Relevant bibliographies by topics / Protein-ligand complex

Contents

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

Academic literature on the topic 'Protein-ligand complex'

Author: Grafiati
Published: 4 June 2021
Last updated: 26 April 2022

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Journal articles on the topic "Protein-ligand complex"

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Roche, Olivier, Ryuichi Kiyama, and Charles L. Brooks. "Ligand−Protein DataBase: Linking Protein−Ligand Complex Structures to Binding Data." Journal of Medicinal Chemistry 44, no. 22 (October 2001): 3592–98. http://dx.doi.org/10.1021/jm000467k.

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Debreczeni, Judit É., and Paul Emsley. "Ligand complex structures in protein crystallography." Acta Crystallographica Section D Structural Biology 73, no. 2 (February 1, 2017): 77–78. http://dx.doi.org/10.1107/s2059798317001644.

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Karthikeyan, Muthukumarasamy, Deepak Pandit, and Renu Vyas. "Protein Ligand Complex Guided Approach for Virtual Screening." Combinatorial Chemistry & High Throughput Screening 18, no. 6 (September 2, 2015): 577–90. http://dx.doi.org/10.2174/1386207318666150703112620.

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Vonrhein, C., O. S. Smart, A. Sharff, C. Flensburg, P. Keller, W. Paciorek, T. O. Womack, and G. Bricogne. "Improving the quality of protein–ligand complex structures." Acta Crystallographica Section A Foundations of Crystallography 68, a1 (August 7, 2012): s87. http://dx.doi.org/10.1107/s0108767312098303.

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Kolář, Michal, Jindřich Fanfrlík, and Pavel Hobza. "Ligand Conformational and Solvation/Desolvation Free Energy in Protein−Ligand Complex Formation." Journal of Physical Chemistry B 115, no. 16 (April 28, 2011): 4718–24. http://dx.doi.org/10.1021/jp2010265.

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Emsley, Paul. "Protein-Ligand Analysis and Validation." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1480. http://dx.doi.org/10.1107/s2053273314085192.

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A number of tools related to handling of ligands have been added to Coot in recent years - these include 2D depictions, ligand binding pocket layout and a ligand scoring system. Coot also incorporates a number interface to other tools (CCP4's Refmac, Molprobity's probe and reduce and the CCDC's Mogul) to generate score for protein ligand complexes. This scoring system has been applied to models (with data) from the PDB. The details of the ligand scoring, and its application to one's own complex structure will be discussed.
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Moriarty, Nigel W., and Paul D. Adams. "High-throughput protein–ligand complex structure solution with Phenix." Acta Crystallographica Section A Foundations and Advances 74, a1 (July 20, 2018): a445. http://dx.doi.org/10.1107/s0108767318095557.

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Sousa, Paulo Robson M., Nelson Alberto N. de Alencar, Anderson H. Lima, Jerônimo Lameira, and Cláudio Nahum Alves. "Protein-Ligand Interaction Study ofCpOGA in Complex with GlcNAcstatin." Chemical Biology & Drug Design 81, no. 2 (November 27, 2012): 284–90. http://dx.doi.org/10.1111/cbdd.12078.

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Masetti, Matteo, Andrea Cavalli, Maurizio Recanatini, and Francesco Luigi Gervasio. "Exploring Complex Protein−Ligand Recognition Mechanisms with Coarse Metadynamics." Journal of Physical Chemistry B 113, no. 14 (April 9, 2009): 4807–16. http://dx.doi.org/10.1021/jp803936q.

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Müller, Ilka. "Guidelines for the successful generation of protein–ligand complex crystals." Acta Crystallographica Section D Structural Biology 73, no. 2 (February 1, 2017): 79–92. http://dx.doi.org/10.1107/s2059798316020271.

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With continuous technical improvements at synchrotron facilities, data-collection rates have increased dramatically. This makes it possible to collect diffraction data for hundreds of protein–ligand complexes within a day, provided that a suitable crystal system is at hand. However, developing a suitable crystal system can prove challenging, exceeding the timescale of data collection by several orders of magnitude. Firstly, a useful crystallization construct of the protein of interest needs to be chosen and its expression and purification optimized, before screening for suitable crystallization and soaking conditions can start. This article reviews recent publications analysing large data sets of crystallization trials, with the aim of identifying factors that do or do not make agoodcrystallization construct, and gives guidance in the design of an expression construct. It provides an overview of common protein-expression systems, addresses how ligand binding can be both help and hindrance for protein purification, and describes ligand co-crystallization and soaking, with an emphasis on troubleshooting.
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Dissertations / Theses on the topic "Protein-ligand complex"

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Qian, Yi. "Flipping a MAGUK switch : complex domain interactions regulating ligand binding to the tumor suppressor Dlg /." view abstract or download file of text, 2006. http://proquest.umi.com/pqdweb?did=1251819311&sid=1&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2006.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 68-71). Also available for download via the World Wide Web; free to University of Oregon users.
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Fujishima, Sho-hei. "Development of Protein Labeling Methods for Functional Analyses in Biological Conditions." 京都大学 (Kyoto University), 2012. http://hdl.handle.net/2433/157618.

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Spitzmüller, Andreas [Verfasser], and Gerhard [Akademischer Betreuer] Klebe. "Knowledge-based Optimization of Protein-Ligand-Complex Geometries / Andreas Spitzmüller. Betreuer: Gerhard Klebe." Marburg : Philipps-Universität Marburg, 2011. http://d-nb.info/1014851696/34.

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Holmes, Peter. "Structure and mode of action of the TolA-TolB complex from Pseudomonas aeruginosa." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:cccb0c88-5c89-4d21-81eb-70ebf513c7ab.

