Relevant bibliographies by topics / Conformational characterization

Academic literature on the topic 'Conformational characterization'

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Published: 14 March 2023

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Journal articles on the topic "Conformational characterization"

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Seidler, Clarissa A., Janik Kokot, Monica L. Fernández-Quintero, and Klaus R. Liedl. "Structural Characterization of Nanobodies during Germline Maturation." Biomolecules 13, no. 2 (February 17, 2023): 380. http://dx.doi.org/10.3390/biom13020380.

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Camelid heavy-chain antibody variable domains (VHH), nanobodies, are the smallest-known functional antibody fragments with high therapeutic potential. In this study, we investigate a VHH binding to hen egg-white lysozyme (HEL). We structurally and dynamically characterized the conformational diversity of four VHH variants to elucidate the antigen-binding process. For two of these antibodies, not only are the dissociation constants known, but also the experimentally determined crystal structures of the VHH in complex with HEL are available. We performed well-tempered metadynamics simulations in combination with molecular dynamics simulations to capture a broad conformational space and to reconstruct the thermodynamics and kinetics of conformational transitions in the antigen-binding site, the paratope. By kinetically characterizing the loop movements of the paratope, we found that, with an increase in affinity, the state populations shift towards the binding competent conformation. The contacts contributing to antigen binding, and those who contribute to the overall stability, show a clear trend towards less variable but more intense contacts. Additionally, these investigated nanobodies clearly follow the conformational selection paradigm, as the binding competent conformation pre-exists within the structural ensembles without the presence of the antigen.
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Paz, Aviv, Derek P. Claxton, Jay Prakash Kumar, Kelli Kazmier, Paola Bisignano, Shruti Sharma, Shannon A. Nolte, et al. "Conformational transitions of the sodium-dependent sugar transporter, vSGLT." Proceedings of the National Academy of Sciences 115, no. 12 (March 5, 2018): E2742—E2751. http://dx.doi.org/10.1073/pnas.1718451115.

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Sodium-dependent transporters couple the flow of Na+ ions down their electrochemical potential gradient to the uphill transport of various ligands. Many of these transporters share a common core structure composed of a five-helix inverted repeat and deliver their cargo utilizing an alternating-access mechanism. A detailed characterization of inward-facing conformations of the Na+-dependent sugar transporter from Vibrio parahaemolyticus (vSGLT) has previously been reported, but structural details on additional conformations and on how Na+ and ligand influence the equilibrium between other states remains unknown. Here, double electron–electron resonance spectroscopy, structural modeling, and molecular dynamics are utilized to deduce ligand-dependent equilibria shifts of vSGLT in micelles. In the absence and presence of saturating amounts of Na+, vSGLT favors an inward-facing conformation. Upon binding both Na+ and sugar, the equilibrium shifts toward either an outward-facing or occluded conformation. While Na+ alone does not stabilize the outward-facing state, gating charge calculations together with a kinetic model of transport suggest that the resting negative membrane potential of the cell, absent in detergent-solubilized samples, may stabilize vSGLT in an outward-open conformation where it is poised for binding external sugars. In total, these findings provide insights into ligand-induced conformational selection and delineate the transport cycle of vSGLT.
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Dong, Qiwen, Kai Wang, Bin Liu, and Xuan Liu. "Characterization and Prediction of Protein Flexibility Based on Structural Alphabets." BioMed Research International 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/4628025.

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Motivation.To assist efforts in determining and exploring the functional properties of proteins, it is desirable to characterize and predict protein flexibilities.Results.In this study, the conformational entropy is used as an indicator of the protein flexibility. We first explore whether the conformational change can capture the protein flexibility. The well-defined decoy structures are converted into one-dimensional series of letters from a structural alphabet. Four different structure alphabets, including the secondary structure in 3-class and 8-class, the PB structure alphabet (16-letter), and the DW structure alphabet (28-letter), are investigated. The conformational entropy is then calculated from the structure alphabet letters. Some of the proteins show high correlation between the conformation entropy and the protein flexibility. We then predict the protein flexibility from basic amino acid sequence. The local structures are predicted by the dual-layer model and the conformational entropy of the predicted class distribution is then calculated. The results show that the conformational entropy is a good indicator of the protein flexibility, but false positives remain a problem. The DW structure alphabet performs the best, which means that more subtle local structures can be captured by large number of structure alphabet letters. Overall this study provides a simple and efficient method for the characterization and prediction of the protein flexibility.
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Siddiqui, Mahtab Z. "Dehydrophenylalanine analogues: conformational characterization." International Journal of Biological Macromolecules 26, no. 1 (October 1999): 17–21. http://dx.doi.org/10.1016/s0141-8130(99)00063-x.

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SENGE, MATHIAS O., INES BISCHOFF, NORA Y. NELSON, and KEVIN M. SMITH. "Synthesis, Reactivity and Structural Chemistry of 5,10,15,20-Tetraalkylporphyrins." Journal of Porphyrins and Phthalocyanines 03, no. 02 (February 1999): 99–116. http://dx.doi.org/10.1002/(sici)1099-1409(199902)3:2<99::aid-jpp109>3.0.co;2-6.

