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Relevant bibliographies by topics / Hydrophobic Cluster Analysis

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Academic literature on the topic 'Hydrophobic Cluster Analysis'

Author: Grafiati

Published: 4 June 2021

Last updated: 3 February 2022

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Journal articles on the topic "Hydrophobic Cluster Analysis"

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Coutinho, Pedro M., and Peter J. Reilly. "Structural similarities in glucoamylases by hydrophobic cluster analysis." "Protein Engineering, Design and Selection" 7, no. 6 (1994): 749–60. http://dx.doi.org/10.1093/protein/7.6.749.

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Lemesle-Varloot, L., V. Bissery, A. Morgat, C. Gaboriaud, and J. P. Mornon. "Hydrophobic cluster analysis: a tool for protein modeling." Journal of Molecular Graphics 7, no. 3 (September 1989): 171. http://dx.doi.org/10.1016/0263-7855(89)80024-4.

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Raimbaud, E., A. Buléon, S. Perez, and B. Henrissat. "Hydrophobic cluster analysis of the primary sequences of α-amylases." International Journal of Biological Macromolecules 11, no. 4 (August 1989): 217–25. http://dx.doi.org/10.1016/0141-8130(89)90072-x.

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Bitard-Feildel, Tristan, Magdalena Heberlein, Erich Bornberg-Bauer, and Isabelle Callebaut. "Detection of orphan domains in Drosophila using “hydrophobic cluster analysis”." Biochimie 119 (December 2015): 244–53. http://dx.doi.org/10.1016/j.biochi.2015.02.019.

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Matsumoto, H., Ismail E. Rozi, K. Tsugika, Y. Seki, and K. Soda. "3P074 Analysis of Contributions of Hydrophobic Cluster Residues to Protein Folding." Seibutsu Butsuri 44, supplement (2004): S208. http://dx.doi.org/10.2142/biophys.44.s208_2.

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Woodcock, Steve, Jean-Paul Mornon, and Bernard Henrissat. "Detection of secondary structure elements in proteins by hydrophobic cluster analysis." "Protein Engineering, Design and Selection" 5, no. 7 (1992): 629–35. http://dx.doi.org/10.1093/protein/5.7.629.

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Silva, Pedro J. "Assessing the reliability of sequence similarities detected through hydrophobic cluster analysis." Proteins: Structure, Function, and Bioinformatics 70, no. 4 (October 5, 2007): 1588–94. http://dx.doi.org/10.1002/prot.21803.

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Kellenberger, Stephan, James W. West, Todd Scheuer, and William A. Catterall. "Molecular Analysis of the Putative Inactivation Particle in the Inactivation Gate of Brain Type IIA Na+ Channels." Journal of General Physiology 109, no. 5 (May 1, 1997): 589–605. http://dx.doi.org/10.1085/jgp.109.5.589.

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Fast Na+ channel inactivation is thought to involve binding of phenylalanine 1489 in the hydrophobic cluster IFM in LIII-IV of the rat brain type IIA Na+ channel. We have analyzed macroscopic and single channel currents from Na+ channels with mutations within and adjacent to hydrophobic clusters in LIII-IV. Substitution of F1489 by a series of amino acids disrupted inactivation to different extents. The degree of disruption was closely correlated with the hydrophilicity of the amino acid at position 1489. These mutations dramatically destabilized the inactivated state and also significantly slowed the entry into the inactivated state, consistent with the idea that F1489 forms a hydrophobic interaction with a putative receptor during the fast inactivation process. Substitution of a phe residue at position 1488 or 1490 in mutants lacking F1489 did not restore normal inactivation, indicating that precise location of F1489 is critical for its function. Mutations of T1491 disrupted inactivation substantially, with large effects on the stability of the inactivated state and smaller effects on the rate of entry into the inactivated state. Mutations of several other hydrophobic residues did not destabilize the inactivated state at depolarized potentials, indicating that the effects of mutations at F1489 and T1491 are specific. The double mutant YY1497/8QQ slowed macroscopic inactivation at all potentials and accelerated recovery from inactivation at negative membrane potentials. Some of these mutations in LIII-IV also affected the latency to first opening, indicating coupling between LIII-IV and channel activation. Our results show that the amino acid residues of the IFM hydrophobic cluster and the adjacent T1491 are unique in contributing to the stability of the inactivated state, consistent with the designation of these residues as components of the inactivation particle responsible for fast inactivation of Na+ channels.

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Henrissat, Bernard, Markku Saloheimo, Stéphane Lavaitte, and Jonathan K. C. Knowles. "Structural homology among the peroxidase enzyme family revealed by hydrophobic cluster analysis." Proteins: Structure, Function, and Genetics 8, no. 3 (1990): 251–57. http://dx.doi.org/10.1002/prot.340080307.

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Xiang, Heng, Ruizhi Zhang, Nengzhang Li, and Charles R. Vossbrinck. "Searching for convergent evolution in manganese superoxidase dismutase using hydrophobic cluster analysis." Genetics and Molecular Biology 37, no. 2 (May 13, 2014): 460–70. http://dx.doi.org/10.1590/s1415-47572014005000008.