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Protein-protein interactions (PPIs) across the cell envelope of Gram-negative bacteria are critical for mediating signal transduction pathways that underpin cellular homeostasis. The Ton and Tol Pal systems are two conserved, ancestrally related protein networks that are also required for bacterial pathogenesis. Both Ton and Tol-Pal traverse the periplasm to effect different functions at the outer membrane (OM). Tol-Pal is composed of a homologous complex of three inner membrane proteins, TolQ-TolR-TolA (linked to proton motive force) and two additional periplasmic proteins TolB and Pal. The physiological role of the Tol-Pal system is to stabilise the OM, however the mechanism involved is unknown. TolA is however known to form a crucial protein-protein interaction via its C-terminus with the disordered N-terminus of TolB. Prior to this thesis, determination of the molecular features underlying a protein-protein complex between TolA and an endogenous binding partner TolB had never been accomplished. In this work, I describe the first structure comprising the TolA-TolB complex from Gram negative bacteria. The structure of this complex was determined from Pseudomonas aeruginosa by solution NMR spectroscopy. I determined the interaction between P. aeruginosa TolA and a TolB N terminal peptide to be relatively weak using fluorescence anisotropy. I found that TolB interacts with TolA through an analogous mechanism to that seen in TonB-dependent transporters. Based on these studies and bioinformatics analyses, I hypothesize that the evolutionary resilience of the Tol-Pal system to external pressures is contingent on the preservation of the TolA-TolB interface. Structure-based mutations within the TolA-TolB complex were also evaluated for their effect on in vivo function of the Tol-Pal complex and impact on complex formation in vitro. Taken together, the results demonstrate that protein networks which transduce energy to the OM through PMF-dependent systems in bacterial cells appear to follow a common β-strand augmentation mechanism.
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Sundqvist, Gustav. "Analysis of noncovalent and covalent protein-ligand complexes by electrospray ionisation mass spectrometry." Doctoral thesis, Stockholm : Bioteknologi, Biotechnology, Kungliga Tekniska högskolan, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4728.

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Griswold, Ian James. "The structural role of CheW in the bacterial chemotaxis receptor complex /." view abstract or download file of text, 2001. http://wwwlib.umi.com/cr/uoregon/fullcit?p3018365.

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Thesis (Ph. D.)--University of Oregon, 2001.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 163-175). Also available for download via the World Wide Web; free to University of Oregon users.
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Le, Duc Thanh. "Algorithmes pour le (dés)assemblage d'objets complexes et applications à la biologie structurale." Phd thesis, Institut National Polytechnique de Toulouse - INPT, 2010. http://tel.archives-ouvertes.fr/tel-00538694.

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La compréhension et la prédiction des relations structure-fonction de protéines par des approches in sillico représentent aujourd'hui un challenge. Malgré le développement récent de méthodes algorithmiques pour l'étude du mouvement et des interactions moléculaires, la flexibilité de macromolécules reste largement hors de portée des outils actuels de modélisation moléculaire. L'objectif de cette thèse est de développer une nouvelle approche basée sur des algorithmes de planification de mouvement issus de la robotique pour mieux traiter la flexibilité moléculaire dans l'étude des interactions protéiques. Nous avons étendu un algorithme récent d'exploration par échantillonnage aléatoire, ML-RRT pour le désassemblage d'objets articulés complexes. Cet algorithme repose sur la décomposition des paramètres de configuration en deux sous-ensembles actifs et passifs, qui sont traités de manière découplée. Les extensions proposées permettent de considérer plusieurs degrés de mobilité pour la partie passive, qui peut Æetre poussée ou attirée par la partie active. Cet outil algorithmique a été appliqué avec succès pour l'étude des changements conformationnels de protéines induits lors de la diffusion d'un ligand. A partir de cette extension, nous avons développé une nouvelle méthode pour la résolution simultanée du séquenc¸age et des mouvements de désassemblage entre plusieurs objets. La méthode, nommée Iterative- ML-RRT, calcule non seulement les trajectoires permettant d'extraire toutes les pièces d'un objet complexe assemblé, mais également l'ordre permettant le désassemblage. L'approche est générale et a été appliquée pour l'étude du processus de dissociation de complexes macromoléculaires en introduisant une fonction d'évaluation basée sur l'énergie d'interaction. Les résultats présentés dans cette thèse montrent non seulement l'efficacité mais aussi la généralité des algorithmes proposés.
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Andersson, David. "Multivariate design of molecular docking experiments : An investigation of protein-ligand interactions." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-35736.

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To be able to make informed descicions regarding the research of new drug molecules (ligands), it is crucial to have access to information regarding the chemical interaction between the drug and its biological target (protein). Computer-based methods have a given role in drug research today and, by using methods such as molecular docking, it is possible to investigate the way in which ligands and proteins interact. Despite the acceleration in computer power experienced in the last decades many problems persist in modelling these complicated interactions. The main objective of this thesis was to investigate and improve molecular modelling methods aimed to estimate protein-ligand binding. In order to do so, we have utilised chemometric tools, e.g. design of experiments (DoE) and principal component analysis (PCA), in the field of molecular modelling. More specifically, molecular docking was investigated as a tool for reproduction of ligand poses in protein 3D structures and for virtual screening. Adjustable parameters in two docking software were varied using DoE and parameter settings were identified which lead to improved results. In an additional study, we explored the nature of ligand-binding cavities in proteins since they are important factors in protein-ligand interactions, especially in the prediction of the function of newly found proteins. We developed a strategy, comprising a new set of descriptors and PCA, to map proteins based on their cavity physicochemical properties. Finally, we applied our developed strategies to design a set of glycopeptides which were used to study autoimmune arthritis. A combination of docking and statistical molecular design, synthesis and biological evaluation led to new binders for two different class II MHC proteins and recognition by a panel of T-cell hybridomas. New and interesting SAR conclusions could be drawn and the results will serve as a basis for selection of peptides to include in in vivo studies.
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Malard, Florian. "Structural and dynamic studies of TCTP protein : deciphering a complex interaction network involved in tumor reversion." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS540.