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The synthesis, reactivity and full characterization of a series of meso-tetraalkyl porphyrins and metalloporphyrins with R ≡ n-butyl (6), 2-methyl-propyl (7), isopropyl (8), l-ethyl-propyl (10) and tert-butyl (11) groups are reported. Derivatives of the last of these show considerably bathochromically shifted absorption bands and the crystal structure of Zn ( II )11(pyr) exhibits a severely ruffled macrocycle conformation. Systematic crystallographic studies of the porphyrins showed that the free base porphyrins with R ≡ n-butyl ( H 26), 2-methyl-propyl ( H 27) and 1-ethyl-propyl ( H 210) are planar. A larger conformational variety was found for the metal complexes. While most Ni ( II ) derivatives and Pd ( II )8 showed a ruffled macrocycle conformation with a degree of ruffling exceeding that of meso-unsubstituted porphyrins, both planar and non-planar forms were found for the related Cu ( II ) derivatives. The Zn ( II ) complexes of porphyrins with isopropyl or 1-ethyl-propyl exhibited conformations with variable degree of distortion. Together with comparative structures from the literature, this study provides experimental evidence that considerable conformational flexibility exists for meso-alkylporphyrins with substituents less bulky than tert-butyl groups.
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Dluhy, R. A., D. Moffatt, D. G. Cameron, R. Mendelsohn, and H. H. Mantsch. "Characterization of cooperative conformational transitions by Fourier transform infrared spectroscopy: application to phospholipid binary mixtures." Canadian Journal of Chemistry 63, no. 7 (July 1, 1985): 1925–32. http://dx.doi.org/10.1139/v85-319.

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Temperature-induced cooperative conformational transitions in biopolymers may be examined in aqueous solution by the use of Fourier transform infrared spectroscopy. The transition is described in terms of a two-state model with a fractional population parameter (which describes the degree of transition at various values intermediate between the two limiting cases) that can be generated by a least-squares technique. This procedure allows for calculation of a conformational index without assuming a linear dependence of the infrared parameter on the extent of transition. Calculations based on the Zimm–Bragg theory of cooperative conformational transitions allow thermodynamic quantities to be derived using the conformational index in conjunction with calorimetric measurements.The method is illustrated with data from the gel/liquid-crystalline phase transitions of binary phospholipid vesicles where the use of isotopic substitution allows the conformation of each component of the binary mixture to be independently monitored. The data suggest the coexistence of well-defined structural domains of phospholipid as well as the preferential clustering of one of the lipid components at the interface between the two phases.
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Appendino, G., M. Calleri, G. Chiari, P. Ugliengo, and D. Viterbo. "Conformational characterization of shiromodiol derivatives." Acta Crystallographica Section A Foundations of Crystallography 43, a1 (August 12, 1987): C63. http://dx.doi.org/10.1107/s0108767387083806.

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Takahashi, Ken-ichi, Tosiyuki Noguti, Hironobu Hojo, Tadayasu Ohkubo, and Mitiko G? "Conformational characterization of designed minibarnase." Biopolymers 58, no. 3 (2001): 260–67. http://dx.doi.org/10.1002/1097-0282(200103)58:3<260::aid-bip1003>3.0.co;2-j.

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Yuan, Wen, Jessica Bazick, and Joseph Sodroski. "Characterization of the Multiple Conformational States of Free Monomeric and Trimeric Human Immunodeficiency Virus Envelope Glycoproteins after Fixation by Cross-Linker." Journal of Virology 80, no. 14 (July 15, 2006): 6725–37. http://dx.doi.org/10.1128/jvi.00118-06.

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ABSTRACT The human immunodeficiency virus type 1 (HIV-1) gp120 exterior and gp41 transmembrane envelope glycoproteins assemble into trimers on the virus surface that represent potential targets for antibodies. Potent neutralizing antibodies bind the monomeric gp120 glycoprotein with small changes in entropy, whereas unusually large decreases in entropy accompany gp120 binding by soluble CD4 and less potent neutralizing antibodies. The high degree of conformational flexibility in the free gp120 molecule implied by these observations has been suggested to contribute to masking the trimer from antibodies that recognize the gp120 receptor-binding regions. Here we use cross-linking and recognition by antibodies to investigate the conformational states of gp120 monomers and soluble and cell surface forms of the trimeric HIV-1 envelope glycoproteins. The fraction of monomeric and trimeric envelope glycoproteins able to be recognized after fixation was inversely related to the entropic changes associated with ligand binding. In addition, fixation apparently limited the access of antibodies to the V3 loop and gp41-interactive surface of gp120 only in the context of trimeric envelope glycoproteins. The results support a model in which the unliganded monomeric and trimeric HIV-1 envelope glycoproteins sample several different conformations. Depletion of particular fixed conformations by antibodies allowed characterization of the relationships among the conformational states. Potent neutralizing antibodies recognize the greatest number of conformations and therefore can bind the virion envelope glycoproteins more rapidly and completely than weakly neutralizing antibodies. Thus, the conformational flexibility of the HIV-1 envelope glycoproteins creates thermodynamic and kinetic barriers to neutralization by antibodies directed against the receptor-binding regions of gp120.
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Polêto, Marcelo D., Bruno I. Grisci, Marcio Dorn, and Hugo Verli. "ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories." Bioinformatics 36, no. 11 (February 27, 2020): 3576–77. http://dx.doi.org/10.1093/bioinformatics/btaa130.

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Abstract Motivation The conformational space of small molecules can be vast and difficult to assess. Molecular dynamics (MD) simulations of free ligands in solution have been applied to predict conformational populations, but their characterization is often based on clustering algorithms or manual efforts. Results Here, we introduce ConfID, an analytical tool for conformational characterization of small molecules using MD trajectories. The evolution of conformational sampling and population frequencies throughout trajectories is calculated to check for sampling convergence while allowing to map relevant conformational transitions. The tool is designed to track conformational transition events and calculate time-dependent properties for each conformational population detected. Availability and implementation Toolkit and documentation are freely available at http://sbcb.inf.ufrgs.br/confid Contact marcelo.poleto@ufv.br or bigrisci@inf.ufrgs.br Supplementary information Supplementary data are available at Bioinformatics online.
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Dissertations / Theses on the topic "Conformational characterization"

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Ambrogi, Martina. "Synthesis, characterization and conformational studies of arylbenzylmaleimides." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2012. http://amslaurea.unibo.it/4251/.

