Relevant bibliographies by topics / Mobilité conformational

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Mobilité conformational'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 February 2022

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Journal articles on the topic "Mobilité conformational"

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Košovan, Peter, Zuzana Limpouchová, and Karel Procházka. "Charge Distribution and Conformations of Weak Polyelectrolyte Chains in Poor Solvents." Collection of Czechoslovak Chemical Communications 73, no. 4 (2008): 439–58. http://dx.doi.org/10.1135/cccc20080439.

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In this work we study the effect of mobility of charges in annealed polyelectrolytes on their conformational behavior in poor solvents. A combination of molecular dynamics and Monte Carlo simulation techniques was used to take the dissociation into account. We investigated the relation between the conformation of the polyelectrolyte and the distribution of charges along the chain. The results suggest that in sufficiently poor solvents the local degree of charging differs significantly from the average. When a pearl-necklace conformation is formed, the degree of charging of the pearls is significantly lower than that of the strings. The redistribution of charges stabilizes the pearl-necklace conformation and enables the formation of asymmetric conformations with a single pearl at one chain end and a string at the other end.
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Brewer, Dyanne, Howard Hunter, and Gilles Lajoie. "NMR studies of the antimicrobial salivary peptides histatin 3 and histatin 5 in aqueous and nonaqueous solutions." Biochemistry and Cell Biology 76, no. 2-3 (1998): 247–56. http://dx.doi.org/10.1139/o98-066.

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Conformational studies of the salivary peptides histatin 3 (H3) and histatin 5 (H5) were performed by NMR and circular dichroism (CD) in aqueous and nonaqueous solutions. Histatin 5 has no defined structure in H2O but adopts a more helical conformation in dimethyl sulfoxide and aqueous trifluoroethanol. This is in agreement with the CD analysis, which shows no secondary structure in H2O but increasing helical content in the presence of trifluoroethanol. CD analysis shows that H3 has less propensity to form a helical structure than H5 in similar conditions. The NMR analysis of H3 in H2O at pH 7.4 reveals that its conformational mobility is less than that of H5 as indicated by the observation of backbone cross peaks alphaN (i, i + 1) and NN (i, i + 1) and the slow exchanging amide protons in the C-terminus. However, H3 remains essentially unordered as suggested by the lack of longer range nuclear Overhauser effects (NOEs) in the NOESY spectrum. H3 becomes much more ordered in a mixture of 50:50 H2O - dimethyl sulfoxide as indicated by the numerous NOEs, including several side chain to side chain and side chain to backbone conectivities. Our data suggest that in these conditions H3 contains a turn in the region of K13 to K17 and possibly a 310 helix at the C-terminus. This study demonstrates that H3 and H5 are both conformationally mobile and that each adopt different types of conformations in aqueous and nonaqueous solutions.Key words: histatins, NMR, antimicrobial.
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Camacho, Inês S., Alina Theisen, Linus O. Johannissen, et al. "Native mass spectrometry reveals the conformational diversity of the UVR8 photoreceptor." Proceedings of the National Academy of Sciences 116, no. 4 (2019): 1116–25. http://dx.doi.org/10.1073/pnas.1813254116.

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UVR8 is a plant photoreceptor protein that regulates photomorphogenic and protective responses to UV light. The inactive, homodimeric state absorbs UV-B light, resulting in dissociation into monomers, which are considered to be the active state and comprise a β-propeller core domain and intrinsically disordered N- and C-terminal tails. The C terminus is required for functional binding to signaling partner COP1. To date, however, structural studies have only been conducted with the core domain where the terminal tails have been truncated. Here, we report structural investigations of full-length UVR8 using native ion mobility mass spectrometry adapted for photoactivation. We show that, while truncated UVR8 photoconverts from a single conformation of dimers to a single monomer conformation, the full-length protein exists in numerous conformational families. The full-length dimer adopts both a compact state and an extended state where the C terminus is primed for activation. In the monomer the extended C terminus destabilizes the core domain to produce highly extended yet stable conformations, which we propose are the fully active states that bind COP1. Our results reveal the conformational diversity of full-length UVR8. We also demonstrate the potential power of native mass spectrometry to probe functionally important structural dynamics of photoreceptor proteins throughout nature.
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Schaefer, Ted, Rudy Sebastian, Alberta Lemire, and Glenn H. Penner. "1H and 13C NMR studies of the conformational mobility of 1,2-dimethoxybenzene in solution." Canadian Journal of Chemistry 68, no. 8 (1990): 1393–98. http://dx.doi.org/10.1139/v90-213.