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TCTP est une petite protéine globulaire (20~kDa) qui interagit avec de nombreux partenaires et qui est impliquée dans diverses fonctions cellulaires et physiologiques, avec un rôle bien documenté dans la réversion tumorale qui est un phénomène rare et spontané où une cellule cancereuse perd tout ou partie de son phénotype malin et retrouve des caractéristiques associées aux cellules bénignes telles que la sensibilité à l'apoptose. Dans les cellules cancéreuses, TCTP inhibe la dégradation de MDM2, diminuant ainsi les niveaux de p53 et favorisant le maintien et la progression du cancer. TCTP contient également un motif BH3-like connu pour réguler les membres de la famille Bcl-2 et elle interagit directement avec Bcl-xL et Mcl-1 pour renforcer leurs propriétés anti-apoptotiques. Dans la structure TCTP, le motif BH3-like n'est pas facilement accessible pour une interaction avec un partenaire. Conformément à son importance dans le maintien de la tumeur, TCTP est une cible pharmacologique validée dans le traitement du cancer et fait l’objet d’essais cliniques en cours avec une molécule d'abord connue comme anti-depresseur, la sertraline. Cependant, on en sait peu sur la structure de TCTP en complexe avec ses partenaires, ce qui entrave le développement de médicaments et ne permet pas de comprendre comment TCTP peut s'adapter à une telle variété de partenaires. Ainsi, nous avons étudié le mécanisme moléculaire par lequel TCTP s'associe à des protéines et à des ligands en utilisant diverses méthodes biophysiques (RMN, SAXS, CD, SEC, DSF...). Nous avons démontré que la protéine TCTP se lie à Bcl-xL et à Mcl-1 dans le sillon de liaison des motifs BH3. Dans les complexes, la région BH3-like est engagée dans l'interface intermoléculaire et la structure centrale de TCTP est déstabilisée dans un état de globule fondu (molten-globule). Nous avons en outre montré que seule une forme mineure pré-existante de TCTP, à savoir TCTP*, est compétente pour les interactions avec les partenaires Bcl-xL et Mcl-1. Dans TCTP*, la région BH3-like est détachée du domaine structuré et elle est accessible aux protéines Bcl-xL/Mcl-1 tandis qu'on retrouve un état globule fondu dans la partie globulaire de TCTP*. Nous avons également collecté des données d'interaction préliminaires entre TCTP et la sertraline, des ARN, la protéine YB-1 se liant à l'ARN et le domaine N-terminal de MDM2. Enfin, nous avons caractérisé TCTP phosphorylé (pTCTP) au résidu S46 en utilisant la Plk-1 car cette modification a un impact sur les interactions et est un marqueur de l'aggressivité tumorale. En résumé, ces travaux ont établi la versatilité de TCTP en terme de structure et ont montré que cette versatilité est indispensable pour exercer ses fonctions cellulaires. En conséquence, ceci devrait être pris en compte dans les stratégies de développement de nouvelles molécules thérapeutiques ciblant TCTP
TCTP is a small (20~kDa) globular protein that interacts with many partners with consequences in various cellular and physiological functions, with well-documented roles in tumoral reversion program. Cells that undergo such program spontaneously loose their malignant phenotype and recover characteristics associated with benign cells, such as apoptosis. In cancer cells, TCTP inhibits MDM2 degradation, thus decreasing p53 levels and favoring tumor maintenance and progression. TCTP also contains a BH3-like motif known to regulate Bcl-2 family members and TCTP directly interacts with Bcl-xL and Mcl-1 to reinforce their pro-survival properties. In TCTP structure, the BH3-like motif is not readily accessible for interaction. Consistently with its importance in tumor maintenance, TCTP is a validated pharmacological target in cancer treatment with ongoing clinical trials using the TCTP-targeting antidepressant drug sertraline. However, little is known about TCTP structure in complex with partners, thus impeding the development of drugs and the understanding of how TCTP could adapt to its myriad of partners. Thus, we investigated the molecular mechanism by which TCTP associates with proteins and ligands using various biophysical methods (NMR, SAXS, CD, SEC, DSF...). We have demonstrated that full length TCTP binds to Bcl-xL and Mcl-1 in their BH3-binding groove. In the complexes, the TCTP BH3-like region is engaged in the intermolecular interface and the core TCTP structure is destabilized into a molten-globule (MG) state. We further showed that only a minor pre-existing form of TCTP, namely TCTP*, is competent for interactions with the Bcl-2 protein partners. In TCTP*, the BH3-like region is unpinned and accessible to Bcl-xL/Mcl-1 proteins and the core structure is also in MG state. We also collected preliminary interaction data between TCTP and sertraline, RNA, the RNA binding YB-1 protein and the MDM2 N-terminal domain. Finally, we characterized the Plk-1-mediated S46 phosphorylated TCTP (pTCTP), a marker of tumor aggressivity and its interaction properties. Overall, this work established the structural versatility of TCTP that is mandatory to exert its cellular functions and this versatility should be taken into account in drug-design strategies targeting TCTP
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Alavi, Sarah. "Synthese et evaluation biologique de derives de l’aminobenzosuberone, inhibiteurs puissants et selectifs de l’aminopeptidase N ou CD13." Thesis, Mulhouse, 2013. http://www.theses.fr/2013MULH4071/document.