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From the discoveries of Pasteur, stereochemistry has played an increasingly important role in the chemical sciences. In particular conformational study of molecules with axial chirality is object of intense research. Through Dynamic-NMR analysis and simulation of the spectra, the energy rotational barriers value of conformers are obtained. When this barrier is high sufficiently, atropisomeric stable compounds can be reached. They can be separated and used in stereo-synthesis and in packing processes. 3,4-bis-aryl maleimides, in which the aromatic groups are sufficiently bulky, generate atropisomeric stable configurations, that can be isolated at room temperature. The assignment of absolute configurations is performed through ECD analysis and comparison with computational calculations. The biological activities of maleimide derivatives widen the field of atropisomers application also in biological systems.
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Silenzi, Ilaria. "Synthesis, characterization and conformational studies of bis-phenothiazine-aryl-boranes." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2019. http://amslaurea.unibo.it/19201/.

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This thesis project presents a work based on the study of a particular class of amino-boranes, called bis-phenothiazine-aryl-boranes. The peculiarity of these compounds is the N-B-N chemical moiety and their complex conformational behaviour, due to the combination of steric hindrance and conjugation of the B-N bond. Our work is focused on two main products with different symmetry: bis-phenothiazine-2-methylnaphthyl-borane (2b) and bis-phenothiazine-anthracenyl-borane (2c). We firstly focused our attention on an effective way of synthesis, by optimizing both reaction conditions and purification. The products and co-products of interest were then characterized with NMR, mass spectroscopy and X-Ray diffraction on single crystals. The products were eventually analysed through conformational studies, by experimental techniques, such as dynamic NMR and EXSY, and by a theorical approach with DFT calculations.
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Zych, Andrew John. "Conformational characterization of abiotic secondary structure based on aromatic stacking /." Full text (PDF) from UMI/Dissertation Abstracts International, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3008484.

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Foschi, Simone. "Synthesis, Characterization and Conformational Studies of Modified Carbazole-bis-aryl-boranes." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2020. http://amslaurea.unibo.it/20686/.

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During this project we have synthetized different compounds belonging to the class of amino-boranes for the study of bis-aryl-B=N system. We have decided to keep unchanged the aryl components and change only the amine to observe the effect of that on the B=N bond. The used amines are modified carbazoles with functional groups chosen to amplify or disempower the steric and the conjugation effect. We have found that the evaluation of steric barrier was possible studying the gearing aryls rotation around the C-B bonds, while the conjugation barrier is instead given by the energy needed to break the formal double bond B=N and allow the amine rotation. The work started with a proposed synthesis, improved for every reaction, then the products are characterized by NMR, fluorometric spectroscopy, mass spectrometry and X-Ray diffraction on single crystal. The following study on rotational energy barrier was possible theoretically through DFT calculation and experimentally with techniques like Dynamic NMR and EXSY. The fluorometric analysis was done for the study of the solvatochromic propriety of the products.
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Croasdale, Rebecca Alice. "Characterization of the conformational dynamics of the Nek2 leucine zipper domain." Thesis, University of Leicester, 2013. http://hdl.handle.net/2381/27799.

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Nek2 is a cell cycle regulated protein kinase. Its expression and activity peak in S and G2 phase before the protein is targeted for degradation in mitosis. Nek2 activity promotes centrosome separation and bipolar spindle formation, processes that are essential for maintaining the fidelity of chromosome segregation and cell division. Importantly, Nek2 inhibition results in increased apoptosis and senescence in cancer cell lines and tumour xenografts making Nek2 an attractive target for chemotherapeutic intervention. The α-helix is the most common secondary structure in proteins, with 2-3% of all proteins adopting a coiled-coil structure. The coiled-coil motif mediates a diverse range of functions including DNA transcription, intracellular protein shuttling, membrane signalling, and coordination of the cell cycle. Nek2 contains two coiled-coil motifs in its C-terminal non-catalytic domain, the first of which forms a leucine zipper structure, whilst the second has recently been classified as a SARAH domain. The leucine zipper spans residues 304-340 and is responsible for Nek2 dimerization, autophosphorylation and activation. The Nek2 leucine zipper contains an unusual pattern of charged residues in the dimerization interface. Through studies on isolated fragments, we found that the Nek2 leucine zipper exists primarily as a dimer in solution, albeit with concentration dependent higher order oligomerization. However, the positioning of charged residues enabled the helices to undergo a register shift between two alternative heptad conformations on a timescale of 17s-1. This represents slow-intermediate exchange on the NMR timescale, greatly increasing the transverse and longitudinal relaxation rates leading to enhanced loss of signal intensity. As this precluded structure determination through NMR studies on wild-type fragments, a K309C mutant was generated that ‘locked’ the leucine zipper into one conformation. The significantly reduced relaxation rates confirming the presence of conformational dynamics and making structural determination possible in the future.
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Ieronymaki, Matthaia. "Immunological and Conformational characterization of synthetic peptide probes for autoimmune diseases." Thesis, Cergy-Pontoise, 2016. http://www.theses.fr/2016CERG0831/document.