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1H NMR and 13C NMR spectral data are presented for 1,2-dimethoxybenzene-α,α′-13C, as well as for a number of other anisole derivatives. For the title molecule, the coupling constants between the 13C nucleus in the side chain and the para ring proton or 13C nucleus in the benzene ring show that the expectation value of sin2 θ is very near 0.2 at 300 K, where θ is the angle by which the methoxy groups twist out of the aromatic plane. This value of [Formula: see text] is much larger than that of 0.05 for anisole in solution, emphasizing the greater conformational mobility of the methoxy groups in 1,2-dimethoxybenzene (DMB). Long-range coupling constants between the methyl and ring protons in DMB are also discussed and compared with those in anisole and some of its derivatives. The preponderance of conformations with large values of θ, thought to occur in the vapor, disappears in solution at ambient temperatures. Under these conditions, the molecule is perhaps best described as preferring a planar conformation in which, however, the methoxy groups undergo excursions in θ whose average value is near 25°. Keywords: 1,2-dimethoxybenzene, conformational behaviour, internal mobility, long-range coupling constants, 1H and 13C NMR.
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Crookston, K. P., D. J. Webb, J. Lamarre та S. L. Gonias. "Binding of platelet-derived growth factor-BB and transforming growth factor-β 1 to α2-macroglobulin in vitro and in vivo: comparison of receptor-recognized and non-recognized α2-macroglobulin conformations". Biochemical Journal 293, № 2 (1993): 443–50. http://dx.doi.org/10.1042/bj2930443.

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alpha 2-Macroglobulin (alpha 2M) undergoes a major conformational change when reacting with proteinases or primary amines. This conformational change has been referred to as the ‘slow’ to ‘fast’ transformation based on the increase in alpha 2M mobility shown by non-denaturing PAGE. Previous studies demonstrated that many cytokines, including transforming growth factor beta 1 (TGF-beta 1) and interleukin-1 beta, bind preferentially or exclusively to alpha 2M which has undergone conformational change. In this study, we demonstrate that platelet-derived growth factor-BB (PDGF-BB) also binds preferentially to conformationally transformed alpha 2M (alpha 2M-methylamine, alpha 2M-trypsin) in vitro. Purified 125I-PDGF-BB-alpha 2M-methylamine complex cleared rapidly from the circulation of mice via the alpha 2M receptor/low-density-lipoprotein-receptor-related protein (alpha 2M-R/LRP). In order to determine whether PDGF-BB or TGF-beta 1 binds to native alpha 2M, we defined the native conformation by lack of interaction with alpha 2M-R/LRP instead of electrophoretic mobility. 125I-PDGF-BB was incubated with 4.3 microM native alpha 2M and 0.47 microM alpha 2M-methylamine. The 125I-PDGF-BB distributed evenly between slow-form and fast-form alpha 2M without shifting the electrophoretic mobility of either species. When the mixed preparation was injected intravenously in mice, 125I-PDGF-BB-fast-form-alpha 2M cleared rapidly and selectively from the circulation; 125I-PDGF-BB which was bound to slow-form alpha 2M was stable in the blood (apparently not recognized by alpha 2M-R/LRP). Therefore, while conformationally transformed alpha 2M binds PDGF-BB preferentially in vitro, non-alpha 2M-R/LRP-recognized alpha 2M binds PDGF-BB as well. Binding of 125I-PDGF-BB and 125I-TGF-beta 1 to alpha 2M was demonstrated in vivo by injecting the free growth factors intravenously into mice. Plasma samples which were subjected to non-denaturing PAGE and autoradiography demonstrated binding of both growth factors exclusively to the slow-form of alpha 2M. Therefore, under normal physiological conditions, native alpha 2M (non-alpha 2M-R/LRP-recognized) is the primary form of the proteinase inhibitor functioning as a carrier of PDGF-BB and TGF-beta 1 in the blood.
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Gormal, Rachel S., Pranesh Padmanabhan, Ravikiran Kasula та ін. "Modular transient nanoclustering of activated β2-adrenergic receptors revealed by single-molecule tracking of conformation-specific nanobodies". Proceedings of the National Academy of Sciences 117, № 48 (2020): 30476–87. http://dx.doi.org/10.1073/pnas.2007443117.

