Дисертації з теми "Rhodopsin proteins"
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1
Perera, Mahakumarage Suchithranga, and Mahakumarage Suchithranga Perera. "Investigation of Rhodopsin Activation Using Spectroscopic and Scattering Techniques." Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/622975.
Повний текст джерелаАнотація:
G-protein–coupled receptors are the largest superfamily in the human genome, and involved in critical cellular signaling processes in living cells. Protein structural fluctuations are the key for GPCR function that is driven and modulated by a variety of factors that are not well understood. This dissertation focusses on understanding the activation of GPCRs using the visual receptor, rhodopsin as the prototype. Rhodopsin is an ideal candidate for this study, as it represents the largest class of GPCRs, and is known to demonstrate more noticeable structural changes upon activation compared to the other GPCRs. What structural fluctuations occur, the role of water, and how the retinal cofactor regulates the protein dynamics during rhodopsin activation are specific research problems addressed in this work. Hypothesizing an ensemble activation mechanism, experiments were conducted using a variety of techniques to probe structural and dynamical fluctuations of rhodopsin in native membranes, as well as in membrane mimetics such as detergent micelles. Time-resolved wide-angle X-ray scattering (TR-WAXS), small-angle neutron scattering (SANS), quasielastic neutron scattering (QENS), and electronic spectroscopy are among the prominent techniques used to gain insights into the photo-intermediates that are key to understanding the rhodopsin activation process. The small-angle neutron scattering (SANS) experiments revealed a volumetric expansion of the protein molecule upon photoactivation of rhodopsin. Electronic spectroscopy together with the differential hydration study revealed the crucial role of water in rhodopsin signaling process and signal amplification by water. The quasielastic neutron scattering study conducted on powdered rhodopsin probed the changes in the local dynamics that are regulated by the retinal cofactor of the rhodopsin molecule. The increased local steric crowding in the ligand-free opsin is consistent with collapsing of the apoprotein structure in the absence of the retinal chromophore leading to inactive opsin conformation. Finally, a time-resolved wide-angle X-ray scattering study was conducted using the X-ray free electron laser at the SLAC national laboratory to probe the early structural fluctuations in rhodopsin photoactivation. The preliminary pump-probe experiments conducted on rhodopsin in CHAPS detergent micelles revealed a light-triggered protein quake that occurs during the early activation stages of rhodopsin photoactivation. Thus the protein fluctuations underlying the GPCR function are revealed by neutrons, X-rays, and other photons in a combined implementation of both spectroscopic and scattering techniques as applied to the investigation of rhodopsin activation.
2
Birkholz, Denise A. "Photoreceptor cell fate determination and rhodopsin expression in the developing eye of Drosophila /." Connect to full text via ProQuest. IP filtered, 2005.
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3
Farmer, Nicola Ann. "Folding and assembly of two alpha helical membrane proteins, rhodopsin and bacteriorhodopsin." Thesis, University of Bristol, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.402351.
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4
Murray, Anne Riché. "The functional significance of rhodopsin's N-linked glycosylation." Oklahoma City : [s.n.], 2009.
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5
Zhao, Xinyu. "Characterization of molecular forms of G protein-coupled receptor kinase 1 (rhodopsin kinase) in vertebrate retina and pineal gland /." Thesis, Connect to this title online; UW restricted, 1997. http://hdl.handle.net/1773/6259.
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6
Sapra, K. Tanuj. "Single-Molecule Measurements of Complex Molecular Interactions in Membrane Proteins using Atomic Force Microscopy." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2007. http://nbn-resolving.de/urn:nbn:de:swb:14-1175696409847-74867.
Повний текст джерелаАнотація:
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.
7
Tomasello, Gaia <1981>. "Theoretical insight into the properties of light induced events of photochromic systems and rhodopsin proteins." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1726/1/Tomasello_Gaia_Tesi.pdf.
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8
Tomasello, Gaia <1981>. "Theoretical insight into the properties of light induced events of photochromic systems and rhodopsin proteins." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1726/.
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9
Sapra, K. Tanuj. "Single-Molecule Measurements of Complex Molecular Interactions in Membrane Proteins using Atomic Force Microscopy." Doctoral thesis, Technische Universität Dresden, 2006. https://tud.qucosa.de/id/qucosa%3A24922.
Повний текст джерелаАнотація:
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.
10
Behnke, Craig A. "X-ray crystallographic analysis of three proteins : the novel structures of the corn Hageman factor inhibitor, the G-protein coupled receptor rhodopsin, and the ultra-high resolution structure of carbonic anhydrase /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/9206.
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11
Laricheva, Elena N. "Turning on Fluorescence in Silico: From Radical Cations to 11-cis Locked Rhodopsin Analogues." Bowling Green State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1339787341.
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12
Pérez, María del Carmen Marín. "Benchmarking and applications of a computational photobiology tool for design of novel and highly fluorescent rhodopsin proteins." Doctoral thesis, Università di Siena, 2019. http://hdl.handle.net/11365/1070289.
Повний текст джерелаАнотація:
In recent years, world economy and technological advancement have been transformed by Genomics, which allows us to study, design and build biologically relevant molecules. Genomics is already deeply embedded in industries as diverse as pharmaceutical, food and agricultural, environmental and bio-tech in general. Fast and cheap tools for gene sequencing,
protein expression and analysis are commonly used for high-throughput genomic-related studies. However, due to experimental difficulties and long time scales (e.g., protein crystallization), protein structure determination, and thus the fundamental structure function rationalization, cannot presently be performed at the same fast pace: a fact that is slowing down the discovery of proteins with new features, as well as ex novo design. These difficulties are particularly felt in the field of photobiology, where the crystal structure of Bovine rhodopsin (Rh, retina dim-light visual photo-receptor), still remains the
only structure of a vertebrate photo-receptor sensor available for photobiological studies since the year 2000. Rhodopsins constitute a class of light-triggered proteins that can be found throughout the whole spectrum of living organisms, and represent the perfect blue-print for building light-activated bio-molecular machines. In principle, the problem of not having a sufficient number of rhodopsins molecular structures could be circumvented and overcome with the construction of accurate atomistic computer models of the set of studied photoreceptors, which would allow: (i) in silico fundamental structure-function characterization, (ii) thorough and detailed screening of mutant series, and even (iii) ex novo design. Nevertheless, such models should also be constructed using a fast, relatively cheap, reliable and standardized protocol, of known accuracy. In this thesis, we refine and test the Automatic Rhodopsin Modeling (ARM) computational protocol, which we demonstrate as being capable of helping to address the above issues. Such protocol has the primary target of generating congruous quantum mechanical/molecular mechanical (QM/MM) models of rhodopsins, with the aim of facilitating systematic rhodopsin-mutants studies. The cornerstone of this thesis is the validation of the ARM protocol as a successful attempt to provide a basis for the standardization and reproducibility of rhodopsin QM/MM models, aimed to study the behaviour of photoactive molecules. First, we validate the ARM protocol, which employs a CASPT2//CASSCF/AMBER scheme, for a benchmark set of rhodopsins from different biological kingdoms. We show that ARM is able to reproduce and predict absorption trends in rhodopsin protein sets, with blue-shifted values not much displaced (a few kcal/mol) from the observed data. Secondly, we present how to use this protocol towards a better design of novel mutations as applications for Optogenetics, an innovative biological tool aimed to visualize and control neuron signals through light. Two different microbial rhodopsins are studied:
Krokinobacter eikastus rhodopsin 2 (KR2), a light-driven outward sodium pump, and Anabaena sensory rhodopsin (ASR), a light sensor. In both cases, the qualitative and quantitative information acquired from the ARM-obtained QM/MM models reveal nature (electrostatic or steric) and extent of the mutation-induced changes on the retinal configuration, which, in turn, are the cause of the shift in the absorption wavelength of the relative mutants. Finally, we explore the fluorescence of ASR mutants, particularly useful for the visualization of neuronal activity. The target of this work is to use QM/MM simulations to understand the opposite behaviour observed in two blue-shifted ASR mutants, where one presents a negligible fluorescence, while the other displays one order of magnitude enhanced fluorescence, with respect to the wild type protein. Our QM/MM models show that specific electrostatic and steric interactions control the character mixing of different electronic states, opening a path to the rational engineering of highly fluorescent rhodopsins. In conclusion, within the limits of its automation, the ARM protocol allows the study of ground and excited states of specific photoactive proteins: rhodopsins. This opens the way to an improved molecular-level understanding of rhodopsin photochemistry and photobiology. The results obtained highlight the importance of having a standardized, effective and automatic protocol, which renders this kind of studies more efficient and accessible, by drastically shortening the time required to produce accurate and congruous QM/MM models. For the above reasons the author of the present thesis believes that ARM stands as an important cogwheel in the virtuous cycle between experimental and theoretical work, aimed to prepare the photobiological tools for tomorrow’s needs.
13
Höglund, Pär J. "Identification, Characterization and Evolution of Membrane-bound Proteins." Doctoral thesis, Uppsala universitet, Institutionen för neurovetenskap, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9329.