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Les maladies auto-immunes sont des maladies chroniques et hétérogènes caractérisées par des réactions du système immunitaire acquis contre les propres tissus sains de l'organisme. Ces maladies affectent presque 5% de la population mondiale et en particulier les jeunes adultes. La complexité de leur spectre est énorme et même si leur étiologie est encore incertaine, il a été démontré que des facteurs génétiques et environnementaux sont impliqués dans le déclenchement du mécanisme pathologique. Cependant, il est nécessaire d'utiliser des outils diagnostiques et / ou pronostiques fiables pour le diagnostic précoce avant que des dommages cellulaires irréversibles ne se produisent et pour surveiller la progression de la maladie.De nombreuses études ont mis en évidence la présence de différents auto-anticorps dans le sérum de patients atteints de maladies auto-immunes. Les auto-anticorps qui sont spécifiques d’une maladie peuvent être utilisés en tant que biomarqueurs (BM) pour son diagnostic alors que les auto-anticorps qui diffèrent en fonction de l'état de la maladie peuvent être utilisés dans le suivi des patients. En fait, dans le cas de l'auto-immunité, un BM facilement détectable et fiable peut être représenté par le titre d'un auto-anticorps spécifique.Dans ce contexte, nous nous intéressons à deux maladies différentes, la sclérose en plaques (SEP) et la gammapathie monoclonale, en utilisant l'approche chimique inverse via le criblage de librairies de peptides par des sérums de patients.En particulier, l'importance des anticorps anti-myéline, et surtout, des anticorps anti-MOG (myéline oligodendrocyte glycoprotéine) est toujours l’objet de débats, soulignant la question très controversée d'un rôle pathogène putatif d'anticorps anti-MOG dans la SEP. Dans cette thèse, nous avons étudié le rôle de MOG comme auto-Ag putatif dans la SEP en utilisant le modèle expérimental d’encéphalomyélite auto-immune (EAE). Ainsi, afin d'évaluer la présence d'un mécanisme d’« epitope spreading » des cellules B, à savoir l'apparition d'une réponse dirigée vers des épitopes distincts de l'agent pathogène induisant la réponse immunitaire, nous avons synthétisé et testé en tant que sondes antigéniques cinq peptides synthétiques qui couvrent la séquence 1-117 de MOG.La seconde étude a porté sur la sélection d'un peptide mimant l'épitope minimal reconnu par l'anticorps monoclonal commercial anti- natural killer cell-1 humain (anti-HNK-1) en utilisant la résonance plasmonique de surface (SPR). L’épitope HNK-1 est considéré comme le déterminant antigénique de la glycoprotéine associée à la myéline (MAG), un composant quantitativement mineur des gaines de myéline. On observe que les patients atteints de troubles neurologiques auto-immuns, tels que la gammapathie monoclonale à IgM et la polyneuropathie démyélinisante, développent souvent des anticorps anti-MAG ciblant spécifiquement l’épitope HNK-1. Par conséquent, l'identification et la caractérisation de ces anticorps est pertinente. Le peptide choisi suite à notre étude pourrait ensuite être utilisé chez des patients atteints de troubles neurologiques pour le développement d'un outil de diagnostic fiable ou de surveillance de l'activité de la maladie par l'identification d'anticorps anti-HNK-1 dans le sérum des patients
Autoimmune diseases (ADs) refer to chronic and heterogeneous diseases with acquired immune system’s reactions against the body’s own healthy tissues. ADs affect more than 5% of the population worldwide and especially young adults. The complexity of their spectrum is enormous and even if their etiology is still unclear, it was demonstrated that both genetic and environmental factors are involved in triggering the pathological mechanism. Hence, a reliable diagnostic and/or prognostic tool for an early diagnosis of ADs before irreversible cellular damage occurs and for monitoring their progression is demanded.Numerous studies have revealed the presence of different autoantibodies (auto-Abs) in sera of patients suffering from ADs. Autoantibodies that are specific for a disease can be used as biomarkers (BMs) for its diagnosis while autoantibodies that differ depending on the disease state can be used in the follow up of the patients. Actually, in the case of autoimmunity, an easily detectable and reliable BM may be represented by the titer of a specific auto-Ab.In this context, we aimed to identify target(s) of the response for two different ADs, multiple sclerosis (MS) and monoclonal gammopathy, using the chemical reverse approach, which involves the screening of focused antigen (Ag) libraries with patients’ serum.In particular, the significance of anti-myelin antibodies, and especially, anti- Myelin Oligodendrocyte Glycoprotein (anti-MOG) antibodies is still matter of debate, underscoring the highly controversial issue of a putative pathogenetic role of anti-MOG antibodies in MS. In this thesis we investigated the role of MOG as putative auto-Ag in MS using the experimental autoimmune encephalomyelitis (EAE) model. Moreover, in order to assess the presence of a B-cell epitope spreading mechanism, i.e. the occurrence of a response directed toward epitopes distinct from the disease-inducing agent, we synthesized and tested as antigenic probes also five synthetic peptides covering the 1-117 sequence of MOG.The second issue focused on the selection of a peptide mimicking the minimal epitope recognized by the commercial available monoclonal antibody anti-human natural killer cell-1 (anti-HNK-1) using Surface Plasmon Resonance (SPR) technique. HNK-1 epitope, is considered as the antigenic determinant of myelin-associated glycoprotein (MAG), a quantitatively minor component of myelin sheaths. It is observed that patients affected by autoimmune neurological disorders, such as IgM monoclonal gammopathy and demyelinating polyneuropathy, often develop anti-MAG antibodies specifically targeting the HNK-1 epitope. Accordingly, identification and characterisation of these antibodies is relevant. The selected peptide could be subsequently used in earlier stage patients for the development of a novel and reliable diagnostic tool for anti-HNK-1 antibody identification in sera of patients affected by autoimmune neurological disorders monitoring disease activity
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Fisher, Charles. "Statistical Characterization of Protein Ensembles." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10223.