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None of the current superresolution microscopy techniques can reliably image the changes in endogenous protein nanoclustering dynamics associated with specific conformations in live cells. Single-domain nanobodies have been invaluable tools to isolate defined conformational states of proteins, and we reasoned that expressing these nanobodies coupled to single-molecule imaging-amenable tags could allow superresolution analysis of endogenous proteins in discrete conformational states. Here, we used anti-GFP nanobodies tagged with photoconvertible mEos expressed as intrabodies, as a proof-of-concept to perform single-particle tracking on a range of GFP proteins expressed in live cells, neurons, and small organisms. We next expressed highly specialized nanobodies that target conformation-specific endogenous β2-adrenoreceptor (β2-AR) in neurosecretory cells, unveiling real-time mobility behaviors of activated and inactivated endogenous conformers during agonist treatment in living cells. We showed that activated β2-AR(Nb80) is highly immobile and organized in nanoclusters. The Gαs−GPCR complex detected with Nb37 displayed higher mobility with surprisingly similar nanoclustering dynamics to that of Nb80. Activated conformers are highly sensitive to dynamin inhibition, suggesting selective targeting for endocytosis. Inactivated β2-AR(Nb60) molecules are also largely immobile but relatively less sensitive to endocytic blockade. Expression of single-domain nanobodies therefore provides a unique opportunity to capture highly transient changes in the dynamic nanoscale organization of endogenous proteins.
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Hlaváček, Jan, Ivo Frič, Petr Maloň, Karel Jošt, and Karel Bláha. "Three cyclohexapeptides modelling the oxytocin ring moiety: Synthesis and circular dichroism." Collection of Czechoslovak Chemical Communications 52, no. 7 (1987): 1841–56. http://dx.doi.org/10.1135/cccc19871841.

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A series of cyclic disulfides cysteinyl-triglycyl-asparaginyl-cysteine (Ib), cysteinyl-diglycyl-glutaminyl-asparaginyl-cysteine (Ic), and cysteinyl-glycyl-isoleucyl-glutaminyl-asparaginyl-cysteine (Id) has been prepared. The effect of gradual attachment of side chains to the ring on the peptide backbone and the disulfide group conformation has been studied using circular dichroism. Introduction of side chains reduces substantially the conformational mobility of the backbone , but not enough to let any conformational β-turn type predominate (in polar solvents). Conformation of the disulfide group is essentially independent of the peptide moiety of the molecule and is influenced by specific solvation.
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Grampp, Günter, Van Anh Tran, Petr V. Pantyukhov, and Alexander I. Kokorin. "Intramolecular Mobility in Nitroxide Biradicals with Flexible Linkers." Applied Magnetic Resonance 51, no. 9-10 (2020): 1031–40. http://dx.doi.org/10.1007/s00723-020-01219-9.

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Abstract Intramolecular electron spin exchange has been studied by X-band electron paramagnetic resonance (EPR) spectroscopy in two long-chain flexible nitroxide biradicals existing in fluid solutions in three spectroscopy-different spatial conformations as a function of temperature, solvent viscosity and polarity. Certain thermodynamic parameters of the conformational transitions were calculated from the EPR spectra. The process of spin-exchange in these biradicals dissolved in five different alcohols was compared with that in the non-polar solvents (toluene) and aprotic (acetonitrile), as well as with two other biradicals studied earlier, and with thermodynamic characteristics of the solvents. A distinct correlation was found between macroscopic (solvent viscosity) characteristics of solvents and thermodynamic parameters of the intramolecular conformational transitions.
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Pineda, Agustin O., Zhi-Wei Chen, Alaji Bah, Laura C. Garvey, F. Scott Mathews, and Enrico Di Cera. "Crystal Structure of Thrombin in a Self-inhibited Conformation." Journal of Biological Chemistry 281, no. 43 (2006): 32922–28. http://dx.doi.org/10.1074/jbc.m605530200.

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The activating effect of Na+ on thrombin is allosteric and depends on the conformational transition from a low activity Na+-free (slow) form to a high activity Na+-bound (fast) form. The structures of these active forms have been solved. Recent structures of thrombin obtained in the absence of Na+ have also documented inactive conformations that presumably exist in equilibrium with the active slow form. The validity of these inactive slow form structures, however, is called into question by the presence of packing interactions involving the Na+ site and the active site regions. Here, we report a 1.87Å resolution structure of thrombin in the absence of inhibitors and salts with a single molecule in the asymmetric unit and devoid of significant packing interactions in regions involved in the allosteric slow → fast transition. The structure shows an unprecedented self-inhibited conformation where Trp-215 and Arg-221a relocate >10Å to occlude the active site and the primary specificity pocket, and the guanidinium group of Arg-187 penetrates the protein core to fill the empty Na+-binding site. The extreme mobility of Trp-215 was investigated further with the W215P mutation. Remarkably, the mutation significantly compromises cleavage of the anticoagulant protein C but has no effect on the hydrolysis of fibrinogen and PAR1. These findings demonstrate that thrombin may assume an inactive conformation in the absence of Na+ and that its procoagulant and anticoagulant activities are closely linked to the mobility of residue 215.
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Lee, Sengyong, Tage Carlson, Noah Christian, et al. "The Yeast Heat Shock Transcription Factor Changes Conformation in Response to Superoxide and Temperature." Molecular Biology of the Cell 11, no. 5 (2000): 1753–64. http://dx.doi.org/10.1091/mbc.11.5.1753.

