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Kinesins are motor proteins that convert chemical energy from ATP hydrolysis into mechanical energy used to generate force along microtubules, transporting organelles, vesicles, and proteins within the cell. Kar3 kinesins are microtubule minus-end-directed motors with pleiotropic functions in mating and mitosis of budding and fission yeast. In Saccharomyces cerevisiae, Kar3 is multifunctionalized by two non-catalytic companion proteins, Vik1 and Cik1. A Kar3-like kinesin and a single Vik1/Cik1 ortholog are also expressed by the filamentous fungus Ashbya gossypii, which exhibits different nuclear movement challenges and unique microtubule dynamics from its yeast relatives. We hypothesized that these differences in A. gossypii physiology could translate into interesting and novel differences in its versions of Kar3 and Vik1/Cik1. Presented here is a structural and functional analysis of recombinantly expressed and purified forms of these motor proteins. Compared to the previously published S. cerevisiae Kar3 motor domain structure (ScKar3MD), AgKar3MD displays differences in the conformation of the ATPase pocket. Perhaps it is not surprising then that we observed the maximal microtubule-stimulated ATPase rate (kcat) of AgKar3MD to be approximately 3-fold slower than ScKar3MD, and that the affinity of AgKar3MD for microtubules (Kd,MT) was lower than ScKar3MD. This may suggest that elements that compose the ATPase pocket and that participate in conformational changes required for efficient ATP hydrolysis or products release work differently for AgKar3 and ScKar3. There are also subtle structural differences in the disposition of the secondary structural elements in the small lobe (B1a, B1b, and B1c) at the edge of the motor domain of AgKar3 that may reflect the enhanced microtubule-depolymerization activity that we observed for this motor, or they could relate to its interactions with a different regulatory companion protein than its budding yeast counterpart. Although we were unable to gain experimentally determined high-resolution information of AgVik1, the results of Phyre2-based bioinformatics analyses may provide a structural explanation for the limited microtubule-binding activity we observed. These and other fundamental differences in AgKar3/Vik1 could explain divergent functionalities from the ScKar3/Vik1 and ScKar3/Cik1 motor assemblies. / Thesis (Master, Biochemistry) -- Queen's University, 2012-07-26 10:40:54.738

Non-muscle myosin II (NM-II) is present in every cell type and moves actin filaments to provide contraction within the cell. NM-II has a motor domain, a neck domain that binds two light chains, a long coiled-coil tail domain, and a carboxyl-terminal tailpiece. NM-II forms bipolar filaments by associating near the carboxyl-terminus of the tail. It has long been known that both the formation of bipolar filaments and enzymatic activity of the motor domain are regulated by phosphorylation of one of the neck-binding light chains, known as the regulatory light chain (RLC). This phosphorylation causes a large-scale conformational shift of both the motor domains and the tail domain. However, the mechanism of this regulation and the elements that mediate the autoinhibition remain unknown. We have taken a deletional approach to finding the elements necessary for autoinhibition and regulation of filament assembly. We have used salt- dependent pelleting assays, cell culture, and analytical ultracentrifugation to identify two small regions in the IQ motifs of the neck and the carboxyl-terminal tailpiece that are essential for autoinhibition. Another necessary element for autoinhibition is the fold the coiled coil of the tail back on itself by means of hinge domains. We used internal deletions, pelleting assays, and thermal stability assays to identify and characterize the flexible hinge domains within the coiled-coil tail of NM-II. These hinges consist of low-stability regions of coiled coil, and can be stiffened by introducing mutations that cause the sequence to mimic a more ideal coiled coil. By defining these essential elements of autoinhibition, this work paves the way for a mechanistic understanding of the complex regulation of NM-II in the cell. This dissertation contains unpublished co-authored material. / 2015-07-11