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Conformational ensembles are models of proteins that capture variations in conformation that result from thermal fluctuations. Ensemble based models are important tools for studying Intrinsically Disordered Proteins (IDPs), which adopt a heterogeneous set of conformations in solution. In order to construct an ensemble that provides an accurate model for a protein, one must identify a set of conformations, and their relative stabilities, that agree with experimental data. Inferring the characteristics of an ensemble for an IDP is a problem plagued by degeneracy; that is, one can typically construct many different ensembles that agree with any given set of experimental measurements. In light of this problem, this thesis will introduce three tools for characterizing ensembles: (1) an algorithm for modeling ensembles that provides estimates for the uncertainty in the resulting model, (2) a fast algorithm for constructing ensembles for large or complex IDPs and (3) a measure of the degree of disorder in an ensemble. Our hypothesis is that a protein can be accurately modeled as an ensemble only when the degeneracy of the model is appropriately accounted for. We demonstrate these methods by constructing ensembles for K18 tau protein, \(\alpha\)-synuclein and amyloid beta - IDPs that are implicated in the pathogenesis of Alzheimer's and Parkinson's diseases.
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Niyogi, Sandip. "Synthesis and characterization of molecules to study the conformational barriers of fluorocarbon chains." Thesis, University of North Texas, 2000. https://digital.library.unt.edu/ark:/67531/metadc2511/.

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Fluorocarbons are known to be stiffer than their hydrocarbon analogues, a property that underlines the extensive industrial application of fluorocarbon materials. Although there has been previous studies on the rotational barrier of molecules having fluorocarbon centers, a detailed systematic study is necessary to quantify flurocarbon stiffness. The molecules, Pyrene-(CF2)n-Pyrene, Pyrene-(CF2)n-F, Pyrene-(CH2)n-Pyrene and Pyrene-(CH2)n-H were therefore synthesized to enable the determination of the barrier to rotation of the carbon backbone in fluorocarbons. Conformational studies will be completed with steady-state and time-dependent emission spectroscopy.
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Cherwa, Jr James Edward. "Characterization of Scaffolding Proteins Altered in the Ability to Perform a Critical Conformational Switch." Diss., The University of Arizona, 2009. http://hdl.handle.net/10150/195476.

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Throughout recent history scientists have struggled to elucidate the biochemical and biophysical mechanisms that guide the assembly of macromolecular structures. The early models of "sub-assembly" or "self assembly" attempted to explain how individual components could interact in a precisely regulated manner to form higher-ordered complex biological structures. Subsequent studies, using viral systems as assembly models, demonstrated how protein-protein and protein-nucleic acid interactions assist in lowering the thermodynamic barriers that typically disfavor assembly.Due to their simplicity, viruses provide an ideal system to investigate the biophysical mechanisms that drive the assembly of complex biological structures. Proper virion assembly requires numerous macromolecular interactions that proceed along an ordered morphogenetic pathway. While structural proteins are incorporated into the final product, morphogenesis is equally dependent upon scaffolding proteins, which are not included in the mature virion. Since the identification of scaffolding proteins in the bacteriophage P22, homologues have been discovered in many systems. Scaffolding proteins play multiple roles during morphogenesis by inducing protein conformational switches and lowering the thermodynamic barriers to promote virion assembly, while ensuring the efficiency and fidelity of the final product.
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Braggin, Greg A. "Effect of Surfactant Architecture on Conformational Transitions of Conjugated Polyelectrolytes." DigitalCommons@CalPoly, 2015. https://digitalcommons.calpoly.edu/theses/1411.

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Water soluble conjugated polyelectrolytes (CPEs), which fall under the category of conductive polymers, possess numerous advantages over other conductive materials for the fabrication of electronic devices. Namely, the processing of water soluble conjugated polyelectrolytes into thin film electronic devices is much less costly as compared to the processing of inorganic materials. Moreover, the handling of conjugated polyelectrolytes can be performed in a much more environmentally friendly manner than in the processing of other conjugated polymers because conjugated polyelectrolytes are water soluble, whereas other polymers will only dissolve in toxic organic solvents. The processing of electronic devices containing inorganic constituents such as copper indium gallium selenide (CIGS), is much more expensive and poses much greater environmental risks because toxic metals may be released into landfills or waterways upon cell disposal.75 Because conjugated polyelectrolytes enjoy an assortment of advantages over other materials for the manufacturing of thin film electronic devices, there is globally vested interest in the researching of their properties. Despite the fact that CPEs can serve as efficient electron transport mediums, devices such as organic solar cells cannot realize their highest efficiencies unless the morphology of CPEs is precisely controlled. Charged surfactants can electrostatically and ionically interact with CPEs, and when introduced in specific concentrations, molar ratios, and temperature ranges, will aid in a ‘coil to rod’ transition of the CPE, wherein polymer chains undergo intramolecular transitions to obtain rigid-rod morphologies. The kinetics and thermodynamics of the ‘coil to rod’ transition are heavily dependent upon the type(s) of charged surfactant complexed with the CPE (i.e. on the surfactant architecture). By performing UV/Vis Spectroscopy and Fluorometry on dilute polymer/surfactant solutions, Polarized Optical Microscopy (POM) and Small Angle X-Ray Scattering (SAXS) on high concentration polymer/surfactant solutions, and Differential Scanning Calorimetry (DSC) and X-Ray Diffraction (XRD) on solid-state polymer/surfactant samples, the role of various surfactant architectures on the kinetics and thermodynamics of the ‘coil to rod’ transition was studied. The liquid crystalline physical properties and the extent of solid state crystallinity were also investigated. Through an analysis of the data obtained from these various techniques, it was found that the ‘coil to rod’ transition is progressively favored when the alkyl chain length of a single tailed surfactant is sequentially increased, and that as the concentration of double-tailed surfactant increases, the ‘coil to rod’ transition is negated.
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Books on the topic "Conformational characterization"

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(Editor), Ying Xu, Dong Xu (Editor), and Jie Liang (Editor), eds. Computational Methods for Protein Structure Prediction and Modeling 1: Basic Characterization (Biological and Medical Physics, Biomedical Engineering). Springer, 2006.