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In vitro DNA-binding assays demonstrate that the heat shock transcription factor (HSF) from the yeast Saccharomyces cerevisiae can adopt an altered conformation when stressed. This conformation, reflected in a change in electrophoretic mobility, requires that two HSF trimers be bound to DNA. Single trimers do not show this change, which appears to represent an alteration in the cooperative interactions between trimers. HSF isolated from stressed cells displays a higher propensity to adopt this altered conformation. Purified HSF can be stimulated in vitro to undergo the conformational change by elevating the temperature or by exposing HSF to superoxide anion. Mutational analysis maps a region critical for this conformational change to the flexible loop between the minimal DNA-binding domain and the flexible linker that joins the DNA-binding domain to the trimerization domain. The significance of these findings is discussed in the context of the induction of the heat shock response by ischemic stroke, hypoxia, and recovery from anoxia, all known to stimulate the production of superoxide.
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Dissertations / Theses on the topic "Mobilité conformational"

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Eudes, Richard. "Développements méthodologiques relatifs à l'attribution et à la prédiction des structures secondaires des protéines globulaires : classification structurale de mutations du transporteur CFTR, observées chez des patients atteints de mucoviscidose." Paris 6, 2006. http://www.theses.fr/2006PA066170.

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Albrieux, Florian. "Etude conformationnelle de peptides et protéines par mesure de mobilité ionique couplée à la spectrométrie de masse." Phd thesis, Université Claude Bernard - Lyon I, 2010. http://tel.archives-ouvertes.fr/tel-00594601.

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Ce travail de thèse porte sur l'analyse conformationelle de biomolécules en phase gazeuse. L'étude d'objets complexes en phase gazeuse permet de connaître les facteurs intrinsèques stabilisant leur structure. La première étape de mes travaux a été le couplage entre un appareil de mobilité ionique (IMS) et un appareil de spectrométrie de masse (MS). Nous avons simulé (SimIon) et développé différentes optiques ioniques fonctionnant à haute pression (entonnoirs à ions, piège ionique). Ces modifications expérimentales nous ont permis de commencer des études conformationnelles de biomolécules en phase gazeuse.Les premières expériences avaient pour objectif d'observer les facteurs stabilisants une structure secondaire sur des séries de peptides analogues. La première étude a été réalisée sur des séries de polyalalanines et de polyglycines de formules Arg(Ala)4XxxAla4Lys et Arg(Gly)4Xxx(Gly)4Lys, où Xxx est l'un des 20 acides aminés naturels. Nous nous sommes intéressés à l'influence de l'acide aminé central sur la conformation globale. Puis nous avons observés la stabilité de l'hélice de la partie transmembranaire de la protéine M2 du virus de la grippe A et de différents mutants. Ces études ont permit de montrer l'importance de la solvatation des charges en phase gazeuse.Enfin nous avons initié une étude sur le repliement des protéines en utilisant une protéine modèle, le lysozyme. Nous nous sommes plus particulièrement intéressés aux mécanismes de repliements en fonction du degré d'oxydation de cette dernière
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Chang, Wun-Shaing Wayne. "Conformational mobility and interactions of the serpins." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387511.

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Badyal, Sandip Kaur. "Conformational mobility in the active site of a heme peroxidase." Thesis, University of Leicester, 2008. http://hdl.handle.net/2381/8225.

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Site-directed mutagenesis in recombinant soybean ascorbate peroxidase (rsAPX) has been performed to probe structure/function relationships in this and other heme proteins. In Chapter Two, we present mechanistic, spectroscopic, and structural evidence for peroxide- and ligand-induced conformational mobility of the distal histidine (His-42) in the W41A variant of ascorbate peroxidase. In this variant, His-42 binds “on” to the heme in the oxidised form, duplicating the active site structure of the cytochromes b but, in contrast to cytochromes b, is able to swing “off” the iron during catalysis. Contrary to the widely adopted view of heme enzyme catalysis, these data indicate that strong coordination of the distal histidine to the heme iron does not automatically undermine catalytic activity. In Chapter Three, we have shown that conformational rearrangement in W41A, discussed above, can also be triggered upon reduction of the heme iron. We present structural, spectroscopic and ligand binding data that support dissociation of His-42 from the iron in the ferrous form of W41A. Structural studies provide evidence for formation of a reduced, bis-histidine-ligated species that subsequently decays by dissociation of His-42 from the heme. Collectively, the data provide clear evidence that conformational movement within the same heme active site can be controlled by both ligand binding and metal oxidation state. In Chapter Four, we present evidence for heme oxygenase reactivity in the W41A variant of rsAPX. Crystallographic, spectroscopic, HPLC and MS techniques reveal that the heme is modified on reaction of W41A with tert-butyl hydroperoxide to yield a tert-butyl derivative of biliverdin. Evidence for formation of a hydroperoxo, Compound 0, intermediate is also presented. A common intermediate for the two heme enzymes is proposed. In Chapter Five, we examined the affect of disruption of the conserved distal histidine-asparagine hydrogen bond on active site mobility by formation of a series of asparagine-71 (Asn-71) variants. The spectroscopic data presented provide clear evidence that the conserved distal histidine-asparagine bond is required to maintain the correct orientation of distal histidine in the active site of rsAPX.
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Molano-Arévalo, Juan Camilo. "Conformational Dynamics of Biomolecules by Trapped Ion Mobility Spectrometry Dynamics." FIU Digital Commons, 2018. https://digitalcommons.fiu.edu/etd/3647.