Non-claret disjunctional (Ncd) is a kinesin-14 microtubule motor protein involved in the assembly and stability of meiotic and mitotic spindles in Drosophila oocytes and early embryos, respectively. Ncd functions by cross-linking microtubules through the tail and motor domains. It was originally believed that the role of the Ncd tail domain was to only statically bind microtubules. However, the Ncd tail domain has recently been shown to have properties that stabilize and bundle microtubules, and contribute to the overall motility of the Ncd protein. Continued characterization of the Ncd tail domain is essential to understanding the complete role of Ncd in cell division. This work explored the regulatory function and microtubule binding properties of the Ncd tail domain. Ncd activity is regulated during interphase by nuclear sequestration. GFP-Ncd fusion proteins, containing full length Ncd, individual Ncd domains, or combinations of Ncd domains, were used to identify the presence of a nuclear localization signal (NLS) in the Ncd polypeptide. The nuclear localization of only the GFP fusion proteins containing the Ncd tail sequence indicates that the NLS is contained within the tail domain. Subsequent, experiments performed with GFP fusion proteins containing segments of the tail domain indicate that essential NLS amino acid segments may span the length of the tail domain. Attempts to characterize the microtubule binding properties of the Ncd tail domain, using bacterially expressed MBP-Ncd tail-stalk, were unsuccessful. MBP-Ncd tail-stalk proteins aggregated under binding assay conditions, preventing an accurate determination of the stoichiometric binding relationship between Ncd and the tubulin dimer. / Master of Science

Many active processes in cells are driven by highly specialised motor proteins, which interact with the cytoskeleton: a network of filamentous structures, e.~g.~ actin filaments and microtubules, which organises intracellular transport and largely determines the cell shape. These motor proteins are able to transduce the chemical energy, stored in ATP molecules, to do mechanical work while interacting with a filament. Certain motor proteins, e.~g.~members of the KIN-13 kinesin subfamily, are able to interact specifically with filament ends and induce depolymerisation of the filament ends. One important role for KIN-13 family members is in the mitotic spindle, a microtubule structure that is formed in the process of cell division and is responsible for separation and distribution of the duplicated genetic material to the forming daughter cells. The aim of this work is to develop a theoretical framework capable of describing experimentally observed behaviour and shed light on underlying principles of motor induced filament depolymerisation. We use two different theoretical approaches to describe motor dynamics in this non- equilibrium situation: On the one hand we use phenomenological continuum equations which themselves are to a large extent independent of the underlying molecular details of the system. Molecular details of the system are incorporated in the equations through the specific values of macroscopic parameters which are determined by the underlying details. On the other hand, we use one- and two-dimensional discrete stochastic descriptions of motors on a filament. These kind of descriptions enable us to investigate the effects of different microscopic mechanisms of filament depolymerisation, and to investigate the role of fluctuations on the dynamic behaviour of motor proteins. We additionally discuss filament depolymerisation in the case where motors are not free to move but are fixed to a common anchoring point and depolymerise filaments under the influence of applied forces, mimicking the situation in the mitotic spindle. Our results can be related to recent experiments on members of the KIN-13 subfamily and predictions made in our theory can be tested by further experiments. Although motivated by experiments involving members of the KIN-13 subfamily, our theory is not restricted to these motors but applies in general to associated proteins which regulate dynamics of filament ends.