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Maher, Christopher J., and Elaine R. Mardis. Genomic Landscape of Cancer. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0004.

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The study of cancer genomics has advanced rapidly during the last decade due to the development of next generation or massively parallel technology for DNA sequencing. The resulting knowledge is transforming the understanding of both inherited (germline) genetic susceptibility and the somatic changes in tumor tissue that drive abnormal growth and progression. The somatic alterations in tumor tissue vary depending on the type of cancer and its characteristic “genomic landscape.” New technologies have increased the speed and lowered the cost of DNA sequencing and have enabled high-volume characterization of RNA, DNA methylation, DNA-protein complexes, DNA conformation, and a host of other factors that, when altered, can contribute to the development and/or progression of the cancer. Technologic advances have greatly expanded research on somatic changes in tumor tissue, revealing both the singularity of individual cancer genomes and the commonality of genetic alterations that drive cancer in different tissues.
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Book chapters on the topic "Conformational characterization"

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Franks, Felix. "Conformational Stability Denaturation and Renaturation." In Characterization of Proteins, 95–126. Totowa, NJ: Humana Press, 1988. http://dx.doi.org/10.1007/978-1-59259-437-5_4.

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Fuad, Fazia Adyani Ahmad. "Characterization of Conformational and Oligomeric States of Proteins." In Multifaceted Protocol in Biotechnology, 167–78. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-13-2257-0_14.

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Delaforge, Elise, Tiago N. Cordeiro, Pau Bernadó, and Nathalie Sibille. "Conformational Characterization of Intrinsically Disordered Proteins and Its Biological Significance." In Modern Magnetic Resonance, 1–20. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-28275-6_52-1.

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Delaforge, Elise, Tiago N. Cordeiro, Pau Bernadó, and Nathalie Sibille. "Conformational Characterization of Intrinsically Disordered Proteins and Its Biological Significance." In Modern Magnetic Resonance, 381–99. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-28388-3_52.

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Pinto, Julia C., Jean Jacques Bourguignon, and Camille-Georges Wermuth. "Characterization of the pharmacophoric pattern of acetylcholinesterase inhibitors through conformational analysis." In Trends in QSAR and Molecular Modelling 92, 425–26. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1472-1_104.

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Langer, Thierry, and Camille-Georges Wermuth. "Prolyl-endopeptidase inhibitors: Pharmacophore characterization via conformational analysis and pattern recognition." In Trends in QSAR and Molecular Modelling 92, 427–28. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1472-1_105.

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Hamrick, Grayson S., Casey H. Londergan, and Louise K. Charkoudian. "Heterologous Expression, Purification, and Characterization of Type II Polyketide Synthase Acyl Carrier Proteins." In Methods in Molecular Biology, 239–67. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2273-5_13.

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AbstractThe enzymes that comprise type II polyketide synthases (PKSs) are powerful biocatalysts that, once well-understood and strategically applied, could enable cost-effective and sustainable access to a range of pharmaceutically relevant molecules. Progress toward this goal hinges on gaining ample access to materials for in vitro characterizations and structural analysis of the components of these synthases. A central component of PKSs is the acyl carrier protein (ACP), which serves as a hub during the biosynthesis of type II polyketides. Herein, we share methods for accessing type II PKS ACPs via heterologous expression in E. coli. We also share how the installation of reactive and site-specific spectroscopic probes can be leveraged to study the conformational dynamics and interactions of type II PKS ACPs.
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Baniak, Edmund L., Lila M. Gierasch, Jean Rivier, and Arnold T. Hagler. "NMR analysis and conformational characterization of cyclic antagonists of gonadotropin-releasing hormone." In Peptides, 457–58. Dordrecht: Springer Netherlands, 1988. http://dx.doi.org/10.1007/978-94-010-9595-2_134.

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Ogden, Dylan, and Mahmoud Moradi. "Molecular Dynamics–Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformational Transitions." In Methods in Molecular Biology, 289–309. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1394-8_16.

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Ami, Diletta, and Antonino Natalello. "Characterization of the Conformational Properties of Soluble and by Fourier Transform Infrared Spectroscopy." In Methods in Molecular Biology, 439–54. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-1859-2_26.

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Conference papers on the topic "Conformational characterization"

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Kim, Sungho, Angelica M. Palomino, and Nikolas J. Podraza. "Characterization of Adsorbed Polymer Conformational Response Using Spectroscopic Ellipsometry." In GeoCongress 2012. Reston, VA: American Society of Civil Engineers, 2012. http://dx.doi.org/10.1061/9780784412121.117.

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Koder, Ronald L., David T. Crouse, Derek J. Kosciolek, Ajay V. Sonar, Lori A. Lepak, Peter Schnatz, Igor Bendoym, and Mia C. Brown. "Handheld highly selective plasmonic chem/biosensor using engineered binding proteins for extreme conformational changes." In Plasmonics: Design, Materials, Fabrication, Characterization, and Applications XV, edited by Takuo Tanaka and Din Ping Tsai. SPIE, 2017. http://dx.doi.org/10.1117/12.2273207.

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Couzon, Cecile, Daniel Banks, James Jonkman, Aleksandra Dabkowska, Razvan Nutiu, Yingfu Li, and Cecile Fradin. "Characterization of the conformational changes of a tripartite molecular beacon." In Biomedical Optics 2004, edited by Ammasi Periasamy and Peter T. C. So. SPIE, 2004. http://dx.doi.org/10.1117/12.537423.