Повний текст джерелаАнотація:
Membrane proteins constitute approximately 30% of all genes in the human genome and two large families of membrane proteins are G protein-coupled receptors (GPCRs) and Solute Carriers (SLCs) with about 800 and 380 human genes, respectively. In Papers I, II and IV, we report 16 novel human Adhesion GPCRs found by searches in NCBI and Celera databases. In Paper I, we report eight novel human GPCRs, and six in Paper II. We identified two new human Adhesion GPCRs and 17 mouse orthologs in Paper IV. Phylogenetic analysis demonstrates that the 16 novel human genes are additional members of the Adhesion GPCR family and can be divided into eight phylogenetic groups. EST expression charts for the entire repertoire of Adhesions in human and mouse were established, showing widespread distribution in both central and peripheral tissues. Different domains were found in their N-terminus, some, such as pentraxin in GPR112, indicates that they take part in immunological processes. In Paper III, we discovered seven new human Rhodopsin GPCRs. In Paper V, we present the identification of two new human genes, termed SLC6A17 and SLC6A18 from the Solute Carriers family 6 (SLC6). We also identified the corresponding orthologs and additional genes from the mouse and rat genomes. We analysed, in total, 430 unique SLC6 proteins from 10 animal, one plant, two fungi and 196 bacterial genomes. In Paper VI, we provide the first systematic analysis of the evolutionary history of the different SLC families in Eukaryotes. In all, we analysed 2403 sequences in eight species and we delineate the evolutionary history of each of the 46 SLC families.
14
Wong, Simon Yuk Chun. "A spectrin-like protein in bovine retinal rod photoreceptor outer segments as defined by monoclonal antibodies." Thesis, University of British Columbia, 1988. http://hdl.handle.net/2429/29217.
Повний текст джерелаАнотація:
Biochemical and immunological studies indicate that rod outer segments (ROS) of bovine photoreceptor cells contain a Mr 240,000 polypeptide related to the ∝-subunit of red blood cell (RBC) spectrin. With the use of sodium dodecyl sulfate gel electrophoresis in conjunction with the immunoblotting technique, monoclonal antibody 4B2 was found to bind to a Mr 240,000 polypeptide in ROS that is distinct from the prominent Mr 220,000 concanavalin A binding glycoprotein. The Mr 240,000 polypeptide is highly susceptible to degradation by endogenous proteases. It does not appear to be an integral membrane protein but is tightly membrane associated since it can be partially extracted from ROS membranes with urea in the absence of detergent.
The 4B2 antibody cross-reacted with RBC ghost membranes and bovine brain microsomal membranes. Radioimmune assays and immunoblotting analysis of purified bovine RBC spectrin further revealed that the 4B2 antibody predominantly labelled the ∝-chain of RBC spectrin having an apparent Mr of 240,000. Monoclonal antibody 3A6 was found to bind to a polypeptide with a slightly lower Mr than the 4B2-specific polypeptide. It is also highly susceptible to degradation by endogenous proteases, but unlike the 4B2 antibody, it predominantly labelled the β-chain of RBC spectrin having an apparent M of 220,000. Polyclonal anti-spectrin antibodies that bound to both the ∝ - and β-chain of RBC spectrin predominantly labelled a Mr 240,000 polypeptide of ROS membranes. Two faintly labelled bands in the Mr range of 210,000-220,000 were also observed. These components may represent variants of the β -chain of spectrin that are weakly cross-reacting or present in smaller quantities than the ∝-chain.
Immunocytochemical labelling studies using the 4B2 antibody and immunogold-dextran markers indicated that the ROS spectrin-like protein is preferentially localized in the region where the discs come in close contact to the plasma membrane of ROS. Immunoblotting analysis indicated that rhodopsin and peripherin which constitute over 90% of total disc membrane proteins were selectively solubilized in Triton X-100, whereas a set of polypeptides including the 4B2-specific polypeptide and the Mr 220,000 concanavalin A-binding glycoprotein was only partially soluble. Electron microscopy of a negatively stained Triton-extracted ROS pellet revealed a filamentous network.
These studies indicate that ROS contain a protein related to RBC spectrin, which may constitute a major component of a filamentous network lining the inner surface of the ROS plasma membrane as previously seen by electron microscopy. This membrane skeletal system may serve to stabilize the ordered ROS structure and maintain a constant distance between the rim region of the discs and the plasma membrane.Medicine, Faculty of
Biochemistry and Molecular Biology, Department of
Graduate
15
Nordström, Karl J. V. "Characterization and Evolution of Transmembrane Proteins with Focus on G-protein coupled receptors in Pre-vertebrate Species." Doctoral thesis, Uppsala universitet, Funktionell farmakologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-121696.
Повний текст джерелаАнотація:
G protein-coupled receptors (GPCRs) are one of the largest protein families in mammals. GPCRs are instrumental for hormonal and neurotransmitter signalling and are important in all major physiological systems of the body. Paper I describes the repertoire of GPCRs in Branchiostoma floridae, which is one of the species most closely related species to vertebrates. Mining and phylogenetic analysis of the amphioxus genome showed the presence of at least 664 distinct GPCRs distributed among all the main families of GPCRs; Glutamate (18), Rhodopsin (570), Adhesion (37), Frizzled (6) and Secretin (16). Paper II contains studies of the Adhesion, Methuselah and Secretin GPCR families in nine genomes. The Adhesion GPCRs are the most complex gene family among GPCRs with large genomic size, multiple introns and a fascinating flora of functional domains. Phylogenetic analysis showed Adhesion group V (that contains GPR133 and GPR144) to be the closest relative to the Secretin family among the groups in the Adhesion family, which was also supported by splice site setup and conserved motifs. Paper III examines the repertoire of human transmembrane proteins. These form key nodes in mediating the cell’s interaction with the surroundings, which is one of the main reasons why the majority of drug targets are membrane proteins. We identified 6,718 human membrane proteins and classified the majority of them into 234 families of which 151 belong to the three major functional groups; Receptors (63 groups, 1,352 members), Transporters (89 groups, 817 members) or Enzymes (7 groups, 533 members). In addition, 74 Miscellaneous groups were shown to include 697 members. Paper IV clarifies the hierarchy of the main families and evolutionary origin of majority of the metazoan GPCR families. Overall, it suggests common decent of at least 97% of the GPCRs sequences found in humans, including all the main families.
16
Agathangelou, Damianos. "Anabaena Sensory Rhodopsin : effect of mutations on the ultrafast photo-isomerization dynamics." Thesis, Strasbourg, 2019. http://www.theses.fr/2019STRAE001/document.
Повний текст джерелаАнотація:
ASR, est une protéine photo réceptrice qui lie la base protonée de la rétine de Schiff dans deux conformations de l'état fondamental. La protéine particulière consiste en un système modèle dans lequel I'effet de l'environnement protéique sur la dynamique d'isomérisation des deux isomères peut être étudié. Dans cette thèse, une étude approfondie sur les protéines mutées ponctuellement est présentée, où la variable est l'environnement protéique. Les résultats montrent des différences significatives entre les durées de vie des états excités des deux isomères et les durées de vie plus courtes ou plus longues commentées en termes de mélange électronique Sl/S2. En complément, le développement expérimental d'un spectromètre à absorption transitoire (T.A) et d'un dispositif de spectroscopie électronique bidimensionnelle (2DES) fonctionnant respectivement dans les domaines spectral NIR et UV-Vis. Avec cette configuration, deux impulsions colinéaires à verrouillage de phase d'une durée inférieure à 10fs sont générées, où. la précision interférométrique sur le contrôle du retard entre les deux impulsions de pompe permet d'effectuer des mesures 2DESASR, is a photoreceptor protein that binds the protonated Schiff base of retinal in two ground state conformations. The particular protein consists a model system where the effect of the protein environment on the isomerization dynamics of the two isomers can be investigated. In this thesis an extended study on point mutated proteins is presented where the variable is the protein environment. The results show significant differences between the two isomers excited state lifetimes with the shorter or longer lifetimes commented in terms of Sl/S2 electronic mixing. Supplementary, the experimental development of a Transient absorption spectrometer (T.A) and a Two-dimensional electronic spectroscopy setup (2DES) operating in the NIR and UV-Vis spectral range respectively are described. The 2DES spectrometer is based on translating wedges made out of birefringent material producing two collinear phase-locked pulses with sub-I Ofs duration. The interferometric precision on controlling the delay between the two pump pulses allows to perform 2DES measurements on systems absorbing in the 360-430 nm range allowing to resolve the excitation process spectrally
17
Höglund, Pär J. "Identification, Characterization and Evolution of Membrane-bound Proteins /." Uppsala : Acta Universitatis Upsaliensis Acta Universitatis Upsaliensis, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9329.
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18
Chatterjee, Deep [Verfasser], Harald [Gutachter] Schwalbe, and Josef [Gutachter] Wachtveitl. "Structural and functional characterization of proteins : bovine visual rhodopsin and PaMTH1, a SAM dependent O-methyltransferase / Deep Chatterjee ; Gutachter: Harald Schwalbe, Josef Wachtveitl." Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2016. http://d-nb.info/1120493382/34.
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19
Fernández, Sampedro Miguel Antonio. "Characterization of amino acid changes in visual pigment evolution and interaction with associated proteins." Doctoral thesis, Universitat Politècnica de Catalunya, 2018. http://hdl.handle.net/10803/620622.
Повний текст джерелаАнотація:
Visual opsins are G protein-coupled receptors that function as light photoreceptors in the vertebrate retina. Rhodopsin is the visual pigment located in the rod photoreceptor cells specialized in scotopic vision.