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Le mode d’action des traitements médicaux fait généralement intervenir des interactions entre une (des) molécule(s) et une (des) cible(s) protéique(s) de l’organisme. Au sein de notre équipe, le choix s’est porté vers l’APN, protéine connue depuis les années 2000, pour être impliquée dans les processus d’angiogenèse i.e. la formation de nouveaux vaisseaux sanguins à partir de vaisseaux préexistants, et de migration cellulaire. Compte tenu de la pertinence thérapeutique des fonctions de l’APN et de leur validation lors d’études in vivo, la conception de voies de synthèse simples et efficaces menant à l’inhibiteur le plus puissant et sélectif de l’APN est devenu un des objectifs premier du laboratoire : 3 voies de synthèses sont décrites. Par ailleurs, notre laboratoire s’est intéressé à une nouvelle classe de composés comportant un groupement ferrocényle. En effet, les composés organométalliques suscitent un intérêt grandissant dans le développement de thérapies anticancéreuse ou encore les maladies tropicales. Ses possibilités réactionnelles étendues combinées à ses remarquables propriétés électrochimiques donnent lieu à des molécules nouvelles aux propriétés biologiques étonnantes. Ayant développé la molécule la plus puissante vis-à-vis de l’APN, ses impressionnantes propriétés inhibitrices peuvent être exaltées en créant des molécules à activité duale : inhibitrice de l’APN et cytotoxique vis-à-vis des cellules tumorales. La synthèse de ces composés hybrides ainsi que l’évaluation de leurs effets envers deux cibles, l’APN (porcine et d’Escherichia coli) et les cellules HT1080 (cellules de type fibrosarcome exprimant fortement l’APN), sont décrites dans cette thèse
APN/CD13, a zinc dependent metallo-peptidase ectoenzyme widespread in human tissues is emerging as a new target in cancer therapy. Indeed several studies indicate that APN/CD13 plays an active role in angiogenesis and tumor metastasis. We already prepared a series of (±)-1,4-disubstituted-7-amino-benzocyclohepten-6-ones and discovered the extraordinary inhibitory power of the 1-bromo-4-phenyl derivative (Ki = 60 pM) on mammalian APN/CD13. As recent crystallographic works in collaboration with the Paul Scherrer Institut have revealed that only the (S) enantiomer was efficiently binded to the enzyme active site, we recently developed a new synthetic pathway to prepare this optically pure molecule in benzo-oxepine series. In parallel we prepare analogs equipped with at least one ferrocenyl moiety of potential intrinsic additional cytotoxicity
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Book chapters on the topic "Protein-ligand complex"

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Lowe, Peter N., Cara K. Vaughan, and Tina Daviter. "Measurement of Protein–Ligand Complex Formation." In Protein-Ligand Interactions, 63–99. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-398-5_3.

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Birchenough, Holly L., and Thomas A. Jowitt. "Quartz Crystal Microbalance with Monitoring (QCM-D): Preparing Lipid Layers for the Study of Complex Protein–Ligand Interactions." In Protein-Ligand Interactions, 183–97. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5_7.

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Ratnala, Venkata R. P., and Brian Kobilka. "Understanding the Ligand–Receptor–G Protein Ternary Complex for GPCR Drug Discovery." In Methods in Molecular Biology, 67–77. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-317-6_5.

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Turnbull, Andrew P., and Xiaoqiu Wu. "Studying RNA–Protein Complexes Using." In Protein-Ligand Interactions, 423–46. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5_20.

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Pompey, Shanica N., Peter Michaely, and Katherine Luby-Phelps. "Quantitative Fluorescence Co-localization to Study Protein–Receptor Complexes." In Protein-Ligand Interactions, 439–53. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-398-5_16.

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Folta-Stogniew, Ewa. "Characterization of Protein–Nucleic Acid Complexes by Size-Exclusion Chromatography Coupled with , Absorbance, and Refractive Index Detectors." In Protein-Ligand Interactions, 381–95. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5_18.

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Buxbaum, Engelbert. "Structure of Protein–Ligand Complexes." In Biophysical Chemistry of Proteins, 303–8. Boston, MA: Springer US, 2010. http://dx.doi.org/10.1007/978-1-4419-7251-4_33.

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Bitencourt-Ferreira, Gabriela, Martina Veit-Acosta, and Walter Filgueira de Azevedo. "Electrostatic Energy in Protein–Ligand Complexes." In Methods in Molecular Biology, 67–77. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9752-7_5.

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Bitencourt-Ferreira, Gabriela, Martina Veit-Acosta, and Walter Filgueira de Azevedo. "Hydrogen Bonds in Protein-Ligand Complexes." In Methods in Molecular Biology, 93–107. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9752-7_7.

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Barth, Marie, and Carla Schmidt. "Quantitative Cross-Linking of Proteins and Protein." In Methods in Molecular Biology, 385–400. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1024-4_26.

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AbstractCross-linking, in general, involves the covalent linkage of two amino acid residues of proteins or protein complexes in close proximity. Mass spectrometry and computational analysis are then applied to identify the formed linkage and deduce structural information such as distance restraints. Quantitative cross-linking coupled with mass spectrometry is well suited to study protein dynamics and conformations of protein complexes. The quantitative cross-linking workflow described here is based on the application of isotope labelled cross-linkers. Proteins or protein complexes present in different structural states are differentially cross-linked using a “light” and a “heavy” cross-linker. The intensity ratios of cross-links (i.e., light/heavy or heavy/light) indicate structural changes or interactions that are maintained in the different states. These structural insights lead to a better understanding of the function of the proteins or protein complexes investigated. The described workflow is applicable to a wide range of research questions including, for instance, protein dynamics or structural changes upon ligand binding.
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Conference papers on the topic "Protein-ligand complex"

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Pakpahan, M. T., M. Rusmerryani, K. Kawaguchi, H. Saito, and H. Nagao. "Evaluation of scoring functions for protein-ligand docking." In 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku. American Institute of Physics, 2013. http://dx.doi.org/10.1063/1.4794652.

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Kawaguchi, Kazutomo, Hiroyuki Takagi, Masako Takasu, Hiroaki Saito, and Hidemi Nagao. "Molecular dynamics studies of Hsp90 with ADP: Protein-ligand binding dynamics." In 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku. American Institute of Physics, 2013. http://dx.doi.org/10.1063/1.4794650.