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Ali Khajeh, Jahan, Moussoubaou Atchiba, and Zimei Bu. "Abstract C298: Conformational characterization of tumor suppressor protein Merlin and phosphomimetic Merlin(S518D) mutant in solution." In Abstracts: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics--Oct 19-23, 2013; Boston, MA. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1535-7163.targ-13-c298.

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Vo, Elizabeth Donohue, Juan Luengo, Hong Lin, Jerry Chen, Ben Reid, Brooke McDonough, Norman Fultang, Jillian Silva, and Cameron Pitt. "Abstract LBA007: Discovery and characterization of oncogenic KRAS:RAF1 conformational modulators with in vitro and in vivo MAPK inhibition." In Abstracts: AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; October 7-10, 2021. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1535-7163.targ-21-lba007.

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Albuquerque, Ana Carolina Ferreira de, José Walkimar de Mesquita Carneiro, and Fernando Martins dos Santos Junior. "Estudo do tautomerismo ceto-enólico da 7-epi-clusianona através de cálculos teóricos de deslocamentos químicos de RMN." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol202063.

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The properties of natural products, including their biological and pharmacological activities, are directly correlated with their chemical structures. Thus, a correct structural characterization of these compounds is a crucial step to the understanding of their biological activities. However, despite the recent advances in spectroscopic techniques, structural studies of natural products can be challenging. This way, theoretical calculations of Nuclear Magnetic Resonance (NMR) parameters (such as chemical shifts and coupling constants) have proven to be a powerful and low-cost tool for the aid to experimental techniques traditionally used for the structural characterization of natural products. One of the several applications of quantum-mechanical calculations of NMR parameters is the study of tautomerism. Since chemical shifts are sensitive to the tautomeric equilibrium, this technique can provide crucial informations. In this work, it was applied a protocol for theoretical calculations of ¹³C chemical shifts in order to study the tautomerism of the natural product 7-epi-clusianone, isolated from Rheedia gardneriana. This protocol consists in a Monte Carlo conformational search, followed by geometry optimization and shielding tensors calculations, both using a density functional level of theory. After comparison of theoretical and experimental data, it was possible to confirm the two tautomers present in equilibrium in the experimental solution. Furthermore, this study highlights how this theoretical protocol can be an effective method in identifying the preferred tautomeric form in solution.
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Higashiyama, S., I. Ohkubo, H. Ishiguro, and M. Sasaki. "A NEW FUNCTION OF HUMAN KININOGENS: THE AMINO-TERMINAL REGION OF DOMAIN 1 INVOLVES AN EF HAND-LIKE STRACTURE FOR METAL BINDING." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642851.

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Two types of kininogens in mammalian plasma, high molecular weight (HMW) and low molecular weight (LMW) kininogens, are the precursors of kinin. Especially, HMW kininogen circulates in the plasma as a complex with prekallikrein and factor XI, and functions as a cofactor in the initial phase reactions of intrinsic blood coagulation cascade. Recently, it has been found that the kininogens have inhibitory activity toward cysteine proteinases. The heavy chain portion, which is identical for HMW and LMW kininogens, is composed of three domains, domain 1, 2 and 3. Each the domain 2 and 3 has a reactive site as a cysteine proteinase inhibitor. However, physiological function of domain 1 remains still unknown. By using the antibody recognizing the interaction between HMW kininogen and Ca2+ (anti-HMW kininogen-Ca2+ antibody) as a probe, we newly found the Ca2+ binding site in the domain 1.Anti-HMW kininogen-Ca2+ antibody was isolated from anti-HMW kininogen antiserum as an antibody which bound to a HMW kininogen-Sepharose column equilibrated with 40 mM Tris-HCl buffer, pH 7.5, containing 1.0 M NaCl and 1 mM CaCl2, and was eluted with 3 mM EDTA. Resulting from the characterization by ELISA, this antibody specifically recognized the CB-1 region (CNBr-cleavage fragment 1: 1-160 amino acid sequence) of the heavy chain of kininogen molecules in the presence of Ca2+ or Mg2+. Furthermore, circular dichroism (CD) experiments showed that the conformational changes of HMW kininogen and heavy chain were induced by the addition of metal ions such as Ca2+ or Mg2+, and that this change was due to the conformational change of the CB-1 region. The dissociation constant (Kd) for heavy chain measured by Ca2+ titration analysis by CD at 214 nm was found to be 0.33 ± 0.09 mM. The number of Ca2+ binding sites of heavy chain calculated from Hill plot was 1.15 ± 0.04. The EF handlike structure found in the amino-terminal portion of the heavy chain of kininogen molecules strongly supported the above data. This indicates a possibility that kininogens play an important role as a Ca2+ binding protein.
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Zhao, Yang, and Yun-Sheng Chen. "Nanoscopic imaging of molecular conformations in physiological conditions." In Plasmonics: Design, Materials, Fabrication, Characterization, and Applications XVIII, edited by Takuo Tanaka and Din Ping Tsai. SPIE, 2020. http://dx.doi.org/10.1117/12.2568640.

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Globus, Tatiana, Tatyana Khromova, Rebecca Lobo, Dwight Woolard, Nathan Swami, and Erik Fernandez. "THz characterization of lysozyme at different conformations." In Defense and Security, edited by R. Jennifer Hwu, Dwight L. Woolard, and Mark J. Rosker. SPIE, 2005. http://dx.doi.org/10.1117/12.603581.