Bovine and mouse rhodopsins have been thoroughly used as in vitro and in vivo models for physiological and biochemical characterization. In the last years, different lines of evidence point to significant functional differences among rhodopsins of different species. In this thesis bovine, murine and human rhodopsins were immunopurified and biochemically characterized, revealing differences in their thermal stabilities and retinal release rates. Besides, the Y102H RP-like rhodopsin mutation was introduced in the human and bovine backgrounds to bring up potential phenotypic differences. Therefore, keeping in mind that a large body of studies on human genetic retinal degenerative diseases related with opsins (e.g. retinitis pigmentosa) have used these models, our results suggest that using human rhodopsin for future studies would be advised.
The most important biochemical differences were observed between the diurnal (human and bovine) versus nocturnal (mouse) species, especially in their retinal release rates. In addition, we also found a novel relevant amino acid position that appears to be significantly correlated with rhodopsin molecular adaptation to the nocturnal (L290) and the diurnal (I290) niches throughout terrestrial therian mammals. Previous studies suggested that L290 is present in the inferred therian ancestor rhodopsin in agreement with mammalian “nocturnal bottleneck” theories. Thus, the L290I substitution could have an important role in mammal rhodopsin molecular evolution and adaptation as it is likely to be the result of independent analogous changes, a fact that can be well-appreciated in the primate and rodent orders. This hypothesis was experimentally confirmed by the L290I mutation in murine rhodopsin that resulted in a Meta II decay rate similar to that of bovine rhodopsin.
These results provide support for a role of the Meta II decay rate in rhodopsin evolution, beyond the well-studied ¿max spectral shift used by animal species to adapt to different light environments. Moreover, a novel mechanism is proposed involving a compromise between improving rod protection under bright light in nocturnal species by means of a stabilized Meta II conformation, and a faster dark adaption that occurs under dim-light conditions in diurnal species by means of a faster retinal reléase.
Our statistical analysis found three new candidate positions for positive selection in the mammal therian branch. The reverse mutations (F13M, Q225R and A346S) were introduced into bovine rhodopsin and the expressed proteins were immunopurified to functionally and biochemically characterize the consequences of these ancestral changes. Position 225 appears to be important for the function of the protein affecting the G-protein activation process, and position 346 would also regulate functionality of the receptor by enhancing G-protein activation and presumably affecting protein phosphorylation by rhodopsin kinase. Position 13 was shown to be very important for the proper folding and glycosylation of rhodopsin as only in the engineered thermally stable double Cys mutant (N2C/N282C) background was able to be regenerated with 11-cis-retinal. Similarly a double Cys mutation (W90C/A169C) previously proposed for the green cone opsin was biochemically analyzed confirming the formation (at least partially) of this bond.
Finally, a recently detected interaction between the membrane protein peripherin-2 and rhodopsin was functionally studied, showing reduced G-protein activation, by rhodopsin, in presence of peripherin-2 when the two proteins were in a partially solubilised system. These results could have physiological implications in the desensitization process involving rhodopsin on the rim of discs of photoreceptor cells.Los opsinas visuales son receptores acoplados a proteína G que funcionan como fotoreceptores en retinas de vertebrados. La rodopsina es el pigmento visual de los bastones, células fotoreceptoras especializadas en la visión escotópica. Las rodopsinas bovina y murina han sido ampliamente usadas como modelos para caracterización bioquímica y fisiológica. En esta tesis, las rodopsinas bovina, murina y humana fueron inmunopurificadas y caracterizadas bioquímicamente, revelando diferencias en su estabilidad térmica y en la tasa de salida de retinal. Además, la mutación tipo RP Y102H se introdujo en las rodopsinas humana y bovina para revelar potenciales diferencias fenotípicas. Teniendo en cuenta que una gran parte de estudios en enfermedades genéticas degenerativas de la retina humana relacionadas con opsinas (Ej. Retinitis Pigmentosa) han usado estos modelos, los resultados sugieren que el uso de rodopsinas humanas en estudios futuros sería aconsejable. Las mayores diferencias bioquímicas fueron observadas entre especies diurnas (humano y vaca) en comparación con la nocturna (ratón), especialmente en las tasas de salida de retinal. Además, se encontró una nueva y relevante posición aminoacídica que parece estar significativamente correlacionada con la adaptación molecular de la rodopsina a la nocturnidad (L290) y a la diurnidad (I290) a lo largo de los mamíferos terios terrestres. Estudios previos sugieren que L290 estaba presente en la rodopsina ancestrales inferidas, en concordancia con las teorías del ?cuello de botella nocturno?en mamíferos. La substitución L290I podría haber tenido un importante papel en la adaptación y la evolución molecular de las rodopsina de mamíferos al ser probablemente el resultado de cambios análogos independientes, hecho que puede ser apreciado en los órdenes de primates y roedores. Esta hipótesis fue confirmada experimentalmente mediante la mutación L290I en rodopsina murina que resultó en una tasa de decaimiento del Meta II similar al de rodopsina bovina. Estos resultados dan apoyo al papel de la tasa de decaimiento del Meta II en la evolución de la rodopsina, más allá del bien estudiado desplazamiento espectral de ¿max relacionado con la adaptación a diferentes niveles de luz ambiental. Además, se propone un nuevo mecanismo que implica un compromiso entre la protección en bastones ante luz brillantes en especies nocturnas mediante una estabilización de la conformación Meta II, y una adaptación a la oscuridad más rápida bajo condiciones de luz tenue en especies diurnas mediante una salida de retinal más rápida. Análisis estadístico encontraron tres nuevas posiciones candidatas a haber sido positivamente seleccionadas en la rama de los mamíferos terios. Las mutaciones reversas (F13M, Q225R y A346S) se introdujeron en la rodopsina bovina y se inmunopurificaron para caracterizar estos cambios ancestrales. 225 aparenta ser importante para la funcionalidad de la proteína afectando el proceso de activación de la proteína G, y 346 regularía también la funcionalidad mediante la mejora de la activación de la proteína G y presumiblemente afectando la fosforilación por parte de la rodopsina kinasa. La posición 13 es muy importante para el correcto plegamiento y glicosilación de la rodopsina al solo poder ser regenerada con 11-cis-retinal al insertar la doble mutación de Cys (N2C/N282C) termalmente estable. De manera similar una doble mutación de Cys (W90C/A169C) previamente propuesta para la opsina verde de conos fue analizada bioquímicamente confirmando la formación (al menos parcialmente) de este enlace. Finalmente, la interacción entre la periferina-2 y la rodopsina se estudió funcionalmente. Se detectó una reducción en la activación de la proteína G por la rodopsina, cuando las dos proteínas están en un sistema parcialmente solubilizado. Estos resultados podrían tener implicaciones fisiológicas en el proceso de desensibilización que implica la rodopsina en el borde de los discos de las células fotorreceptoras.
20
Ni, Lina. "Maintenance of Visual Sensitivity in the Drosophila Eye: A Dissertation." eScholarship@UMMS, 2010. https://escholarship.umassmed.edu/gsbs_diss/457.
Повний текст джерелаАнотація:
High visual sensitivity is a common but important characteristic of animal eyes. It is especially critical for night vision. In animal eyes, photoreceptors are the first to receive the incoming rays of light and they convert the light signals to electrical signals before passing the information to interneurons in the eye and finally to the brain.
To function in dim light conditions, photoreceptors have developed high sensitivities to light. It is reported that both mammalian rod photoreceptors and Drosophilaphotoreceptors can detect single photons.
The high sensitivities of photoreceptors largely depend on a high content of rhodopsin, a light-stimulated G protein-coupled receptor (GPCR), in light sensory organelles, outer segments in mammals and rhabdomeres in Drosophila. Two shared characteristics, the tightly packed photoreceptive membrane and the high concentration of rhodopsin in the membrane, work together to enable the photoreceptors to achieve the high content of rhodopsin in photosensory organelles in both mammals and Drosophila. In this thesis, I have used the Drosophilaeye as a model system to study the molecular mechanisms required for the maintenance of these two characteristics.
In the second chapter, I present a new molecular mechanism of preventing Gq-mediated rhabdomeral degeneration. A new gene named tadr (for torn and diminished rhabdomeres), when mutated, leads to visual sensitivity reduction and photoreceptor degeneration. Degeneration in the tadr mutant is characterized by shrunken and disrupted rhabdomeres. The TADR protein interacts in vitro with the major light receptor Rh1 rhodopsin, and genetic reduction of the Rh1 level suppresses the tadr-induced degeneration, suggesting the degeneration is Rh1-dependent. Nonetheless, removal of phospholipase C (PLC), a key enzyme in phototransduction, and that of Arr2 fail to inhibit rhabdomeral degeneration in the tadr mutant background. Biochemical analyses reveal that, in the tadr mutant, the Gq protein of Rh1 is defective in dissociation from the membrane during light stimulation. Importantly, reduction of Gq level by introducing a hypomorphic allele of Gαq gene greatly inhibits the tadr degeneration phenotype. These results may suggest that loss of a potential TADR-Rh1 interaction leads to an abnormality in the Gqsignaling, which in turn triggers rhabdomeral degeneration independent of the PLC phototransduction cascade. We propose that TADR-like proteins may also protect photoreceptors from degeneration in mammals including humans.