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Dissertations / Theses on the topic "Hydrophobic Cluster Analysis"

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Le, Tuan Khanh. "Hydrophobic Cluster analysis : prédiction de structures secondaires à partir d'une séquence unique : implémentation de la procédure "Secondary Structure Prediction" (SSP)." Paris 6, 2003. http://www.theses.fr/2003PA066541.

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Albeau, Karine. "Analyse à grande échelle des textures des séquences protéiques via l'approche Hydrophobic Cluster Analysis (HCA)." Phd thesis, Université de Versailles-Saint Quentin en Yvelines, 2005. http://tel.archives-ouvertes.fr/tel-00011139.

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Découper, a priori et de façon précise, les séquences en domaines est d'une grande importance dans le champ de la biologie, notamment pour optimiser les études de génomique structurale et de génomique fonctionnelle. Différentes approches basées sur la composition en acides aminés, la complexité de la séquence ou la construction de modèles 3D ab initio, ont été développées par le passé. Nous proposons, dans le cadre de ce travail, une approche nouvelle et originale pour le découpage automatique et sensible des séquences protéiques en domaines structurés distincts par exploitation de leur texture. Cette approche bénéficie de l'information de voisinage 2D apportée par la méthodologie « Hydrophobic Cluster Analysis » (HCA). La distribution des différentes catégories d'amas hydrophobes, tels que définis par l'intermédiaire de HCA, ainsi que l'analyse de leurs caractéristiques en termes de structures secondaires, permettent d'appréhender de façon différenciée les textures des régions globulaires, non globulaires et/ou désordonnées, répétitives, passages membranaires isolés ou multiples.... L'approche développée, DomHCA, permet in fine de segmenter une séquence protéique en une série de régions et sous-régions caractérisées par des textures précises, segmentation qui, appliquée à l'échelle des génomes, autorise une comparaison rapide et originale de l'ensemble des séquences. Une des applications concerne les séquences du génome de Plasmodium falciparum qui, par leurs fortes proportions en acides aminés N et K, rendent les méthodes classiques de détection de similarité peu efficaces.

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Levivier, Emilie. "Exploration des similitudes de séquences protéiques à haut niveau de divergence évolutive : perspectives de l'approche Hydrophobic Cluster Analysis (HCA)." Paris 7, 2003. http://www.theses.fr/2003PA077069.

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Hennetin, Jérôme. "Texture hydrophobe HCA des séquences protéiques : regards sur les introns." Paris 7, 2003. http://www.theses.fr/2003PA077055.

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

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Dulin, Fabienne. "Exploration des caractéristiques tridimensionnelles des amas protéiques hydrophobes issus du formalisme "Hydrophobic Cluster Analysis" (HCA) : modélisation de formes oligomériques solubles du peptide Aβ impliqué dans la maladie d'Alzheimer, et identification d'un 'point chaud" commun à différentes protéines amyloïdes." Paris 6, 2006. http://www.theses.fr/2006PA066465.

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Nous avons d’abord exploré les caractéristiques 3D des amas d’acides aminés hydrophobes issus de la méthode "Hydrophobic Cluster Analysis" (HCA), au travers d’une représentation originale en tesselation de Voronoï. Chaque amas peut être ainsi caractérisé dans ses conformations  ou  et ses affinités préférentielles pour d’autres amas peuvent être décrites. Le repliement protéique peut alors être décrit comme l’assemblage de ces amas HCA 3D. Nous avons ensuite construit, en utilisant des outils d’alignement tels que HCA, des modèles 3D des formes oligomériques solubles du peptide A. Ce peptide, impliqués dans la maladie d’Alzheimer, serait neurotoxique sous cette forme soluble. Ce travail nous a permis de proposer une hypothèse expliquant le comportement différencié de p3, sans la région N-terminale d’A. Enfin, nous avons pu mettre en évidence la présence d’un ou plusieurs "points chauds" communs aux protéines amyloïdes, pouvant être à l’origine de leur propriété à former des fibres.

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Bissery, Véronique. "Contribution au développement de la méthode Hydrophobic Cluster Analysis HCA d'exploitation des séquences de protéines : application à la superfamille des récepteurs des hormones stéroïdiennes et de l'acide rétinoi͏̈que, modélisation du domaine de liaison à l'hormone du récepteur androgène." Paris 5, 1989. http://www.theses.fr/1989PA05P625.

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Carrière, Cathelène. "Caractérisation des structures et fonctions de la phosphorylase kinase." Paris 6, 2008. http://www.theses.fr/2008PA066419.