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Šeklić, Dragana, Milena Jovanović, Nevena Milivojević, and Marko Živanović. "PLATINUM(IV) COMPLEX AND ITS CORRESPONDING LIGAND SUPPRESS CELL MOTILITY AND PROMOTE EXPRESSION OF FRIZZLED-7 RECEPTOR IN COLORECTAL CANCER CELLS." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.288s.

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Suppression of cell movement is an imperative in the effectiveness of future generations of chemotherapeutics. Frizzled 7 receptor (FZD7), as the first protein of Wnt/β-catenin signaling cascade, plays a significant role in regulation of cell differentiation, proliferation, and cell migration. This study aimed to investigate the potential effects of platinum (IV) complex: [PtCl4 (dbu-S, S-eddp)] – C1, and its corresponding ligand – L1 on cell movement, as well as the FZD7 expression and localization after treatments on two human colorectal carcinoma cell lines (HCT-116, SW-480). A Wound healing assay was used to examine cell migration, while FZD7 protein expression was examined by immunofluorescence. Chemical compounds, especially L1, reduced cell motility of both tested cell lines. They showed a particularly good effect on HCT-116 cells, increasing protein expression of the antimigratory marker FZD7 whose localization was observed on the cell membrane of HCT-116 cells. Suppression of cell movement was significantly lower in SW-480 cells after treatments, when compared to HCT-116, with an obvious decrease of FZD7 receptor expression and its localization in the cytoplasm of these cells. Our results indicate that among the examined treatments, the ligand showed more significant results in the suppression of HCT-116 cell movement, most likely through the stimulation of differentiation, which is indicated by the promotion of FZD7 expression.
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Koller, E., and F. Koller. "LIPOPROTEIN BINDING TOHUMAN PLATELETS IS LOCATED AT GPIIb/IIIa COMPLEX." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643702.

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Human Platelets possess specific binding sites for low density lipoproteins (LDL) and high density lipoproteins(HDL)(1). Binding of both classes of plasma lipoproteins, though competitive, has been shown by several groups to facilitate platelet activation.Isolated washed platelets occasionally aggregate upon addition of high concentrations of LDL even in the absence of known platelet activators. The proteins responsible for this binding have been visualized by ligand blotting (2). Both types of ligand specifically bind to two glycoproteins with molecular weights of 135 and 115 kD, respectively. The conditions of binding to these two proteins, however, markedly differ from those known for other lipoprotein receptors.Following extensive purification, these two species are still present at concentrations relative to each other that depend markedly on the conditions of purification. The purified, solubilized receptor was tested under various conditions, including in the absence and presence of calcium, after disulfide-reduction, and following chymotrypsin digestion. In parallel experiments, the same preparations were tested with respect to binding of fibrinogen, different lectins, and thealloantibody anti-PlAI . The results strongly support the assumption, that the two protein bands associated with lipoprotein binding are constituents of the GP-IIb/IIIa complex.These first results may have greatimplications for our understanding ofthe mechanism by which lipoproteins facilitate platelet stimulation.
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Brewer, Bryson M., Yandong Gao, Rebecca M. Sappington, and Deyu Li. "Microfluidic Molecular Trap: Probing Extracellular Signaling by Selectively Blocking Exchange of Specific Molecules in Cell-Cell Interactions." In ASME 2013 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/imece2013-64489.

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Communication among cell populations is achieved via a wide variety of soluble, extracellular signaling molecules [1]. In order to investigate the role of specific molecules in a cellular process, researchers often utilize in vitro cell culture techniques in which the molecule under question has been removed from the signaling pathway. Traditionally, this has been accomplished by eliminating the gene in the cell that is responsible for coding the targeted ligand/receptor by using modern DNA technology such as gene knockout; however, this process is expensive, time-consuming, and labor intensive. Previously, we have demonstrated a microfluidic platform that uses a semi-permeable barrier with embedded receptor-coated nanoparticles to selectively remove a specific molecule or ligand from the extracellular signaling pathway in a cell co-culture environment [2]. This initial proof-of-principle was conducted using biotinylated nanoparticles and fluorescently tagged avidin molecules, as the avidin/biotin complex is the strongest known non-covalent interaction between a protein and a ligand (Dissociation constant kd = 10−15 M). Also, the trap was only effective for short time periods (<15 min) because the high concentration of fluorescently tagged avidin molecules required for visualization quickly saturated the barrier. However, nearly all biologically relevant ligand-receptor interactions have lower binding affinities than the avidin-biotin complex, with dissociation constants that are larger by several orders of magnitude. In addition, many in vitro cell culture experiments are conducted over multiple hours or days. Thus, a practically useful molecular trap device must be able to operate in a lower binding affinity regime while also lasting for extended time periods. Here we present results in which a biotinylated-particle barrier was used to successfully block lower concentrations of fluorescently tagged avidin for multiple days, showcasing the applicability of the device for long term experiments. In addition, we introduce a modified molecular trap in which the protein A/goat IgG complex was used to demonstrate the effectiveness of the platform for lower binding affinity protein-ligand interactions. These results indicate the potential usefulness of the microfluidic molecular trap platform for probing extracellular signaling pathways.
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Chang, Jeng-Shian, Chih-Kai Yang, Sheng D. Chao, and Kuang-Chong Wu. "Finite-Element Simulation on Electrothermal Effects for Immuno-Biosensors." In ASME 2008 First International Conference on Micro/Nanoscale Heat Transfer. ASMEDC, 2008. http://dx.doi.org/10.1115/mnht2008-52195.