In the third chapter, I present a Drosophila CUB- and LDLa-domain transmembrane protein CULD that counteracts the visual arrestin Arr1-mediated endocytosis to retain rhodopsin in rhabdomeral membrane. CULD is mostly localized in rhabdomeres, but is also detected in scarce rhodopsin endocytic vesicles that contain Arr1. An intracellular region of CULD interacts with Arr1 in vitro. In both culdmutant and knockdown flies, a large amount of rhodopsin is mislocalized in the cell body of photoreceptors through lightdependent, Arr1-mediated endocytosis, leading to reduction of photoreceptor sensitivity. Expressing a wild-type CULD protein in photoreceptors, but not a mutant variant lacking the Arr1-interacting site, rescues both the rhodopsin mislocalization and the low sensitivity phenotypes. Once rhodopsin has been internalized in adult mutant flies, it is reversed only by expression of CULD but not by blocking endocytosis, suggesting that CULD promotes recycling of endocytosed rhodopsin to the rhabdomere. Our results demonstrate an important role of CULD in the maintenance of membrane rhodopsin density and photoreceptor sensitivity. We propose that a common cellular function of CUB- and LDLa-domain proteins, in both mammals and invertebrates, is to concentrate receptors including GPCRs in particular regions of cell membrane.
In summary, the work addressed in this thesis has identified new molecular mechavii nisms underlying the maintenance of visual sensitivity in Drosophila, either through preventing Gq-mediated rhabdomeral degeneration or through antagonizing arrestin-mediated rhodopsin endocytosis. This work has advanced our understanding of visual biology and the general regulatory mechanisms of GPCR signaling, and may provide valuable clues to pathologic studies of human retinal degeneration disorders.
21
Choi, Eun-Jung. "Comparison of the effects of a processing sequence and a nuclear export element on ribozyme activity in transfected cells." [Gainesville, Fla.] : University of Florida, 2004. http://purl.fcla.edu/fcla/etd/UFE0007401.
Повний текст джерелаАнотація:
Thesis (M.S.)--University of Florida, 2004.Typescript. Title from title page of source document. Document formatted into pages; contains 68 pages. Includes Vita. Includes bibliographical references.
22
Mielke, Thorsten. "Untersuchungen zur Struktur und Dynamik der cytoplasmatischen Loopbereiche des G-Protein-gekoppelten Rezeptors Rhodopsin." [S.l. : s.n.], 2000. http://www.diss.fu-berlin.de/2000/98/index.html.
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23
McCarthy, Nina E. M. "Mechanistic studies on rhodopsin kinase : a farnesylated protein." Thesis, University of Southampton, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.266389.
Повний текст джерела
24
Felce, James H. "A survey of G protein-coupled receptor stoichiometry." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:ae078d13-fef7-4f1f-a8ea-c2e5412f59ff.
Повний текст джерелаАнотація:
G-protein coupled receptors (GPCRs) represent the largest family of transmembrane proteins in the human genome. Their biological and medical significance has driven extensive research into their structure and function, yet a number of important aspects of their behaviour remain unresolved. Arguably the most contentious debate in the field concerns whether or not the receptors form stable homo- and hetero-oligomeric interactions, and there is currently no consensus on the extent or purpose of GPCR oligomerisation. In this thesis, the ‘typical’ stoichiometry of Rhodopsin family GPCRs is investigated via the examination of more than 60 receptors natively expressed by human HEK 293T cells using bioluminescence resonance energy transfer (BRET). Assaying receptors in the cells in which they are natively expressed maximises the likelihood of authentic assembly and trafficking while simultaneously providing an unbiased cross-section of the whole GPCR family. In order to make such an investigation possible, the sensitivity of existing BRET approaches for partial homodimers had to be, and was, confirmed, and a complementary competition-based BRET method suitable for a semi high-throughput analysis was developed. Application of these assays to the HEK 293T GPCR repertoire revealed that the Rhodopsin family is very predominantly monomeric but contains a small fraction of independently evolved dimers comprising small phylogenetic clusters of receptors. The mechanism of Rhodopsin family dimerisation was in some cases found to be reliant on interactions between transmembrane helices, in contrast to other families of GPCRs, which were observed or are known to be exclusively dimeric due to interactions between their N-terminal domains. The mechanism of dimerisation in Rhodopsin family GPCRs may preclude constitutive dimerisation but allow heterodimerisation of closely related receptors, as observed for a subset of receptors using a third type of assay designed to detect heterodimers. Taken together, these observations suggest a model of GPCR evolution in which dimers either have a selective disadvantage compared to monomers, or for which dimerisation offers no apparent selective advantage. These findings suggest that receptor stoichiometry is at least partly responsible for several of the remarkable features of GPCR family structure, including the very large size of the family as a whole, the great diversity of Rhodopsin family GPCRs, and the origins of sensory receptors.
25
King, Alistair James. "Purification and characterisation of phosphatases responsible for the dephosphorylation of phospho-opsin in bovine rod outer segments." Thesis, University of Southampton, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.295710.
Повний текст джерела
26
Fransen, Maikel Peter. "Stabilizing the G protein-coupled receptor rhodopsin/heterotrimeric G protein transducin signalling complex." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610816.
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27
Nishioku, Yoshinori. "Energetics, Conformational Changes and Protein-Protein Interaction in the Photolysis of Octopus Rhodopsin." 京都大学 (Kyoto University), 2002. http://hdl.handle.net/2433/149563.
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28
Radhakrishnan, Varsha. "Molecular characterization and expression of Gq/11 protein in fishes /." View online, 2007. http://ecommons.txstate.edu/bioltad/4.
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29
Noche, Ramil Romare. "In Vivo Analysis of Zebrafish Exo-rhodopsin Protein and Suprachiasmatic Nucleus Function." Case Western Reserve University School of Graduate Studies / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=case1212772912.
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30
Inoue, Keiichi. "Studies on signal transduction dynamics between sensory rhodopsin 2 and transducer protein." 京都大学 (Kyoto University), 2007. http://hdl.handle.net/2433/136784.
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31
Gragg, Megan Ellen. "Mutant Rhodopsins in Autosomal Dominant Retinitis Pigmentosa Display Variable Aggregation Properties." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1522935340252319.
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32
Li, Xiang. "G-Protein Modulation of Ion Channels and Control of Neuronal Excitability by Light." Case Western Reserve University School of Graduate Studies / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=case1174263213.
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33
Angel, Thomas Emil. "Spectrophotometric, Mass Spectrometeric and Structural Studies of the Prototypical G Protein Coupled Receptor Rhodopsin." Thesis, Montana State University, 2007. http://etd.lib.montana.edu/etd/2007/angel/AngelT0507.pdf.
Повний текст джерелаАнотація:
Rhodopsin is the integral membrane protein responsible for black and white vision in low light conditions and is found at high concentration in the mammalian retina. Rhodopsin is a prototypical member of the G protein coupled receptor super family that control much of physiology. Improved understanding of rhodopsin signal transduction and amplification via coupling to the heterotrimeric G protein transducin may reveal conserved activation mechanisms that are relevant to other members of the GPCR super family. Described here are several studies that examine the molecular determinants responsible for heterotrimeric G protein coupling to metarhodopsin II, the active photointermediate of bovine rhodopsin. Employing uv-visible spectroscopy we have investigated the nature of the interaction between the C-terminal tail of transducin and metarhodopsin II. We have provided evidence that suggests the orientation of transducin when it interacts with metarhodopsin II. Mass spectrometry is a powerful technique for characterizing intact and digested proteins. We have optimized mass spectral methods for investigating integral membrane proteins, utilizing rhodopsin as a model system. The mass spectrometric studies provide the foundation for future investigations into agonist and antagonist interactions and the related G protein coupled receptors using molecular crosslinking. Development and validation of new tools for generating structural constraints for conformational states of proteins that are not amiable to more traditional structural determination techniques are described. Antibody imprinting studies on rhodopsin were advanced with the work presented here. The x-ray crystal structure of the anti-rhodopsin antibody K42-41L in complex with a synthetic epitope mimetic peptide is described. These studies led to the generation of a model of the third cytoplasmic loop of the photointermediate metarhodopsin I and constraints on the conformational changes in metarhodopsin II.
34
Ruprecht, Jonathan James. "Investigating the structure of an intermediate state of the G protein-coupled receptor rhodopsin." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614750.
Повний текст джерела
35
Tan, Yi Lei. "Structural and Biophysical Characterisation of Denatured States and Reversible Unfolding of Sensory Rhodopsin II." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/289718.