The work presented in this thesis was inspired by one of the most fascinating classes of naturally occurring molecules: bipedal motor proteins from the kinesin, dynein and myosin superfamilies walk along cellular tracks, carrying out essential tasks, such as vesicle transport, muscle contraction or force generation. Although a few synthetic mimicks based on DNA have been described, small-molecule analogues that exhibit the most important characteristics of the biological walkers were still missing until recently. In this thesis, the design, synthesis and operation of several small-molecule walker-track systems is described. All presented systems share a similar molecular architecture, featuring disulfide and hydrazone walker-track linkages, yet deviate fundamentally in the mechanism and energy input that is required for directional walker transport. Chapter I includes an overview of the biological walker proteins, as well as a comprehensive review of the DNA-based mimicks published to date. A set of fundamental walker characteristics is identified and special emphasis is given to the underlying physical mechanisms. Chapter II describes a series of experiments, which lay the groundwork for all smallmolecule walker systems presented in the following Chapters of this thesis. The mutually exclusive nature of disulfide and hydrazone exchange under basic and acidic reaction conditions, was demonstrated using an unprecedented type of macrocycle. The first small-molecule walker-track system is described in Chapter III. Due to the passive nature of both the track and the walker unit, an oscillation of acidic and basic reaction conditions led to a directionally un-biased, intramolecular ‘diffusion’ of the walker unit along the track. Using an irreversible redox-reaction for one of the foot-track exchange reactions conferred a certain degree of directionality to the walking sequence, with the oxidant iodine providing the chemical fuel for the underlying Brownian information ratchet mechanism. Chapter IV contains a comprehensive investigation of the dynamic properties of a series of walker-track conjugates derived from the walker-track conjugate presented in Chapter III. The most significant observation was that ring strain appears to be a requirement for the emergence of directional bias, a phenomenon that has also been found in biological walkers. In Chapter V a different type of walker-track conjugate is described, in which the track plays an active role and light is used as the fuel required for directional walker transport. The key for achieving directionality was the presence of a stilbene unit as part of the molecular track, through which ring strain could be induced in the isomer where the walker unit bridges the E-stilbene linkage. Significantly, the underlying Brownian energy ratchet mechanism allowed walker transport in either direction of the molecular track. Chapters II to V are presented in the form of articles that have recently been published or will be published in due course in peer-reviewed journals. No attempt has been made to re-write this work out of context, other than to avoid repetition, insert crossreferences to other Chapters (where appropriate) and to ensure consistency of presentation throughout this thesis. Chapters II, III, IV and V are reproduced in the Appendix, in their published formats. The Outlook contains closing remarks about the scope and significance of the presented work as well as ideas for the design and operation of a next generation of small-molecule walkers, some of which are well under way in the laboratory.

The number of motor proteins attached to cellular cargos is widely believed to influence intracellular transport processes and may play a role in transport regulation. However, to date, investigating the biophysics of multiple-motor dynamics has been challenging since the number of motors responsible for cargo motion is not easily characterized. This work examines the transport properties of structurally-defined motor complexes containing two kinesin-1 motors, from both an experimental and theoretical perspective. Motor complexes were synthesized using DNA as a molecular scaffold and engineered DNA-conjugated protein polymers as linkers to couple motors to scaffolds. After anchoring the motor complexes to a bead their dynamic properties were measured using an automated optical trapping instrument that could be used to perform both static (increasing load) and force-feedback (constant load) optical trapping experiments. Data from these experiments is compared to predictions from a microscopic transition rate model of multiple kinesin dynamics. Together, these studies uncovered that multiple kinesins typically cannot cooperate since the microtubule-bound configuration of a motor complex often prevents both kinesins from sharing cargo loads. Furthermore, multiple-motor behaviors are influenced by the fact that motor complexes display hysteretic force-velocity behaviors when applied loads change rapidly in time. Overall, such behaviors suggest the number of kinesins on a cargo will not be a key determinant of intracellular transport processes, and in turn, will not contribute appreciably to mechanisms that regulate cargo motion. However, this work also provides evidence that processive microtubule motors that are less efficient than kinesin (e.g., dynein) will cooperate productively, produce greater responses to motor number, and may therefore act as a regulator of cargo transport.