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For a diffusion-limited protein, the diffusion boundary layer of the analyte formed on the reaction surface hinders the binding reaction from association and dissociation. With a non-uniform AC electric field, the electrothermal force generates a pair of stirring vortices to increase the transport of the analytes to the reaction surface and thus to enhance the association or dissociation of analyte-ligand complex. This work simulates a 2-dimensional full scale finite element analysis of the binding reaction kinetics of two commonly used proteins, CRP and IgG, by applying a non-uniform AC electric field. In addition to the electrothermal stirring effect, the blocking effect of the flow field due to the existence of the reaction surface at different positions of the micro-channel could cause different degrees of enhancement to the association and the dissociation. The largest enhancement is found at the position near the negative electrode. The initial slope of the curve of the analyte-ligand complex versus time can be raised up to 5.166 times for CRP and 1.934 times for IgG in association; and 3.744 times for CRP and 1.277 times for IgG in dissociation, respectively, with a field 15 Vrms peak-to-peak and operating frequency 100 kHz.
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Rasulev, Bakhtiyor. "APPLICATION OF COMBINED DATA-DRIVEN COMPUTATIONAL CHEMISTRY AND CHEMINFORMATICS APPROACHES TO PREDICT PROPERTIES OF MATERIALS." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac,, 2021. http://dx.doi.org/10.46793/iccbi21.002r.

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For the last two decades, breakthrough research has been going on in all aspects of materials science at accelerated pace. New materials of unprecedented functionality and performance are being developed and characterized. Moreover, the new materials with improved functionality are in high demand in the marketplace and this need increases in an exponential way for the new materials of desired functionality and performance. Here we show the application of combined computational and cheminformatics methods in various materials properties prediction, including organometallic materials, polymeric materials and nanomaterials. Since most of the materials are complex entities from a chemical point of view, the investigation of them requires an interdisciplinary approach, involving multiple aspects ranging from physics and chemistry to biology and informatics. In this report we show how the combination of computational chemistry, available experimental data, machine learning and cheminformatics approaches can help in materials research and properties assessment, such as physico-chemical properties, toxicity, and biological activity. We discuss here a few case studies where data-driven models developed to reveal the relationships between the physicochemical properties, biological activity and structural characteristics, by application quantum chemical, protein-ligand docking, cheminformatics approaches and developed nanodescriptors.
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Imai, Yohsuke, Hitoshi Kondo, Young Ho Kang, Takuji Ishikawa, Chwee Teck Lim, and Takami Yamaguchi. "A Numerical Model of Adhesion Property of Malaria Infected Red Blood Cells in Micro Scale Blood Flows." In ASME 2009 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2009. http://dx.doi.org/10.1115/sbc2009-206456.

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Infection by malaria parasite changes mechanical properties of red blood cells (RBCs). Infected red blood cells (IRBCs) lose the deformability but also develop the ability to cytoadhere and rosetting. These outcomes can lead to microvascular blockage [1]. The stiffness of IRBCs [2] and its effects on the flow in micro channels [3] were studied with recent experimental techniques. The cytoadherence and rosetting properties of IRBCs have also been studied experimentally. The cytoadherence is mediated by the interaction of the parasite protein PfEMP1 with several endothelial adhesion molecules, such as CD36, intercellular adhesion molecule-1 (ICAM-1), P-selectin, and vascular cell adhesion molecule-1 (VCAM-1) [4]. In particular, the ligand-receptor interaction between PfEMP1 and CD36 shows tight adhesion [5]. Microvascular blockage may be a hemodynamic problem, involving the interactions between IRBCs, healthy RBCs (HRBCs) and endothelial cells (ECs) in flowing blood, but however experimental techniques have several limitations to this topic. First, it is still difficult to observe the RBC behavior interacting with many other cells even with the recent confocal microscopy. Second, the three-dimensional information on flow field is hardly obtained. Third, capillaries in human body are circular channels with complex geometry, but such complex channels cannot be created in micro scale. Instead, numerical modeling can overcome these problems. We presented a two-dimensional hemodynamic model involving adhesive interactions [6]. In this paper, we propose a three-dimensional model of the adhesive interactions for micro scale hemodynamics in malaria infection.
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Hsu, Kai-Cheng, Yen-Fu Chen, and Jinn-Moon Yang. "Binding Affinity Analysis of Protein-Ligand Complexes." In 2008 2nd International Conference on Bioinformatics and Biomedical Engineering. IEEE, 2008. http://dx.doi.org/10.1109/icbbe.2008.46.

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Stern, David M., Sara Rimon, Todd Scott, and Peter P. Nawroth. "MODULATION OF ENDOTHELIAL CELL COAGULANT PROPERTIES." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642946.