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One of the main goals in structural biology is to understand the folding mechanisms and three-dimensional structure of biomolecules. Many biomolecular systems adopt multiple structures as a function of their microenvironment, which makes them difficult to be characterized by traditional structural biology tools (e.g., NMR, X-ray crystallography). As an alternative, complementary tools that can capture and sample multiple conformations needed to be developed. In the present work, we pioneered the application of a new variant of ion mobility spectrometry, trapped ion mobility spectrometry (TIMS), which provides high mobility resolving power and the possibility to study kinetically trapped intermediates as a function of the starting solution (e.g., pH and organic content) and gas-phase conditions (e.g., collisional activation, molecular dopants, hydrogen/deuterium back-exchange). When coupled to mass spectrometry (TIMS-MS), action spectroscopy (IRMPD), molecular dynamics and biochemical approaches (e.g., fluorescence lifetime spectroscopy), a comprehensive description of the biomolecules dynamics and tridimensional structural can be obtained. These new set of tools were applied for the first time to the study of Flavin Adenine Dinucleotide (FAD), Nicotineamide Adenine Dinucleotide (NAD), globular protein cytochrome c (cyt c), the 31 knot YibK protein, 52 knot ubiquitin C terminal hydrolase (UCH) protein, and the 61 knot halo acid dehydrogenase (DehI) protein.
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Bouakil, Mathilde. "Étude de la conformation et de la dynamique conformationnelle de molécules biologiques en phase gazeuse." Thesis, Lyon, 2020. http://www.theses.fr/2020LYSE1145.

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Les protéines sont des molécules dont la structure est liée à leur fonction dans les organismes vivant. Cette thèse porte sur la caractérisation de ces structures et de leur dynamique et s'inscrit dans le développement de l'analyse par spectrométrie de masse en biologie structurale. La spectrométrie de masse couplée à des techniques de spectroscopie optique résolue en temps permet de mettre en lumière les mécanismes d'absorption, de relaxation et de transfert de charges photo-induits impliqués dans la dynamique conformationnelle et électronique de ces molécules biologiques. Ces approches expérimentales avec la combinaison de techniques de biologie moléculaire (expression, gel électrophorèse, dichroïsme circulaire, etc.) sont présentées en début de manuscrit. C'est par l'étude de l'activation photo-induite de chromophores utilisés pour l'analyse de la structure de protéines qu'a commencé ce travail de thèse. Les mécanismes d'absorption de photons et de relaxation non radiative de chromophores greffés sur des peptides ont été sondés. Nous avons ensuite sondé les mécanismes de transferts de charges photo-induits au sein de petits peptides afin de comprendre l'influence de la taille de ces systèmes et de la composition en acides aminés sur la dynamique conformationnelle de ces peptides. Ceci a nécessité le montage d'un dispositif pompe-sonde pour l'étude de la dynamique de transfert de charge. Enfin nous nous sommes intéressés à un processus de changement de conformation du peptide PUMA, présent dans les organismes de mammifères et impliqué dans la régulation de l'apoptose, en utilisant la spectrométrie de mobilité ionique comme sonde de conformation et de dynamique structurale
Protein functions in living organism are governed by their 3D structure. This thesis focuses on the characterization of protein conformation and conformational dynamics by means of mass spectrometry, and participates to the development of tools for structural biology. Mass spectrometry coupled to time resolved optical spectroscopy can set light on mechanisms associated with conformational dynamics: photon absorption, electronic relaxation, photo-induced charge transfer, etc. Experimental approaches combining mass spectrometry, optics and molecular biology (protein expression, gel electrophoresis, circular dichroism, etc.) will be presented in the first section of this manuscript. This thesis work was initiated by the study of the photo-induced activation of the chromophores which were used, at ILM, for action-FRET and more generally for the exploration of the proteins structure. The mechanisms of photon absorption and non-radiative relaxation were studied for chromophores grafted on multiple peptides. We then probed the photo-induced intramolecular charge transfer and associated conformational dynamics in series of small peptides in order to understand the influence of the system size and composition on its structural dynamics. The latter experiment required the implementation of a two-color pump-probe setup. Finally, we used ion mobility spectrometry to probe and investigate the conformational space and dynamics of the PUMA peptide, ubiquitous in mammalian organisms and associated to the regulation of apoptosis
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Faull, Peter Allen. "Exploring gas-phase protein conformations by ion mobility-mass spectrometry." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/3851.