The exquisite frequency selectivity and amplification characteristics of mammalian hearing intimately depend on the fast electromechanical motion of the outer hair cells in the cochlea. This membrane based process, termed electromotility, is driven by the protein prestin which is uniquely present in the OHC lateral wall. Voltage dependent motility, in OHCs and mammalian cells expressing prestin, is accompanied by intramembranous charge movement which is widely considered a signature of electromotility and prestin function. How prestin converts changes in membrane potential into axial length changes of OHCs is currently not understood at the molecular level. Many electromotility models predict that prestin conformational changes are the underlying mechanism connecting charge movement and motility. Currently, however, only indirect evidence for a prestin conformational change is available. Various experiments have indicated that the oligomeric states of prestin may be an important determinant of function. Numerous reports have provided varying estimates of prestin oligomeric state. However, estimates have been based on measurements performed outside the membrane making, firm biophysical conclusions difficult. Biophysical studies of prestin function have demonstrated its dependence on membrane properties. Alterations of membrane cholesterol affect voltage dependence of charge movement and motility. In addition cholesterol manipulations cause spatial redistribution of prestin and possibly change prestin oligomeric state. However, the underlying cause for prestin sensitivity to cholesterol and its relation to membrane distribution is unknown. We have applied single molecule fluorescence (SMF) imaging, single particle tracking (SPT), and Förster resonance energy transfer (FRET) to investigate prestin interactions at the molecular level. The results of our SMF experiments have suggested that prestin forms mainly tetramers and dimers in the cell membrane. Using SPT to map the trajectories of prestin in the membrane, we have found that prestin undergoes diffusion in and hops between membrane confinements of varying size. In addition, we have found that cholesterol affects the size and confinement strength of the compartments but does not affect the diffusivity within the compartments. Finally, using a combination of electrophysiology and FRET we have demonstrated that prestin undergoes voltage dependent structural changes. In total, our results refine our molecular understanding of prestin function.

Orientador: Mário Tyago Murakami / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-19T22:14:14Z (GMT). No. of bitstreams: 1 Pinto_AlineSampaio_M.pdf: 3074349 bytes, checksum: 0fdb140ae2fd1c1975ba6cde0cf00bca (MD5) Previous issue date: 2012 / Resumo: As miosinas formam uma superfamília de proteínas de alto peso molecular com atividade mecanoquímica capaz de hidrolisar a molécula de ATP e de interagir com os filamentos de actina. A estrutura das miosinas pode ser divida de modo geral em cabeça motora, pescoço e cauda. São conhecidas 35 classes de miosinas em eucariotos sendo a classe II de miosinas denominada miosinas convencionais e as demais chamadas de não convencionais. Em plantas são somente encontradas as miosinas não convencionais de classe VIII e XI. A classe VIII caracteriza-se por sua alta processividade sobre os filamentos de actina e a classe XI é a maior classe em número de genes, tendo uma estrutura muito semelhante às miosinas de classe V. Uma terceira classe, a classe XIII, foi posteriormente descoberta e somente foi encontrada no gênero Acetabularia apresentando dois genes, porém essa classificação é controversa havendo aqueles que dizem que as miosinas da classe XIII possuem tanta afinidade filogenética com as da classe XI que elas deveriam compor uma única classe. As miosinas VIII e XI desempenham papéis chave no transporte direcional de componentes intracelulares em plantas, principalmente devido às grandes dimensões das células de plantas que não sobrevivem utilizando somente a difusão como mecanismo de transporte intracelular. Neste trabalho, buscamos selecionar os melhores representantes de cada classe a partir de análises in silico para desenvolvermos os testes de expressão, purificação e análises biofísicas. Os domínios selecionados, cauda globular (GT), dilute e SH3, foram clonados em pET28a e pET28aSUMO, os testes de expressão com diversas cepas de E coli, mostraram que o domínio dilute expressa em grande quantidade na fração solúvel, porém forma agregados impedindo as análises biofísicas e os ensaios de cristalização. O domínio SH3 também foi obtido na forma solúvel, porém em pouca quantidade e apresentou migração anômala no gel, sendo identificado a partir de análises de espectrometria de massas. Foram realizados testes iniciais de cristalização para o domínio SH3, mas não resultou na formação de cristais adequados a difração de raios X. A cauda globular foi obtida apenas na fração insolúvel e submetida a procedimentos de refolding para sua solubilização. Mesmo conseguindo o reenovelamento da construção, a mesma se manteve agregada inviabilizando os testes de cristalização. Por outro