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As the cells forming the luminal vascular surface, endothelium is strategically located to play a role in the regulation of coagulation. Participation of endothelium in coagulation involves specific receptors on the cell surface functioning at the level of initiation and propagation of hemostatic reactions. In the anticoagulant protein C pathway, for example, the receptor thrombomodulin initiates thrombin-mediated activation of protein C and a binding site for protein S on bovine endothelium promotes assembly of the functional activated protein C/protein S complex. Endothelium also synthesizes, stores and releases functional protein S constitutively and in response to specific stimuli such as norepinephrine.Since activation of protein C requires thrombin formation in proximity to the vessel wall, we have examined procoagulant reactions on the endothelial cell surface. Endothelium provides a receptor for Factor IX/IXa which is relatively selective for the enzyme form and facilitates Factor IXa-VIII-mediated activation of Factor X. Half-maximal Factor Xa formation occurs at a Factor IXa concentration of 0.4nM on endothelium, whereas lOnM is required on liposomes. This concentration of Factor IXa corresponds to that which results in half-maximal occupancy of endothelial cell Factor IXa binding sites in the presence of Factors VIII and X, thus correlating kinetics and binding measurements. Crosslinking and ligand blotting studies have shown that the receptor is a protein with a molecular weight of ∼160,000. The clinical significance of this receptor is suggested by the moderately severe bleeding disorder observed in a patient with hemophilia B due to an abnormal Factor IX molecule, Factor IXalabama (Factor IXala). Although the coagulant activity of Factor IXala is only mildly decreased on phospholipids, it is severely impaired on endothelium. The affinity of Factor IXala for the endothelial cell Factor X activation complex is decreased by 20-fold compared with the normal enzyme and the binding affinity is similarly decreased. Since the molecular defect in Factor IXala has been previously shown to consist of a single point mutation in the growth factor domain, this indicates a role for the growth factor domain in receptor, recognition.The picture of endothelial cell coagulant properties which emerges from these and other studies is one in which endothelium has either an anticoagulant or procoagulant potential, depending on modulation of receptor expression and release of secreted products. In the quiescent state, anticoagulant mechanisms predominate with only limited amounts of procoagulant activity: there is little tissue factor activity and only a basal level of receptors for Factor IX/lXa. Activation of endothelium by Tumor Necrosis Factor (TNF) or Interleukin 1 can shift this balance. Tissue factor synthesis and expression occurs in a dose-dependent manner, being half-maximal at a TNF concentration of about 150pM. TNF also increases the number of Factor IX/lXa binding sites. Concomitant with enhancement of endothelial cell procoagulant properties is a suppression of cell surface cofactor activity for the anticoagulant protein C pathway. Endothelial cell-dependent, thrombin-mediated activated protein C formation is decreased by 70-80% and activated protein C-protein S-mediated Factor Va inactivation decreases by over 90%. Following the in vivo infusion of Interleukin 1, similar changes in endothelial cell coagulant properties were observed on aortic segments with fibrin deposition occurring on the functionally altered, but morphologically intact endothelium. This modulation of endothelial cell coagulant properties could underlie the prothrombotic state associated with inflammatory disorders and could also explain the recently observed selective intravascular thrombosis of tumor vasculature seen in vivo in meth A sarcomas after administration of TNF.Thus, although endothelium was initially felt to be hemostatically inert, this apparent lack of activity actually masks a delicate balance of procoagulant and anticoagulant mechanisms. The balance can be effectively shifted by physiologic mediators, such as monokines, which alter receptor expression on the endothelial cell surface. Changes in endothelial cell hemostatic properties may be an early indicator of vessel wall disease and underlie the pathogenesis of localized thrombotic processes.
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Reports on the topic "Protein-ligand complex"

1

Epel, Bernard, and Roger Beachy. Mechanisms of intra- and intercellular targeting and movement of tobacco mosaic virus. United States Department of Agriculture, November 2005. http://dx.doi.org/10.32747/2005.7695874.bard.

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To cause disease, plant viruses must replicate and spread locally and systemically within the host. Cell-to-cell virus spread is mediated by virus-encoded movement proteins (MPs), which modify the structure and function of plasmodesmata (Pd), trans-wall co-axial membranous tunnels that interconnect the cytoplasm of neighboring cells. Tobacco mosaic virus (TMV) employ a single MP for cell- cell spread and for which CP is not required. The PIs, Beachy (USA) and Epel (Israel) and co-workers, developed new tools and approaches for study of the mechanism of spread of TMV that lead to a partial identification and molecular characterization of the cellular machinery involved in the trafficking process. Original research objectives: Based on our data and those of others, we proposed a working model of plant viral spread. Our model stated that MPᵀᴹⱽ, an integral ER membrane protein with its C-terminus exposed to the cytoplasm (Reichel and Beachy, 1998), alters the Pd SEL, causes the Pd cytoplasmic annulus to dilate (Wolf et al., 1989), allowing ER to glide through Pd and that this gliding is cytoskeleton mediated. The model claimed that in absence of MP, the ER in Pd (the desmotubule) is stationary, i.e. does not move through the Pd. Based on this model we designed a series of experiments to test the following questions: -Does MP potentiate ER movement through the Pd? - In the presence of MP, is there communication between adjacent cells via ER lumen? -Does MP potentiate the movement of cytoskeletal elements cell to cell? -Is MP required for cell-to-cell movement of ER membranes between cells in sink tissue? -Is the binding in situ of MP to RNA specific to vRNA sequences or is it nonspecific as measured in vitro? And if specific: -What sequences of RNA are involved in binding to MP? And finally, what host proteins are associated with MP during intracellular targeting to various subcellular targets and what if any post-translational modifications occur to MP, other than phosphorylation (Kawakami et al., 1999)? Major conclusions, solutions and achievements. A new quantitative tool was developed to measure the "coefficient of conductivity" of Pd to cytoplasmic soluble proteins. Employing this tool, we measured changes in Pd conductivity in epidermal cells of sink and source leaves of wild-type and transgenic Nicotiana benthamiana (N. benthamiana) plants expressing MPᵀᴹⱽ incubated both in dark and light and at 16 and 25 ᵒC (Liarzi and Epel, 2005 (appendix 1). To test our model we measured the effect of the presence of MP on cell-to-cell spread of a cytoplasmic fluorescent probe, of two ER intrinsic membrane protein-probes and two ER lumen protein-probes fused to GFP. The effect of a mutant virus that is incapable of cell-to-cell spread on the spread of these probes was also determined. Our data shows that MP reduces SEL for cytoplasmic molecules, dilates the desmotubule allowing cell-cell diffusion of proteins via the desmotubule lumen and reduces the rate of spread of the ER membrane probes. Replicase was shown to enhance cell-cell spread. The data are not in support of the proposed model and have led us to propose a new model for virus cell-cell spread: this model proposes that MP, an integral ER membrane protein, forms a MP:vRNAER complex and that this ER-membrane complex diffuses in the lipid milieu of the ER into the desmotubule (the ER within the Pd), and spreads cell to cell by simple diffusion in the ER/desmotubule membrane; the driving force for spread is the chemical potential gradient between an infected cell and contingent non-infected neighbors. Our data also suggests that the virus replicase has a function in altering the Pd conductivity. Transgenic plant lines that express the MP gene of the Cg tobamovirus fused to YFP under the control the ecdysone receptor and methoxyfenocide ligand were generated by the Beachy group and the expression pattern and the timing and targeting patterns were determined. A vector expressing this MPs was also developed for use by the Epel lab . The transgenic lines are being used to identify and isolate host genes that are required for cell-to-cell movement of TMV/tobamoviruses. This line is now being grown and to be employed in proteomic studies which will commence November 2005. T-DNA insertion mutagenesis is being developed to identify and isolate host genes required for cell-to-cell movement of TMV.
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Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593390.bard.