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Mosca, A., S. Viganò D'Angelo, and A. D'Angelo. "ACTIVATION OF PROTEIN C INDUCES CHANGES IN ITS INTRINSIC FLUORESCENCE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644302.

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Upon activation with either thrombin (T) or thrombin-thrombo modulin complex (T-TM), the zymogen protein C (PC) is transformed into a serine-protease, activated protein C(APC), by release of a small activation peptide. The rate of PC activation changes dramatically with T or with T-TM as a function of the Ca++ concentration in the activation medium, suggesting a configurational change of the zymogen in the presence of Ca++ . It has been shown that Ca++ binding to one single high-affinity binding site of gla-domainless PC is accompanied by a significant decrease of the intrinsic fluo rescence emission intensity of the protein and that the high-affinity binding site is retained following activation of gla-domain-less PC (J. Biol. Chem: 258; 5554, 1983). In the present work we have investigated the fluorescence properties of PC in order to answer the following questions: 1) is there a difference in the fluorescence properties of PC as compared to APC? 2) is there a difference between the conformational changes of PC activated with T or T-TM? From our experimental data we conclude that : a) the fluorescence emission intensity of fully activated PC is about 54% of the PC zymogen fluorescence intensity (λexc 280 nm, λ em 345 nm, 0.6 μuM PC or APC in 20 mMTris-HCl, 0.1 M NaCl, pH 7.8 at 25°C) ; b) during activation of PC (2 μM) with T-TM (150 nM) in the presence of 2 mM Ca++ , there is a good correlation (r=0.959) between fluorescence quenching and degree of PC activation, as measured by the rate of cleavage of the chromogenic substrate S-2238; c) the maximal fluorescence quench of PC activated with T or T-TM are virtually identical. Preliminary data suggest that Ca++ affects differently the fluorescence emission properties of PC and APC. These results suggest that evaluation of the fluorescence properties of PC might represent a valuable tool for the characterization of abnormal PC molecules.
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Reports on the topic "Conformational characterization"

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Ashani, Y., and I. Silman. Characterization by NMR and Fluorescence Spectroscopy of Differences in the Conformation of Non-aged and Aged Organophosphoryl Conjugates of AChE. Fort Belvoir, VA: Defense Technical Information Center, September 1985. http://dx.doi.org/10.21236/ada202381.

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Ashani, Y., and I. Silman. Characterization by NMR and Fluorescence Spectroscopy of Differences in the Conformation of Non-Aged and Aged Organophosphoryl Conjugates of AChE. Fort Belvoir, VA: Defense Technical Information Center, March 1990. http://dx.doi.org/10.21236/ada238708.

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Sadot, Einat, Christopher Staiger, and Mohamad Abu-Abied. Studies of Novel Cytoskeletal Regulatory Proteins that are Involved in Abiotic Stress Signaling. United States Department of Agriculture, September 2011. http://dx.doi.org/10.32747/2011.7592652.bard.

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In the original proposal we planned to focus on two proteins related to the actin cytoskeleton: TCH2, a touch-induced calmodulin-like protein which was found by us to interact with the IQ domain of myosin VIII, ATM1; and ERD10, a dehydrin which was found to associate with actin filaments. As reported previously, no other dehydrins were found to interact with actin filaments. In addition so far we were unsuccessful in confirming the interaction of TCH2 with myosin VIII using other methods. In addition, no other myosin light chain candidates were found in a yeast two hybrid survey. Nevertheless we have made a significant progress in our studies of the role of myosins in plant cells. Plant myosins have been implicated in various cellular activities, such as cytoplasmic streaming (1, 2), plasmodesmata function (3-5), organelle movement (6-10), cytokinesis (4, 11, 12), endocytosis (4, 5, 13-15) and targeted RNA transport (16). Plant myosins belong to two main groups of unconventional myosins: myosin XI and myosin VIII, both closely related to myosin V (17-19). The Arabidopsis myosin family contains 17 members: 13 myosin XI and four myosin VIII (19, 20). The data obtained from our research of myosins was published in two papers acknowledging BARD funding. To address whether specific myosins are involved with the motility of specific organelles, we cloned the cDNAs from neck to tail of all 17 Arabidopsis myosins. These were fused to GFP and used as dominant negative mutants that interact with their cargo but are unable to walk along actin filaments. Therefore arrested organelle movement in the presence of such a construct shows that a particular myosin is involved with the movement of that particular organelle. While no mutually exclusive connections between specific myosins and organelles were found, based on overexpression of dominant negative tail constructs, a group of six myosins (XIC, XIE, XIK, XI-I, MYA1 and MYA2) were found to be more important for the motility of Golgi bodies and mitochondria in Nicotiana benthamiana and Nicotiana tabacum (8). Further deep and thorough analysis of myosin XIK revealed a potential regulation by head and tail interaction (Avisar et al., 2011). A similar regulatory mechanism has been reported for animal myosin V and VIIa (21, 22). In was shown that myosin V in the inhibited state is in a folded conformation such that the tail domain interacts with the head domain, inhibiting its ATPase and actinbinding activities. Cargo binding, high Ca2+, and/or phosphorylation may reduce the interaction between the head and tail domains, thus restoring its activity (23). Our collaborative work focuses on the characterization of the head tail interaction of myosin XIK. For this purpose the Israeli group built yeast expression vectors encoding the myosin XIK head. In addition, GST fusions of the wild-type tail as well as a tail mutated in the amino acids that mediate head to tail interaction. These were sent to the US group who is working on the isolation of recombinant proteins and performing the in vitro assays. While stress signals involve changes in Ca2+ levels in plants cells, the cytoplasmic streaming is sensitive to Ca2+. Therefore plant myosin activity is possibly regulated by stress. This finding is directly related to the goal of the original proposal.
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