lado foram analisadas as interações da cauda globular da miosina XIh com presas identificadas por duplo-híbrido realizado pelo nosso grupo com a miosina humana Va. Três das proteínas que interagiram com a miosina Va humana também mostraram sinais de interação com a miosina XIh de Arabidopsis, indicando que mesmo havendo diferenças nas sequências polipeptídicas entre as classes de miosina, a estrutura terciária se mantém permitindo que ambas apresentem interações com algumas proteínas em comum / Abstract: Myosins belong to a superfamily of high molecular weight proteins, presenting mechanochemical activity by hydrolyzing ATP molecule and ability to interact with actin filaments. The myosin structure can be divided into motor head, neck and tail. 35 myosin classes are known in eukaryotic cells, where class II is known as conventional myosins and all others, as unconventional myosins. Plants possess only unconventional myosins including classes VIII and XI. The class VIII, is characterized by its high processivity on actin filaments while class XI possesses multiple genes and its protein structure is very similar to class V myosins. A third class, XIII, was later discovered and only found in Acetabularia genome presenting two genes. However this classification is controversial, because some studies shown that class XIII myosins share such high phylogenetic similarity with class XI that they should form the same class. Myosins VIII and XI play key roles on directional intracellular components transport in plants, mainly due to the large plant cell size which would not survive only by the diffusion mechanism for intracellular transport. In this work, we have selected the best representative targets of each class from in silico analyses to develop the protein expression, purification and biophysical characterization. The selected domains (globular tail (GT), dilute and SH3) were cloned into pET28a and pET28aSUMO expression vectors. Results of expression tests with several E coli strains, showed that dilute domain is expressed in large amounts in the soluble fraction; however, it aggregates preventing biophysical analysis and crystallization trials. The SH3 domain, expressed in low soluble concentration, presented an abnormal migration in SDS-PAGE and its identity was confirmed by mass spectrometry analysis. Initial crystallization tests were conducted with SH3 domain, but owing to the low protein concentration only clear drops have appeared, and no crystals or aggregates were observed. The globular tail domain, obtained only in insoluble fraction, was subjected to refolding procedures/ techniques in order to recover its native-like state; however, even the refolded protein displayed secondary structure, the protein remained aggregated. Furthermore, we analyzed the interactions between of myosin XIh globular tail with pre-identified proteins by yeast two-hybrid conducted by our group with human myosin Va. Three proteins that interacted with human myosin Va also showed interaction with Arabidopsis myosin XIh, indicating that despite of differences in polypeptide sequences between the classes XI and V, the tertiary structure may be maintained allowing both of them to have interactions with common proteins / Mestrado / Bioquimica / Mestre em Biologia Funcional e Molecular

Familial Hypertrophic cardiomyopathy (HCM) causes ventricle walls to thicken and often leads to sudden death especially in adults. Mutations in the subfragment 2 (S2) of β-cardiac myosin are implicated in the genetic disorder. This S2 region is a coiled-coil rod region resulting from the dimeric form of myosin II. It has been proposed that an elastic quality allows normal S2 to absorb force during the powerstroke according to the sliding filament model. To test the flexibility of single molecules of S2 against levels of physiological force, the Gravitational Force Spectrometer (GFS) is being developed. This novel system employs a standard microscope on an equatorial mount that allows the spectrometer to be rotated freely in space. Stationary glass beads are attached to a microscope slide where the molecule is tethered between the stationary bead and a smaller mobile bead. The GFS is oriented so that the force of gravity can act on the mobile bead and so impart a small force to the tethered subfragment. Additionally, a video system in conjunction with ImageJ software makes a distance measurement of the molecule possible with a resolution of around 11 nm. The S2 can be stretched parallel or perpendicular to the coiled coil to elucidate different structural properties of the rod. This study is the first to show structural evidence that S2 in vertebrate skeletal myosin uncoils proportionally to physiological force loads. Because of this, the usefulness and promise of the novel GFS is highlighted, and the biological role of S2's flexibility can be directly commented on. If the dimer undergoes uncoiling at physiological force loads as shown, then it is reasonable to think that this might occur in nature in response to the stress of the powerstroke on a single molecule. This unwinding could be to absorb force as a mechanism to protect the muscle fiber.