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The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mutant receptors, cell lines and pheromone glands (at tissue and organism levels) against selected, designed compounds to confirm if compounds are agonists or antagonists. (2) The elucidation ofthemolecular regulationmechanisms of PBAN-R by:(a) age-dependence of gene expression; (b) the effect of hormones and; (c) PBAN-R characterization in male hair-pencil complexes. Background to the topic Insects have several closely related G protein-coupled receptors (GPCRs) belonging to the pyrokinin/PBAN family, one with the ligand pheromone biosynthesis activating neuropeptide or pyrokinin-2 and another with diapause hormone or pyrokinin-1 as a ligand. We were unable to identify the diapause hormone receptor from Helicoverpa zea despite considerable effort. A third, related receptor is activated by a product of the capa gene, periviscerokinins. The pyrokinin/PBAN family of GPCRs and their ligands has been identified in various insects, such as Drosophila, several moth species, mosquitoes, Triboliumcastaneum, Apis mellifera, Nasoniavitripennis, and Acyrthosiphon pisum. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates pheromone production in moths plus other functions indicating the pleiotropic nature of these ligands. Based on the alignment of annotated genomic sequences, the primary and secondary structures of the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors found in vertebrates. Major conclusions, solutions, achievements Evolutionary trace analysisof receptor extracellular domains exhibited several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding. Through site-directed point mutations, the 3rd extracellular domain of PBAN-R was shown to be critical for ligand selection. We identified three receptors that belong to the PBAN family of GPCRs and a partial sequence for the periviscerokinin receptor from the European corn borer, Ostrinianubilalis. Functional expression studies confirmed that only the C-variant of the PBAN-R is active. We identified a non-peptide agonist that will activate the PBAN-receptor from H. zea. We determined that there is transcriptional control of the PBAN-R in two moth species during the development of the pupa to adult, and we demonstrated that this transcriptional regulation is independent of juvenile hormone biosynthesis. This transcriptional control also occurs in male hair-pencil gland complexes of both moth species indicating a regulatory role for PBAN in males. Ultimate confirmation for PBAN's function in the male tissue was revealed through knockdown of the PBAN-R using RNAi-mediated gene-silencing. Implications, both scientific and agricultural The identification of a non-peptide agonist can be exploited in the future for the design of additional compounds that will activate the receptor and to elucidate the binding properties of this receptor. The increase in expression levels of the PBAN-R transcript was delineated to occur at a critical period of 5 hours post-eclosion and its regulation can now be studied. The mysterious role of PBAN in the males was elucidated by using a combination of physiological, biochemical and molecular genetics techniques.
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Eyal, Yoram, and Sheila McCormick. Molecular Mechanisms of Pollen-Pistil Interactions in Interspecific Crossing Barriers in the Tomato Family. United States Department of Agriculture, May 2000. http://dx.doi.org/10.32747/2000.7573076.bard.

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During the evolutionary process of speciation in plants, naturally occurring barriers to reproduction have developed that affect the transfer of genes within and between related species. These barriers can occur at several different levels beginning with pollination-barriers and ending with hybrid-breakdown. The interaction between pollen and pistils presents one of the major barriers to intra- and inter-specific crosses and is the focus of this research project. Our long-term goal in this research proposal was defined to resolve questions on recognition and communication during pollen-pistil interactions in the extended tomato family. In this context, this work was initiated and planned to study the potential involvement of tomato pollen-specific receptor-like kinases (RLK's) in the interaction between pollen and pistils. By special permission from BARD the objectives of this research were extended to include studies on pollen-pistil interactions and pollination barriers in horticultural crops with an emphasis on citrus. Functional characterization of 2 pollen-specific RLK's from tomato was carried out. The data shows that both encode functional kinases that were active as recombinant proteins. One of the kinases was shown to accumulate mainly after pollen germination and to be phosphorylated in-vitro in pollen membranes as well as in-vivo. The presence of style extract resulted in dephosphorylation of the RLK, although no species specificity was observed. This data implies a role for at least one RLK in pollination events following pollen germination. However, a transgenic plant analysis of the RLK's comprising overexpression, dominant-negative and anti-sense constructs failed to provide answers on their role in pollination. While genetic effects on some of the plants were observed in both the Israeli and American labs, no clear functional answers were obtained. An alternative approach to addressing function was pursued by screening for an artificial ligand for the receptor domain using a peptide phage display library. An enriched peptide sequence was obtained and will be used to design a peptide-ligand to be tested for its effect o pollen germination and tube growth. Self-incompatibility (SI) in citrus was studied on 3 varieties of pummelo. SI was observed using fluorescence microscopy in each of the 3 varieties and compatibility relations between varieties was determined. An initial screen for an S-RNase SI mechanism yielded only a cDNA homologous to the group of S-like RNases, suggesting that SI results from an as yet unknown mechanism. 2D gel electrophoresis was applied to compare pollen and style profiles of different compatibility groups. A "polymorphic" protein band from style extracts was observed, isolated and micro-sequenced. Degenerate primers designed based on the peptide sequence date will be used to isolate the relevant genes i order to study their potential involvement in SI. A study on SI in the apple cultivar Top red was initiated. SI was found, as previously shown, to be complete thus requiring a compatible pollinator variety. A new S-RNase allele was discovered fro Top red styles and was found to be highly homologous to pear S-RNases, suggesting that evolution of these genes pre-dated speciation into apples and pears but not to other Rosaceae species. The new allele provides molecular-genetic tools to determine potential pollinators for the variety Top red as well as a tool to break-down SI in this important variety.
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