Повний текст джерелаАнотація:
Our understanding of the folding of membrane proteins lags behind that of soluble proteins due to the challenges posed by the exposure of hydrophobic regions during in vitro chemical denaturation and refolding experiments. While different folding models are accepted for soluble proteins, only the two-stage model and the long-range interactions model have been proposed so far for helical membrane proteins. To address our knowledge gap on how different membrane proteins traverse their folding landscapes, Chapter 2 investigates the structural features of SDS-denatured states and the kinetics for reversible unfolding of sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis. pSRII is difficult to denature, and only SDS can dislodge the retinal chromophore without rapid aggregation. Even in 30% SDS (0.998 $\mathit{\Chi}_{SDS}$), pSRII retains the equivalent of six out of seven transmembrane helices, while the retinal binding pocket is disrupted, with transmembrane residues becoming more solvent-exposed. Folding of pSRII from an SDS-denatured state harbouring a covalently-bound retinal chromophore shows deviations from an apparent two-state behaviour. SDS denaturation to form the sensory opsin apo-protein is reversible. This chapter establishes pSRII as a new model protein which is suitable for membrane protein folding studies and has a unique folding mechanism that differs from those of bacteriorhodopsin and bovine rhodopsin. In Chapter 3, SDS-denatured pSRII, acid-denatured pSRII and sensory opsin obtained by hydroxylamine-mediated bleaching of pSRII were characterised by solution state NMR. 1D $^1$H and $^{19}$F NMR were first used to characterise global changes in backbone amide protons and tryptophan side-chains. Residue-specific changes in backbone amide chemical shifts and peak intensities in 2D [$^1$H,$^{15}$N]-correlation spectra were analysed. While only small changes in the chemical environment of backbone amides were detected, changes in backbone amide dynamics were identified as an important feature of SDS- and acid-denatured pSRII and sensory opsin. $^{15}$N relaxation experiments were performed to study the backbone amide dynamics of SDS-denatured pSRII, reflecting motions on different timescales, including fast fluctuations of NH bond vectors on the ps-ns timescale and the lack of exchange contributions on the µs timescale. These studies shed insight on differences in the unfolding pathways under different denaturing conditions and the crucial role of the retinal chromophore in governing the structural integrity and dynamics of the pSRII helical bundle. Hydrogen bonds play fundamental roles in stabilising protein secondary and tertiary structure, and regulating protein function. Successful detection of hydrogen bonds in denatured states and during protein folding would contribute towards our understanding on the unfolding and folding pathways of the protein. Previous studies have demonstrated residue-specific detection of stable and transient hydrogen bonds in small globular proteins by measuring $^1{\it J}_{NH}$ scalar coupling constants using NMR. In Chapter 4, different methods for measuring $^1{\it J}_{NH}$ scalar coupling were explored using RalA, a small GTPase with a mixed alpha/beta fold, as proof-of-concept. Detection of hydrogen bonds was then attempted with OmpX, a beta-barrel membrane protein, both in its folded state in DPC micelles and in the urea-denatured state. While $^1{\it J}_{NH}$ measurement holds promise for studying hydrogen bond formation, further optimisation of NMR experiments and utilisation of perdeuterated samples are required to improve the precision of such measurements in large detergent-membrane protein complexes. Naturally occurring split inteins can mediate spontaneous trans-splicing both in vivo and in vitro. Previous studies have demonstrated successful assembly of proteorhodopsin from two separate fragments consisting of helices A-B and helices C-G via a splicing site in the BC loop. To complement the in vitro unfolding/folding studies, pSRII assembly in vivo was attempted by introducing a splicing site in the loop region of the beta-hairpin constituting the BC loop of pSRII. The expression conditions for the N- and C-terminal pSRII-intein segments were optimised, and the two segments co-expressed. However, the native chromophore was not observed. Further optimisation is required for successful in vivo trans-splicing of pSRII and application of this approach towards understanding the roles of helices and loops in the folding of pSRII.
36
Royant, Antoine. "Etudes structurales du photocycle de la bactériorhodopsine, et de la rhodopsine sensorielle II." Université Joseph Fourier (Grenoble), 2001. http://www.theses.fr/2001GRE10094.
Повний текст джерела
37
Jia, Xiaofei. "X-ray crystallographic studies of cellular retinoic acid-binding protein II mutants designed as rhodopsin mimics." Diss., Connect to online resource - MSU authorized users, 2008.
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38
Sharples, Jonathan M. "The conformation of the β-ionone ring region of the chromophore of rhodopsin, in the dark and meta-I photostates." Thesis, University of Oxford, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.275206.
Повний текст джерела
39
Cheng, Cheng. "Theoretical investigation of protein functions related to electron and ion transports working in thermal fluctuation." Kyoto University, 2019. http://hdl.handle.net/2433/242631.
Повний текст джерела
40
Gautier, Antoine. "Structure determination of the seven-helix transmembrane protein receptor sensory rhodopsin II by solution-state NMR spectroscopy." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611417.
Повний текст джерела
41
Madathil, Sineej. "Modular Switches in Protein Function: A Spectroscopic Approach." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-25977.
Повний текст джерелаАнотація:
Understanding the molecular basis of protein function is a challenging task that
lays the foundation for the pharmacological intervention in many diseases originating
in altered structural states of the involved proteins. Dissecting a complex functional
machinery into modules is a promising approach to protein function. The motivation
for this work was to identify minimal requirements for “local” switching processes in
the function of multidomain proteins that can adopt a variety of structural substates
of different biological activity or representing intermediates of a complex reaction
path. For example, modular switches are involved in signal transduction, where
receptors respond to ligand-activation by specific conformational changes that are
allosterically transmitted to “effector recognition sites” distant from the actual
ligand-binding site. Heptahelical receptors have attracted particular attention due to
their ubiquitous role in a large variety of pharmacologically relevant processes.
Although constituting switches in their own right, it has become clear through
mutagenesis and functional studies that receptors exhibit substates of partial
active/inactive structure that can explain biological phenotypes of different levels of
activity. Here, the notion that microdomains undergo individual switching processes
that are integrated in the overall response of structurally regulated proteins is
addressed by studies on the molecular basis of proton-dependent (chemical) and
force-dependent (mechanical) conformational transitions.
A combination of peptide synthesis, biochemical analysis, and secondary
structure sensitive spectroscopy (Infrared, Circular dichroism, Fluorescence) was
used to prove the switching capability of putative functional modules derived from
three selected proteins, in which conformational transitions determine their function
in transmembrane signaling (rhodopsin), transmembrane transport
(bacteriorhodopsin) and chemical force generation (kinesin-1). The data are then
related to the phenotypes of the corresponding full length-systems. In the first two
systems the chemical potential of protons is crucial in linking proton exchange
reactions to transmembrane protein conformation. This work addresses the
hypothesized involvement of lipid protein interactions in this linkage (1). It is shown
here that the lipidic phase is a key player in coupling proton uptake at a highly
conserved carboxylic acid (DRY motif located at the C-terminus of helix 3) to conformation during activation of class-1 G protein coupled receptors (GPCRs)
independently from ligand protein interactions and interhelical contacts. The data
rationalize how evolutionary diversity underlying ligand-specifity can be reconciled
with the conservation of a cytosolic ‘proton switch’, that is adapted to the general
physical constraints of a lipidic bilayer described here for the prototypical class-1
GPCR rhodopsin (2).
Whereas the exact sequence of modular switching events is of minor
importance for rhodopsin as long as the final overall active conformation is reached,
the related heptahelical light-transducing proton pump bacteriorhodopsin (bR),
requires the precise relative timing in coupling protonation events to
conformationtional switching at the cytosolic, transmembrane, and extracellular
domains to guarantee vectorial proton transport. This study has focused on the
cytosolic proton uptake site of this retinal protein whose proton exchange reactions at
the cytosolic halfchannel resemble that of rhodopsin. It was a prime task in this work
to monitor in real time the allosteric coupling between different protein regions. A
novel powerful method based on the correlation of simultaneously recorded infrared
absorption and fluorescence emission changes during bR function was established
here (3), to study the switching kinetics in the cytosolic proton uptake domain
relative to internal proton transfer reactions at the retinal and its counter ion. Using
an uptake-impaired bR mutant the data proves the modular nature of domain
couplings and shows that the energy barrier of the conformational transition in the
cytosolic half but not its detailed structure is under the control of proton transfer
reactions at the retinal Schiff base and its counter ion Asp85 (4).
Despite the different functions of the two studied retinal proteins, the
protonation is coupled to local switching mechanisms studied here at two levels of
complexity, [a] a single carboxylic acid side chain acting as a lipid-dependent proton
switch [b] a full-length system, where concerted modular regions orchestrate the
functional coupling of proton translocation reactions. Switching on the level of an
individual amino acid is shown to rely on localizable chemical properties (charge
state, hydrophobicity, rotamer state). In contrast, switching processes involving
longer stretches of amino acids are less understood, less generalizable, and can
constitute switches of mechanical, rather than chemical nature. This applies
particularly to molecular motors, where local structural switching processes are directly involved in force generation. A controversy exists with respect to the
structural requirements for the cooperation of many molecular motors attached to a
single cargo. The mechanical properties of the Hinge 1 domain of kinesin-1 linking
the “neck” and motor domain to the “tail” were addressed here to complement single
molecule data on torsional flexibility with secondary structure analysis and thermal
stability of peptides derived from Hinge 1 (5). It is shown that the Hinge 1 exhibits
an unexpected helix-forming propensity that resists thermal forces but unfolds under
load. The data resolve the paradox that the hinge is required for motor cooperation,
whereas it is dispensable for single motor processivity, clearly emphasizing the
modular function of the holoprotein. However, the secondary-structural data reveal
the functional importance of providing high compliance by force-dependent
unfolding, i.e. in a fundamentally different way than disordered domains that are
flexible but yet do not support cooperativity.
42
Gulati, Sahil Gulati. "Modulating G Protein-Coupled Receptor Signaling Pathways with Selective Chemical- and Protein-Based Effector Molecules." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1530642105672697.