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Analysis and characterisation of biomolecules using mass spectrometry has advanced over the past decade due to improvements in instrument design and capability; relevant use of complementary techniques; and available experimental and in silico data for comparison with cutting-edge research. This thesis presents ion mobility data, collected on an in-house modified QToF mass spectrometer (the MoQTOF), for a number of protein systems. Two haemoproteins, cytochrome c and haemoglobin, have been characterised and rotationally-averaged collision cross-sections for a number of multimeric species are presented. Intact multiply-charged multimers of the form [xCyt c + nH]z+ where x = 1 (monomer), x = 2 (dimer) and x = 3 (trimer) for cytochrome c have been elucidated and for species with x ≥ 2, reported for the first time. Fragment ions possibly attributed to a novel fragmentation mechanism, native electron capture dissociation, are reported with a brief discussion into their possible production from the dissociation of the gas-phase dimer species. Haemoglobin monomer globin subunits, dimers and intact tetramer have been successfully transferred to the gas phase, and their cross-sections elucidated. Comparisons with in silico computational data have been made and a discussion of the biologically-active tetramer association/dissociation technique is presented. Three further proteins have been studied and their gas-phase collision cross-sections calculated. Two regions of the large Factor H (fH) complement glycoprotein, fH 10-15 and fH 19-20, have been characterised for the first time by ion mobility-mass spectrometry. Much work using nuclear magnetic resonance spectroscopy has previously been achieved to produce structural information of these protein regions, however further biophysical characterisation using mass spectrometry may aid in greater understanding of the interactions these two specific regions have with other biomolecules. The DNA-binding core domain of the tumour suppressor p53 has been characterised and cross-sections produced in the presence and absence of the zinc metal ion that may control the domain’s biological activity. Within this core domain, p53 inactivation mutations have been shown to occur in up to 50% of human cancers, therefore the potential exists to further cancer-fighting activity through research on this region. Anterior Gradient-2 (AGR2) protein facilitates downregulation of p53 in an as yet unclear mechanism. Recent work using peptide aptamers has demonstrated that this downregulation can be disrupted and levels of p53 restored. Collision cross-sections for six peptide aptamers have been calculated, as well as cross-sections for multimers of AGR2 protein. A complex between one aptamer with the protein has also been elucidated. Use of the commercially available Synapt HDMS ion mobility-mass spectrometer at Waters MS Technologies Centre (Manchester, UK) allowed data to be collected for both Factor H protein regions and for the DNA-binding core domain of p53. Data are compared in the appropriate chapters with data collected using the MoQTOF.
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Jin, Lan. "Investigating glycosaminoglycan conformations by ion mobility mass spectrometry and nuclear magnetic resonance." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/12304.

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The aim of this project is to develop and test methodologies for conformational studies of free and bound GAGs. Gas phase conformations of heparin-derived oligosaccharides were studied by using Ion Mobility Mass Spectrometry (IMMS) and molecular modelling. Gas phase conformations were modelled using the AMBER force field. Their theoretical collision cross-sections were compared with the IMMS data and a good agreement was obtained. The gas phase conformations of heparin oligosaccharides were more compact than those observed in solution or crystal structures of heparin-protein complexes. This was attributed to the effects of sodium cations interacting with the negatively charged sulphate and carboxyl groups of oligosaccharides. Adiabatic maps of dihedral angles vs. potential energy of disaccharide fragments of the tetrasaccharides were calculated in the absence of the sodium cations. New NMR methods for the measurement of scalar and dipolar 1H-1H coupling constants and 13C-13C coupling constants in natural abundance 13C samples were developed. Performance of these methods was tested extensively. Solution conformation of the fully sulphated heparin-derived tetrasaccharide was studied by NMR spectroscopy. 1H-1H scalar coupling constants were used to characterize the dynamic equilibria of flexible monosaccharide rings. 1H-1H and 1H-13C RDCs were used in the study of the conformation of the glycosidic linkages. RDC-refined structures were obtained from molecular dynamics with explicit water and sodium cations. Interactions of the heparin-derived fully sulphated tetrasaccharide with factor H modules, fH~19, 20 and fH~7, were studied using AUTODOCK. Conformation of a spin-labelled heparin-derived fully sulphated disaccharide was studied by NMR and molecular modelling.
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Kalapothakis, Jason Michael Drosos. "Investigations of peptide structural stability in vacuo." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/5670.

