms associated to kinesins and vesicular and mitochondrial transports. Other works showed that FEZ1 superexpression interfere in the life cycle of some viral types such as HIV and JCV. FEZ1 is able to interact with more than 51 different proteins and participates in several cellular processes. We observed that FEZ1 has a mobile molecular structure, is a member of the natively unfolded protein class, and can form dimers in solution. This observation is in agreement with its capacity to interact with a large number of different proteins. The capacity of FEZ1 to interact with other proteins is influenced by different PKC isoforms phosphorylation in its C-terminal region. FEZ1 interacts and co-localizes with NEK1 and CLASP2 in a centrossomal candidate region of mammalian cells. These interactions are dependent of a coiled coil inside the C-terminal region of FEZ1, and occur in dependence of coiled coil regions of NEK1 and CLASP2. The interaction between FEZ1 and CLASP2 is abolished after FEZ1 phosphorylation by PKC. The FEZ1 overexpression causes the flower like phenotype observed in cells of some leukemias. We observed that FEZ1 interacts and co-localizes with _ and _-tubulins and that the phenotype formation in HEK293 cells is mediated by an atypical organization of microtubule spindles, caused by overexpression of FEZ1. The flower like phenotype formation is influenced by activation of PKC and PI3K pathways. The data generated by our work indicate that FEZ1 is an intrinsically unfolded protein, that works in cellular processes associated to the cytoskeleton in conjunct with NEK1 and CLASP2, and that defects in its regulation, maybe via the PKC or PI3K pathways, causes alterations in microtubule organization and formation of the "flower like" nuclei. / Doutorado / Bioquimica / Doutor em Biologia Funcional e Molecular

Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) exist as interconverting conformational ensembles, without a single fixed three-dimensional structure in vivo. The focus in the literature up to this point has been primarily on IDPs that are mostly or entirely disordered. Therefore, we have an incomplete understanding of the incidence and functional relevance of IDPRs in proteins that have regions of both order and disorder. This work explores these populations, by examining IDPRs in the Protein Data Bank (PDB) and in enzymes. By applying disorder prediction methods combined with an analysis of missing regions in crystal structure data, this work shows that enzymes have a similar incidence and length of IDPRs as do non-enzymes, and that these IDPRs are correlated with functions related to macromolecular metabolism, signaling, and regulation. Furthermore, extensive analyses of missing regions with conflicting information between multiple structures in the PDB show that, rather than experimental artifacts, this ambiguity most likely arises due to partially or conditionally disordered regions. This work documents the first proteome level study of protein intrinsic disorder in enzyme populations and demonstrates a novel way of analyzing missing regions in the PDB. Furthermore, an extensive literature search as part of this work provides information for 1127 IDPs with experimental evidence documented in the literature, 96 of which are enzymes. The results contained herein present a new model of the protein universe, where disorder is directed by evolution in both non-enzymes and enzymes to make the most of limited proteomes in complex organisms through complicated signaling networks and tightly controlled regulation.

No description available.

COR15A is a cold regulated disordered protein from Arabidopsis thaliana that contributes to freezing tolerance in plants by protecting membranes. It belongs to the (LEA) Late Embryogenesis Abundant group of proteins that accumulate during the later stage of seed development and are expressed in various parts of the plant. During freezing-induced cellular dehydration, COR15A transitions from a disordered structure to a mostly α-helical structure that binds and stabilizes chloroplast membranes when cells dehydrate due to freezing. We hypothesize that increasing the transient α-helicity of COR15A under normal conditions will increase its ability to bind and protect chloroplast membranes when cells are frozen. To test this hypothesis, conserved glycine residues were mutated to alanine to increase α-helicity. NMR spectroscopy was used to examine structural changes of these mutants compared to wildtype in 0% and 20% TFE. The impact of these mutations on the stability of model membranes during a freeze-thaw cycle was investigated by fluorescence spectroscopy. The results of these experiments showed the mutants had a higher content of α-helical secondary structure than wildtype in 0% and 20% TFE. Increased α-helicity of the COR15A mutants improved membrane stabilization during freezing. Altogether, our results suggest the conserved glycine residues are important for maintaining the disordered structure of the protein.

No description available.