Повний текст джерела
43
Madathil, Sineej. "Modular Switches in Protein Function: A Spectroscopic Approach." Doctoral thesis, Technische Universität Dresden, 2009. https://tud.qucosa.de/id/qucosa%3A25175.
Повний текст джерелаАнотація:
Understanding the molecular basis of protein function is a challenging task that
lays the foundation for the pharmacological intervention in many diseases originating
in altered structural states of the involved proteins. Dissecting a complex functional
machinery into modules is a promising approach to protein function. The motivation
for this work was to identify minimal requirements for “local” switching processes in
the function of multidomain proteins that can adopt a variety of structural substates
of different biological activity or representing intermediates of a complex reaction
path. For example, modular switches are involved in signal transduction, where
receptors respond to ligand-activation by specific conformational changes that are
allosterically transmitted to “effector recognition sites” distant from the actual
ligand-binding site. Heptahelical receptors have attracted particular attention due to
their ubiquitous role in a large variety of pharmacologically relevant processes.
Although constituting switches in their own right, it has become clear through
mutagenesis and functional studies that receptors exhibit substates of partial
active/inactive structure that can explain biological phenotypes of different levels of
activity. Here, the notion that microdomains undergo individual switching processes
that are integrated in the overall response of structurally regulated proteins is
addressed by studies on the molecular basis of proton-dependent (chemical) and
force-dependent (mechanical) conformational transitions.
A combination of peptide synthesis, biochemical analysis, and secondary
structure sensitive spectroscopy (Infrared, Circular dichroism, Fluorescence) was
used to prove the switching capability of putative functional modules derived from
three selected proteins, in which conformational transitions determine their function
in transmembrane signaling (rhodopsin), transmembrane transport
(bacteriorhodopsin) and chemical force generation (kinesin-1). The data are then
related to the phenotypes of the corresponding full length-systems. In the first two
systems the chemical potential of protons is crucial in linking proton exchange
reactions to transmembrane protein conformation. This work addresses the
hypothesized involvement of lipid protein interactions in this linkage (1). It is shown
here that the lipidic phase is a key player in coupling proton uptake at a highly
conserved carboxylic acid (DRY motif located at the C-terminus of helix 3) to conformation during activation of class-1 G protein coupled receptors (GPCRs)
independently from ligand protein interactions and interhelical contacts. The data
rationalize how evolutionary diversity underlying ligand-specifity can be reconciled
with the conservation of a cytosolic ‘proton switch’, that is adapted to the general
physical constraints of a lipidic bilayer described here for the prototypical class-1
GPCR rhodopsin (2).
Whereas the exact sequence of modular switching events is of minor
importance for rhodopsin as long as the final overall active conformation is reached,
the related heptahelical light-transducing proton pump bacteriorhodopsin (bR),
requires the precise relative timing in coupling protonation events to
conformationtional switching at the cytosolic, transmembrane, and extracellular
domains to guarantee vectorial proton transport. This study has focused on the
cytosolic proton uptake site of this retinal protein whose proton exchange reactions at
the cytosolic halfchannel resemble that of rhodopsin. It was a prime task in this work
to monitor in real time the allosteric coupling between different protein regions. A
novel powerful method based on the correlation of simultaneously recorded infrared
absorption and fluorescence emission changes during bR function was established
here (3), to study the switching kinetics in the cytosolic proton uptake domain
relative to internal proton transfer reactions at the retinal and its counter ion. Using
an uptake-impaired bR mutant the data proves the modular nature of domain
couplings and shows that the energy barrier of the conformational transition in the
cytosolic half but not its detailed structure is under the control of proton transfer
reactions at the retinal Schiff base and its counter ion Asp85 (4).
Despite the different functions of the two studied retinal proteins, the
protonation is coupled to local switching mechanisms studied here at two levels of
complexity, [a] a single carboxylic acid side chain acting as a lipid-dependent proton
switch [b] a full-length system, where concerted modular regions orchestrate the
functional coupling of proton translocation reactions. Switching on the level of an
individual amino acid is shown to rely on localizable chemical properties (charge
state, hydrophobicity, rotamer state). In contrast, switching processes involving
longer stretches of amino acids are less understood, less generalizable, and can
constitute switches of mechanical, rather than chemical nature. This applies
particularly to molecular motors, where local structural switching processes are directly involved in force generation. A controversy exists with respect to the
structural requirements for the cooperation of many molecular motors attached to a
single cargo. The mechanical properties of the Hinge 1 domain of kinesin-1 linking
the “neck” and motor domain to the “tail” were addressed here to complement single
molecule data on torsional flexibility with secondary structure analysis and thermal
stability of peptides derived from Hinge 1 (5). It is shown that the Hinge 1 exhibits
an unexpected helix-forming propensity that resists thermal forces but unfolds under
load. The data resolve the paradox that the hinge is required for motor cooperation,
whereas it is dispensable for single motor processivity, clearly emphasizing the
modular function of the holoprotein. However, the secondary-structural data reveal
the functional importance of providing high compliance by force-dependent
unfolding, i.e. in a fundamentally different way than disordered domains that are
flexible but yet do not support cooperativity.
44
Gloriam, David E. "G Protein-Coupled Receptors; Discovery of New Human Members and Analyses of the Entire Repertoires in Human, Mouse and Rat." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Universitetsbiblioteket [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6745.
Повний текст джерела
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Gushchin, Ivan. "Etudes structurales des rhodopsines microbiennes et des autres protéines membranaires au moyen de la cristallographie aux rayons X et de la modélisation informatique." Thesis, Grenoble, 2014. http://www.theses.fr/2014GRENY075/document.
Повний текст джерелаАнотація:
Chaque cellule vivante sur notre Terre est entourée d'une membrane lipidique. Les protéines résidant dans la membrane exécutent multitude de fonctions essentielles pour la survivance de la cellule. Parmi eux sont le transport actif et passif dans et hors de la cellule, la signalisation et la catalyse des réactions.Une des plus grandes familles de protéines membranaires sont rhodopsins microbiennes, qui utilisent l'énergie de la lumière pour leur fonction. Les membres de cette famille comptent parmi eux les pompes de protons, cations et anions, entraînée par l'illumination, les canaux ioniques activés par l'illumination et, finalement, photorécepteurs. Bien que les aspects fondamentaux de leur fonctionnement ont été connus depuis un certain temps, il ya une abondance de questions sans réponse. Dans cette thèse, plusieurs structures de rhodopsines microbiennes (y compris la première structure de protéorhodopsine et la première structure de la pompe à sodium) sont présentés et analysés. Les structures ouvrent la voie pour comprendre les similitudes et les différences entre les différents rhodopsines microbiennes et pour exploiter cette connaissance pour créer de meilleurs instruments à base de rhodopsines microbiennes pour des applications biologiques, par exemple, dans le domaine de optogenetics.Alors que la première partie de ce travail porte sur les nouvelles structures de rhodopsines microbiennes, la deuxième partie présente l'approche de simulation pour comprendre la signalisation en fonction des rhodopsines sensorielles dans phototaxie. Les domaines HAMP des protéines transductrices des signals des rhodopsines sensorielles sont étudiés au moyen de la dynamique moléculaire, et il est démontré que les simulations peuvent être utilisés pour la construction et la validation des structures atomiques des domaines de signalisation, ainsi que pour la compréhension des changements conformationnels associée à signalisation, initié par les transformations des rhodopsine sensorielles.La troisième et la dernière partie décrit le travail sur la protéine IPCT-DIPPS de Archaeoglobus fulgidus, une enzyme catalysant deux étapes consécutives de di-inositol-phosphate biosynthèse. La structure résolue peut servir de modèle pour comprendre le mécanisme catalytique de transférases CDP-alcool, une grande famille de protéines comptant des milliers de membres, parmi lesquels sont cinq protéines humaines, qui catalysent les étapes majeures de la biosynthèse des lipides. La structure a également été utilisé pour prédire les sites de liaison des ligands sur le site actif de l'enzyme et pour proposer le mécanisme d'action catalytique.Pour résumer, cette thèse présente les études structurales de diverses protéines membranaires par la cristallographie aux rayons X et la modélisation qui font progresser notre compréhension des aspects fondamentaux et pratiques de fonctionnement des protéines membranairesEvery living cell on Earth is surrounded by a lipid membrane. Proteins residing in the membrane perform a variety of functions crucial for the cell's survival. Among them are active and passive transport in and out of the cell, signaling and reaction catalysis.One of the largest membrane protein families are microbial rhodopsins, which utilize light energy for their function. Members of this family count among them light-driven proton, cation and anion pumps, light-gated ion channels and photoreceptors. While the basic aspects of their functioning have been known for some time, there is a plenty of unanswered questions. In this dissertation, several structures of microbial rhodopsins (among them the first proteorhodopsin structure and the first light-driven sodium pump structure) are presented and analyzed. The structures open the way for understanding the similarities and differences between the various microbial rhodopsins and for exploiting this understanding to create better microbial rhodopsin-based instruments for biological applications, for example, in the field of optogenetics.While the first part of this work deals with the novel structures of microbial rhodopsins, the second part presents the simulation approach for understanding the sensory rhodopsin-based signaling in phototaxis. The HAMP domains of the sensory rhodopsin transducer protein are studied by means of molecular dynamics, and it is demonstrated that the simulations may be used for building and validating the atomic structures of signaling domains, as well as for understanding the signaling-associated conformational changes, initiated by light-driven sensory rhodopsin transformations.The third and the last part describes the work on the Archaeoglobus fulgidus IPCT-DIPPS proteins, an enzyme catalyzing two consecutive steps of di-inositol-phosphate biosynthesis. The determined structure may serve as a model for understanding the catalytic mechanism of CDP-alcohol transferases, a large family of proteins counting thousands of members, among which are five human proteins that catalyze the major steps of lipid biosynthesis. The structure was also used to predict the binding sites of the ligands at the enzyme active site and to propose the mechanism of catalytic action.To sum up, this dissertation presents the structural studies of various membrane proteins by means of X-ray crystallography and modeling that advance our understanding of fundamental and practical aspects of membrane protein functioning
46
Waterstradt, Katja. "Der Einfluss des Cholesterolgehaltes der Diskmembranen des Stäbchenaußensegmentes auf die ersten Schritte der visuellen Signaltransduktion." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2009. http://dx.doi.org/10.18452/15949.