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Gas-phase analytical techniques provide very valuable tools for tackling the structural complexity of macromolecular structures such as those encountered in biological systems. Conformational dynamics of polypeptides and polypeptide assemblies underlie most biological functionalities, yet great difficulties arise when investigating such phenomena with the well-established techniques of X-ray crystallography and NMR. In areas such as these ion mobility interfaced with mass spectrometry (IMMS) and molecular modelling can make a significant contribution. During an IMMS experiment analyte ions drift in a chamber filled with an inert gas; measurement of the transport properties of analyte ions under the influence of a weak electric field can lead to determination of the orientationally-averaged collision cross-section of all resolved ionic species. A comparison with cross-sections estimated for model molecular geometries can lead to structural assignments. Thus IMMS can be used effectively to separate gas-phase ions based on their conformation. The drift tube employed in the experiments described herein is thermally regulated, which also enables the determination of collision cross-sections over a range of temperatures, and can provide a view of temperature-dependent conformational dynamics over the experimental (low microsecond) timescale. Studies described herein employ IMMS and a gamut of other MS-based techniques, solution spectroscopy and – importantly – molecular mechanics simulations to assess a) conformational stability of isolated peptide ions, with a focus on small model peptides and proteins, especially the Trp cage miniprotein; and b) structural characteristics of oligomeric aggregates of an amyloidogenic peptide. The results obtained serve to clarify the factors which dominate the intrinsic stability of non-covalent structure in isolated peptides and peptide assemblies. Strong electrostatic interactions are found to play a pivotal role in determining the conformations of isolated proteins. Secondary structures held together by hydrogen bonding, such as helices, are stable in the absence of solvent, however gas-phase protein structures display loss of their hydrophobic cores. The absence of a polar solvent, “self-solvation” is by far the most potent force influencing the gas-phase configuration of these systems. Geometries that are more compact than the folded state observed in solution are routinely detected, indicating the existence of intrinsically stable compact non-native states in globular proteins, illuminating the nature of proteins’ ‘unfolded’ states.
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Sevostiyanova, Anastasia K. "Mechanism of Antitermination by NusG-like Proteins and the Role of RNAP Conformational Mobility in Transcription Cycle." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1281629313.

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Book chapters on the topic "Mobilité conformational"

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Käiväräinen, Alex I. "Conformational Mobility of Proteins." In Solvent-Dependent Flexibility of Proteins and Principles of Their Function. Springer Netherlands, 1985. http://dx.doi.org/10.1007/978-94-009-5197-6_3.

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Ellwood, Paul, Catriona M. Spencer, Neil Spencer, J. Fraser Stoddart, and Ryszard Zarzycki. "Conformational Mobility in Chemically-Modified Cydodextrins." In The Pedersen Memorial Issue. Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2532-1_6.

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DeBrosse, Charles W., Judith C. Hempel, and Kenneth D. Kopple. "Conformational mobility in the vasopressin series." In Peptides. Springer Netherlands, 1988. http://dx.doi.org/10.1007/978-94-010-9595-2_18.

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Steitz, T. A., R. Harrison, I. T. Weber, and M. Leahy. "Ligand-Induced Conformational Changes in Proteins." In Ciba Foundation Symposium 93 - Mobility and Function in Proteins and Nucleic Acids. John Wiley & Sons, Ltd., 2008. http://dx.doi.org/10.1002/9780470720752.ch3.

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Wyttenbach, Thomas, and Michael T. Bowers. "Gas-Phase Conformations: The Ion Mobility/Ion Chromatography Method." In Topics in Current Chemistry. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/3-540-36113-8_6.

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Miller, I. R., V. Brumfeld, and R. Korenstein. "Conformation and Mobility of Membrane Proteins in Electric Fields." In Advances in Chemistry. American Chemical Society, 1994. http://dx.doi.org/10.1021/ba-1994-0235.ch006.

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Espinet, Pablo, and Juan A. Casares. "Conformational Mobility in Chelated Square-Planar Rh, Ir, Pd, and Pt Complexes." In Fluxional Organometallic and Coordination Compounds. John Wiley & Sons, Ltd, 2005. http://dx.doi.org/10.1002/0470858451.ch4.

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Harrington, William F., Hitoshi Ueno, and Tian Yow Tsong. "Cross-Bridge Movement in Muscle and the Conformation of the Myosin Hinge." In Ciba Foundation Symposium 93 - Mobility and Function in Proteins and Nucleic Acids. John Wiley & Sons, Ltd., 2008. http://dx.doi.org/10.1002/9780470720752.ch11.

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Bradbury, E. Morton. "Conformations and Flexibilities of Histones and High Mobility Group (HMG) Proteins in Chromatin Structure and Function." In Ciba Foundation Symposium 93 - Mobility and Function in Proteins and Nucleic Acids. John Wiley & Sons, Ltd., 2008. http://dx.doi.org/10.1002/9780470720752.ch14.

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Phillips, Shawn T., James N. Dodds, Jody C. May, and John A. McLean. "Isomeric and Conformational Analysis of Small Drug and Drug-Like Molecules by Ion Mobility-Mass Spectrometry (IM-MS)." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9089-4_9.

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Conference papers on the topic "Mobilité conformational"

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Shahbazi, Zahra, Horea T. Ilies¸, and Kazem Kazerounian. "Protein Molecules as Natural Nano Bio Devices: Mobility Analysis." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13021.

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Proteins are nature’s nano-robots in the form of functional molecular components of living cells. The function of these natural nano-robots often requires conformational transitions between two or more native conformations that are made possible by the intrinsic mobility of the proteins. Understanding these transitions is essential to the understanding of how proteins function, as well as to the ability to design and manipulate protein-based nano-mechanical systems [1]. Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOF) with considerable computational implications. On the other hand, real protein molecules appear to exhibits a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of Hydrogen bonds during the folding process.
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Babkov, Lev M., and Ekaterina A. Martynova. "Optical spectra and conformational mobility of benzophenone." In Saratov Fall Meeting '99, edited by Vladimir L. Derbov, Leonid A. Melnikov, and Vladimir P. Ryabukho. SPIE, 2000. http://dx.doi.org/10.1117/12.380124.

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Chu, Benjamin, and Zhulun Wang. "Electrophoretic mobility and conformational changes of DNA in agarose gels." In Moscow - DL tentative, edited by Sergei A. Akhmanov and Marina Y. Poroshina. SPIE, 1991. http://dx.doi.org/10.1117/12.57294.

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Babkov, Lev M., E. S. Vedyaeva, I. I. Gnatyuk, Galina A. Puchkovska, S. V. Truhachev, and J. I. Kukielski. "Investigation of conformational mobility of 4-pentyl-4'-cyanobiphenyl by IR spectroscopy methods." In XV International School on Spectroscopy of Molecules and Crystals, edited by Galina A. Puchkovska and Sergey A. Kostyukevych. SPIE, 2002. http://dx.doi.org/10.1117/12.486660.

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Andreadi, Nikolai, Artem Mitrofanov, Petr Matveev, and Nataliya Borisova. "The role of ligand conformational mobility in the process of An(III)/Ln(III) extraction." In RAD Conference. RAD Centre, 2021. http://dx.doi.org/10.21175/rad.abstr.book.2021.33.3.

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Tagawa, Norio, Tadao Tateyama, Atsunobu Mori, Nagayoshi Kobayashi, Yoshinobu Fujii, and Masako Ikegami. "Spreading of Novel Cyclotriphosphazine-Terminated PFPE Films on Carbon Surfaces." In STLE/ASME 2003 International Joint Tribology Conference. ASMEDC, 2003. http://dx.doi.org/10.1115/2003-trib-332.

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Spreading characteristics of novel cyclotriphosphazine-terminated Perfluoropolyether (PFPE) films on carbon surfaces were investigated experimentally by using a scanning micro-ellipsometer. The apparent diffusion coefficients of novel lubricants were also studied in order to evaluate the spreading speed and they were compared to the conventional Zdol. It was found that the mobility of cyclotriphosphazine-terminated PFPE films is lower than that of Zdol. This characteristics is dependent on the interactions between the end groups of the lubricants and carbon surfaces and it is found that the tendency of “work of adhesion” for the lubricants has a good correlation with the mobility tendency of the lubricants. In addition, the monolayer film thickness of novel lubricant films as well as conventional Zdol was identified, which was extracted using Matano interface method. As a result, the existing conformation of novel cyclotriphosphazine-terminated PFPE film on carbon surfaces could be estimated, based on the monolayer film thickness results.
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Tagaya, Yoichi, Yasunaga Mitsuya, Susumu Ogata, Hedong Zhang, and Kenji Fukuzawa. "Effects of Molecular Conformations and Functional Endgroups on Nanoscale Mobility of Lubricant Molecules on Magnetic Disks." In 2006 IEEE International Symposium on MicroNanoMechanical and Human Science. IEEE, 2006. http://dx.doi.org/10.1109/mhs.2006.320267.

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Xue-song Ye, Peng Wang, Tao Zhou, Jun Liu, and Feng Liu. "Molecular mechanism for conformation mobility of the active center of glucose oxidase adsorbed on single wall carbon nanotubes." In 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2009. http://dx.doi.org/10.1109/iembs.2009.5333338.

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