Повний текст джерелаАнотація:
Das Außensegment der Stäbchenzelle ist aus einem Stapel von flachen Membransäckchen, den Diskmembranen, aufgebaut. Entlang dessen existiert ein Cholesterolgradient mit 24 mol% Cholesterol in den basalen Diskmembranen und 5 mol% in den apikalen. Das Außensegment enthält alle Proteine der Signaltransduktion. Der Photorezeptor Rhodopsin ist als integrales Membranprotein in die Diskmembran eingebettet. Das G-Protein Transducin und das Effektorprotein, die Phosphodiesterase (PDE), sind periphere Proteine mit Lipidankern und somit reversibel mit der Membranoberfläche assoziiert. Um den Einfluss des Cholesterolgehaltes der Diskmembranen auf diese drei Proteine zu untersuchen, wurden Diskmembranen mit unterschiedlichem Cholesterolgehalt präpariert (Simulation des Cholesterolgradienten). Die Untersuchungen zur transversalen Verteilung des Cholesterols in der Diskmembran ergaben eine schnelle Transmembranbewegung mit einer Halbwertzeit von weniger als einer Minute bei 35 °C. Desweiteren konnte gezeigt werden, dass es zu kopfgruppenspezifischen Wechselwirkungen von Cholesterol mit dem Phospholipid Phosphatidylcholin kommt. Cholesterol verschiebt das Meta I-Meta II-Gleichgewicht (nach Lichtaktivierung von Rhodopsin) auf die Seite von Meta I (inaktiv). In dieser Arbeit konnte jedoch gezeigt werden, dass durch die Anwesenheit des Transducins das Gleichgewicht vollständig auf die Seite von Meta II (aktiv) verschoben wird, da Transducin spezifisch die Meta-II-Form stabilisiert. Somit kann die verminderte Meta II-Bildung des Rezeptors in Diskmembranen mit hohem Cholesterolgehalt durch Transducin ausgeglichen werden. Lediglich die Geschwindigkeit der Transducinaktivierung ist verlangsamt. Durch den erhöhten Cholesterolgehalt werden die Membraneigenschaften für eine Bindung der beiden peripheren Proteine Transducin und PDE über deren Lipidanker optimiert. Somit kann die Signaltransduktion auch in den basalen Diskmembranen des Stäbchenaußensegmentes stattfinden.The rod outer segment consists of a stack of flat membrane saccules called disc membranes. Along this stack a cholesterol gradient exists with 24 mol% cholesterol in the basal and only 5 mol% in the apical disc membranes. The outer segment contains all the proteins necessary for signal transduction. The photoreceptor rhodopsin as integral membrane protein is embedded in the disc membrane. The G protein transducin and the effector protein phosphodiesterase (PDE) are soluble proteins with lipid modifications, which are associated reversibly to the membrane surface. Disc membranes with different cholesterol contents were prepared to simulate the cholesterol gradient along the rod outer segment and to investigate the influence of disc membrane cholesterol content of these three proteins. Investigations of the transversal distribution of cholesterol in the disc membrane revealed a fast transmembrane movement with a half life of less than one minute at 35 °C. Further, head group specific interactions between cholesterol and phosphatidylcholine could be shown. The Meta I Meta II equilibrium after light activation of rhodopsin was shifted to the Meta I (inactive) site in membranes with high cholesterol. In this work it was shown that in the presence of transducin this equilibrium is shifted completely to the Meta II (active) site because transducin stabilizes specifically the Meta II form of the receptor. Hence the reduced Meta II formation in disc membranes with high cholesterol could be compensated by transducin. The speed of transducin activation is decelerated. By the increased cholesterol content membrane properties are optimized to the binding of transducin and PDE via their lipid modifications. Thus the signal transduction can take place also in disc membranes with high cholesterol.
47
Campagna, Anne. "Structural analysis of protein interaction networks." Doctoral thesis, Universitat Pompeu Fabra, 2012. http://hdl.handle.net/10803/84111.
Повний текст джерелаАнотація:
Interactions between proteins give rise to many functions in cells. In the lastdecade, highthroughput experiments have identified thousands of protein interactions, which are often represented together as large protein interaction networks. However, the classical way of representing interaction networks, as nodes and edges, is too limited to take dynamic properties such as compatible and mutually exclusive interactions into account. In this work, we study protein interaction networks using structural information. More specifically, the analysis of protein interfaces in threedimensional protein structures enables us to identify which interfaces are compatible and which are not. Based on this principle, we have implemented a method, which aims at the analysis of protein interaction networks from a structural point of view by (1) predicting possible binary interactions for proteins that have been found in complex experimentally and (2) identifying possible mutually exclusive and compatible complexes. We validated our method by using positive and negative reference sets from literature and set up an assay to benchmark the identification of compatible and mutually exclusive structural interactions. In addition, we reconstructed the protein interaction network associated with the G proteincoupled receptor Rhodopsin and defined related functional submodules by combining interaction data with structural analysis of the network. Besides its established role in vision, our results suggest that Rhodopsin triggers two additional signaling pathways towards (1) cytoskeleton dynamics and (2) vesicular trafficking.Las funciones de las proteínas resultan de la manera con la que interaccionan entre ellas. Los experimentos de alto rendimiento han permitido identificar miles de interacciones de proteínas que forman parte de redes grandes y complejas. En esta tesis, utilizamos la información de estructuras de proteínas para estudiar las redes de interacciones de proteínas. Con esta información, se puede entender como las proteínas interaccionan al nivel molecular y con este conocimiento se puede identificar las interacciones que pueden ocurrir al mismo tiempo de las que están incompatibles. En base a este principio, hemos desarrollado un método que permite estudiar las redes de interacciones de proteínas con un punto de vista mas dinámico de lo que ofrecen clásicamente. Además, al combinar este método con minería de la literatura y Los datos de la proteomica hemos construido la red de interacciones de proteínas asociada con la Rodopsina, un receptor acoplado a proteínas G y hemos identificado sus sub--‐módulos funcionales. Estos análisis surgieron una novel vıa de señalización hacia la regulación del citoesqueleto y el trafico vesicular por Rodopsina, además de su papel establecido en la visión.
48
Borshchevskiy, Valentin. "L'obtention des données cristallographiques de qualité supérieure des états fonctionnels de la bactériorhodopsine." Thesis, Grenoble, 2013. http://www.theses.fr/2013GRENY007.
Повний текст джерелаАнотація:
La synthèse de l'adénosine triphosphate (ATP) est un événement clé dans la bioénergétique cellulaire. ATP synthesis est possible quand un gradient de potentiel électrochimique de protons est présent sur les membranes des cellules ou des organelles. Ce gradient est produit par les réactions d'oxydoréduction ou les réactions photochimiques qui sont contrôlées par l'enzyme. Bactériorhodopsine (bR) est la protéine la plus simple et la plus étudiée qui convertit l'énergie lumineuse en potentiel électrochimique. bR est un protéine transmembranaire de Halobacterium salinarum. bR absorbe des photons de lumière et transmet un proton à partir du cytoplasme vers l'espace extracellulaire. Grâce à sa disponibilité en relativement grandes quantités, la procédure de purification facile et stable, bR reste un des protéines membranaire les plus étudiés au cours des 40 dernières années.Pour comprendre le mécanisme moléculaire de la bR fonctionnement il faut connaître les changements structurels, provoqués par l'absorption de photon, qui accompagnent le cycle de travail des protéines et poussent à transporter le proton. Cela implique l'obtention des structures cristallographiques de bR état fonctionnel avec une résolution atomique. Selon cette approche, il est important d'avoir les cristaux protéiques très ordonnés et les méthodes de fixage des molécules de protéines dans les états intermédiaires. Les méthodes de fixage dans des conditions cryogéniques ont été développées précédemment. Les cristaux de la qualité désirée peuvent être obtenus par la cristallisation in meso où lipide mésophase bicontinue est utilisé pour la cristallisation des protéines membranaires.Le mécanisme de la cristallisation in meso est actuellement étudié pauvrement. Cette situation limite grandement son application potentielle pour des protéines membranaires. Malgré ses limites l’approche in meso a récemment permis d'obtenir les structures de base ainsi que les structures intermédiaires des états de bR. Cependant, différents groupes de scientifiques ont publié de différents structures cristallographiques des mêmes états intermédiaires. Les mécanismes de protons transport proposés par des auteurs différents sont contradictoires. Les raisons de l'absence de consensus dans les structures intermédiaires restent floues. Les raisons possibles discutées dans la littérature sont: la qualité insuffisante de la diffraction des cristaux protéiques, twinning merohedral et détérioration des cristaux par l'irradiation de rayonnement X, ainsi que la génération de nouvelles protéines états provoqués par rayons X.L'objectif de l'étude était de trier les raisons de contradictions dans le domaine de l'analyse cristallographique de bR états fonctionnels et de trouver des moyens de surmonter les problèmes connexes. Ceci implique plusieurs sous-objectifs distincts: l'étude de twinning merohedral de bR cristaux; étude des changements dans la structure bR induit par les 'irradiation de rayonnement X; étude des changements structurels dans bR par les petites doses de radiations. Un autre objectif de ce travail était d'étudier un rôle de molécules de la matrice de in meso cristallisation dans la stabilisation des cristaux de protéines membranairesThe synthesis of adenosine triphosphate (ATP) is a key event in the cell bioenergetics. ATP synthesis is only possible when a proton electrochemical potential gradient is present on the membranes of cell or organelle. This gradient is produced by enzyme-controlled redox or photochemical reactions. Bacteriorhodopsin (bR) is the simplest and most studied protein that converts light energy into electrochemical potential. Being transmembrane protein of Halobacterium salinarum it absorbs light photon and transfers a proton from the cytoplasmic to the extracellular space. Due to its availability of relatively large quantities, easy purification procedure and protein stability bR remains one of the most extensively studied membrane proteins during the past 40 years.Current state of investigated problems. To understand the molecular mechanism of bR functioning is necessary to know the structural changes caused by light absorption which accompany the protein working cycle and lead to the directional transport of the proton. It implies obtaining of X-ray structures of bR functional states with atomic resolution. Following this approach it is important to have highly ordered three-dimensional protein crystals on the one hand and effective methods of trapping protein molecules in intermediate states on the other one. Trapping procedures for bR intermediate states under cryogenic conditions have been developed previously. Crystals of the desired quality can be obtained by in meso crystallization where lipid bicontinuous mesophase is used for the crystallization of membrane proteins. The mechanism of in meso crystallization is currently poorly investigated. This situation greatly limits its potential applicability for membrane proteins. Despite its limitations in meso approach have recently made possible to obtain the ground and some intermediate states structures of bR. However, different scientific groups have published different X-ray models of the same bR intermediate states. The proposed by different authors mechanisms of proton transport are contradictory. The reasons for the lack of the consensus in intermediate structures remain unclear. The possible reasons for this contradiction which have been discussed in literature are: insufficient quality of diffraction data, merohedral twinning and radiation damage of protein crystals, as well as the generation of new protein states caused by X-ray illumination.The aim of the study was to sort out the reasons for contradictions in the field of X-ray crystallographic analysis of bR functional states and to find ways to overcome related problems. This implies several separate subgoals: study of merohedral twinning of bR crystals; study of X-ray-radiation-induced changes in bR structure; study of low-dose radiation-induced structural changes in bR structure. An additional goal of the work was to study a role of molecules of the in meso crystallization matrix in the stabilization of membrane protein crystals
49
Lopes, Gláucia Jansen da Re. "Expressão gênica e protéica de rodopsina em células pigmentares e mecanismos de sinalização intracelular da sua modulação por endotelinas." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/41/41135/tde-09072009-093847/.
Повний текст джерелаАнотація:
Endotelinas (ETs) e sarafotoxinas (SRTXs) pertencem a uma família de peptídeos vasconstritores que podem regular a migração e/ou produção de pigmentos em células pigmentares de vertebrados (cromatóforos). Em peixes teleósteos, ETs/SRTXs induzem a migração de pigmentos. Em melanócitos humanos, as ETs promovem a melanogênese e mitogênese. ETs também regulam a transcrição de diversos genes. Esses efeitos são mediados por diferentes vias de sinalização intracelular, dentre elas a via da fosfolipase C (PLC), da proteína quinase C (PKC) e da cascata de sinalização por proteína quinases ativadas por mitógeno (MAPKs). A rodopsina é um fotopigmento responsável pela detecção de fótons presente nos bastonetes dos olhos dos vertebrados. A modulação da transcrição do gene para rodopsina em peixes teleósteos e mamíferos parece ocorrer através de elementos conservados. Cromatóforos podem responder diretamente à luz, resultando no deslocamento dos grânulos de pigmentos através dos processos dendríticos das células. Essas respostas evocadas por luz são provavelmente mediadas por moléculas fotorreceptoras expressas por essas células. A linhagem celular GEM-81, proveniente de eritroforoma do peixe teleósteo Carassius auratus, assim como os melanócitos B16 de Mus musculus expressam rodopsina e receptores para ETs dos subtipos ETB e ETA, respectivamente. O objetivo deste trabalho foi determinar se: 1) os níveis do RNAm para rodopsina poderiam ser modulados por SRTX S6c em GEM-81 e por ET-1 em B16 e quais os mecanismos de sinalização intracelular envolvidos nessa modulação; 2) os níveis protéicos de rodopsina também poderiam ser modulados por SRTX S6c em GEM-81 e por ET-1 em B16. Através de PCR em tempo real (quantitativo), demonstrou-se que SRTX S6c e ET-1 modulam os níveis do RNAm para rodopsina em GEM-81 e B16, respectivamente, de forma temporal e dose-dependente. Em GEM-81, essa modulação envolve a ativação de uma PKC e da cascata das MAPKs. Já em B16, há o envolvimento de PLC, cálcio como mensageiro intracelular, calmodulina, quinase dependente de cálcio/calmodulina e PKC. Através de ensaios de Western blotting, foi demostrado que na linhagem GEM-81 os níveis protéicos de rodopsina não são significativamente alterados por 24 horas de tratamento com SRTX 10-9M S6c, sugerindo o envolvimento de mecanismos de controle pós-transcricional na modulação da expressão protéica de rodopsina. Nas células B16 cuja extração de proteína total ocorreu 0 ou 6h após o fim do tratamento de 24h com ET-1 10-10M, os níveis protéicos de rodopsina não são significativamente alterados. Já nas células cuja proteína total foi extraída 3h após o fim do tratamento com ET-1, observou-se uma diminuição significativa dos níveis da proteína rodopsina. Esses resultados sugerem o envolvimento de mecanismos de controle pós-transcricional na modulação da expressão protéica de rodopsina, mecanismos estes exacerbados nas células B16 cuja extração de proteína ocorreu 3h após o fim do tratamento.Endothelins (ETs) and sarafotoxins (SRTXs) belong to a family of vasoconstrictor peptides, which can regulate pigment migration and/or production in vertebrate pigment cells (chromatophores). In teleostean fish, ETs/SRTXs induce pigment migration. In human melanocytes, ETs promote melanogenesis and mitogenesis. ETs also regulate the transcription of several genes. These effects are mediated by different intracellular signaling pathways, such as the phospholipase C (PLC), protein kinase C (PKC) and the mitogen-activated protein kinase (MAPK) cascade. Rhodopsin is a photopigment responsible for photon detection, found in vertebrate rod cells. Rhodopsin gene transcription regulation in teleostean fish and mammals seems to occur through conserved elements. Chromatophores can respond directly to light, promoting the migration of pigment granules along the cells dedritic processes. These light-evoked responses are probably mediated by photoreceptive molecules expressed by these cells. The teleost Carassius auratus erythrophoroma cell line, GEM-81 and Mus musculus B16 melanocytes express rhodopsin, as well as the ET receptors, ETB and ETA, respectively. The aim of this study was to determine whether 1) rhodopsin mRNA levels could be modulated by SRTX S6c in GEM-81 cells and ET-1 in B16 cells and the intracellular signaling mechanisms involved; 2) rhodopsin protein levels could also be modulated by SRTX S6c in GEM-81 and ET-1 in B16 cells. Using real time (quantitative) PCR, we demonstrated that SRTX S6c and ET-1 modulate rhodopsin mRNA levels in GEM-81 and B16, respectively, in a time and dose-dependent way. In GEM-81, this modulation involves the activation of a PKC and the MAPK cascade. In B16, it involves PLC, calcium as a second messenger, calmodulin, a calcium/calmodulin dependent kinase and PKC. The Western blotting assays demonstrated that in GEM-81 cells rhodopsin protein levels are not significantly altered by a 24-hour treatment with 10-9M SRTX S6c, suggesting the involvement of post-transcriptional mechanisms in the modulation of rhodopsin expression. In B16 cells, whose total protein was extracted 0 or 6 hours after the 24-hour treatment with 10-10M ET-1, rhodopsin protein levels were not significantly altered. When the cells total protein was extracted 3 hours after the 24-hour treatment with ET-1, a significant reduction in rhodopsin protein levels was observed. These results also suggest the involvement of post-transcriptional mechanisms in the modulation of rhodopsin expression in this cell line. These mechanisms could be somehow exacerbated in B16 cells whose protein was extracted 3 hours after the treatment.
50
Unger, Vinzenz Michael. "Approaches towards a high resolution structure of G protein-coupled receptors : expression of the Dictyostelium discoideum cAMP-receptor 1 in insect cells and electron crystallographic analysis of two - dimensional crystals of bovine rhodopsin." Thesis, University of Cambridge, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.337307.
Повний текст джерела