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La phosphorylase kinase (PhK), enzyme clé de la glycogénolyse, est un complexe hexadécamérique formé de quatre sous-unités différentes (alpha, beta, gamma, delta)4. L’activité catalytique portée par la PhK gamma est modifiée par l’action des sous-unités apparentées alpha et beta (4/5 de la masse de l’enzyme). Des mutations dans la PhK conduisent à une maladie de stockage du glycogène (GSD) de type IX, le désordre le plus répandu dans le métabolisme du glycogène. Peu de choses sont connues sur la structure de l’holoenzyme et sur celle des sous-unités de la PhK (exception faite du domaine catalytique de la PhK gamma et de la PhK delta (calmoduline)). Dans cette thèse, nous avons utilisé des méthodes d’analyse de séquences pour révéler des caractéristiques structurales et fonctionnelles des sous-unités alpha et beta. Nous avons ainsi confirmé l’appartenance du premier domaine (A) à la famille des glucoamylases (Glycosyl Hydrolase 15) et montré que les domaines C et D sont reliés aux protéines « calcineurin B-like », membres de la famille EF-hand impliqués dans la régulation calcium-dépendante de kinases. La plupart des mutations faux-sens affectant la PhK alpha et conduisant à une déficience en PhK sont situées dans les sites actifs de ces domaines, suggérant qu’elles pourraient avoir un impact direct sur leurs fonctions. Par ailleurs, nous avons recalé dans le volume obtenu par cryo-microscopie électronique (résolution 9. 9 Angstrom) les structures 3D des différents domaines de la PhK en nous aidant des contraintes décrites dans la littérature. L’ensemble de ces résultats ouvre de nouvelles perspectives pour comprendre comment les sous-unités de la PhK régulent son activité
Phosphorylase kinase (PhK) is a key enzyme in glycogenolysis. PhK is a hexadecameric complex, made of four different subunits (alpha, beta, gamma, delta)4. Catalytic activity is conferred by the gamma subunit and is modified by the two related regulatory subunits alpha and beta which together account for ~ 4/5 of the PhK mass. Mutations in PhK lead to Glycogen Storage Disease (GSD) type IX, which is the most frequently encountered disorder of glycogen metabolism. The structural features of the quaternary structure of the holoenzyme and the PhK subunits, except for the catalytic domain of the PhK gamma and the PhK delta subunit are poorly understood. Here we have used sensitive methods of sequence analysis to unravel hidden structural and functional features of the PhK alpha and beta subunits. We confirm that the first domain (A) belongs to the glucoamylase family (Glycosyl Hydrolase 15) and show domains C and D are related to calcineurin B-like proteins, which are EF-hand family members involved in the Ca2+-dependent regulation of kinases. Mutations leading PhK deficiency, mostly missense mutations in PhK alpha, are located within the predicted active sites of these domains, suggesting that they may have a direct impact on their predicted functions. Furthermore, we docked the 3D structures of the different PhK domains into the volume obtained by cryo-electron microscopy at 9. 9 Angstrom resolution constraining with various interaction data reported in the literature. Altogether, our findings open new perspectives to understand how the different PhK subunits may regulate the holoenzyme activity

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Book chapters on the topic "Hydrophobic Cluster Analysis"

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Azevedo, Paulo J., Cândida G. Silva, J. Rui Rodrigues, Nuno Loureiro-Ferreira, and Rui M. M. Brito. "Detection of Hydrophobic Clusters in Molecular Dynamics Protein Unfolding Simulations Using Association Rules." In Biological and Medical Data Analysis, 329–37. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11573067_33.

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Vanderheeren, G., and I. Hanssens. "The Perception of Hydrophobic Clusters in the Native and Partially Unfolded States of a Protein." In Proteome and Protein Analysis, 211–24. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-642-59631-5_15.

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Semertzidis, Michel T., Etienne Thoreau, Anne Tasso, Bernard Henrissat, Isabelle Callebaut, and Jean Paul Mornon. "Visualization of Protein Sequences Using the Two-Dimensional Hydrophobic Cluster Analysis Method." In Visualizing Biological Information, 129–44. WORLD SCIENTIFIC, 1995. http://dx.doi.org/10.1142/9789812832054_0012.

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Conference papers on the topic "Hydrophobic Cluster Analysis"

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Chen, Peng-Yu, Wei-Hui Chen, and Che-Wun Hong. "Nanofludic Analysis on Methanol Crossover of Direct Methanol Fuel Cells." In ASME 2008 First International Conference on Micro/Nanoscale Heat Transfer. ASMEDC, 2008. http://dx.doi.org/10.1115/mnht2008-52095.

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Direct methanol fuel cells (DMFCs) are considered as a competitive power source candidate for portable electronic devices. Nafion® has been widely used for the electrolyte of DMFCs because of its good proton conductivity and high chemical and mechanical stability. However, the major problem that must be solved before commercialization is the high methanol crossover through the membrane. There are a number of studies on experiments about the methanol crossover rate through the membrane but only few theoretical investigations have been presented [1–3]. In this paper, an atomistic model [4] is presented to analyze the molecular structure of the electrolyte and dynamic properties of nanofluids at different methanol concentration. In the same time, the nano-scopic phenomenon of methanol crossover through the membrane is observed. The simulation system consists of the Nafion fragments, hydronium ions, water clusters and methanol molecules. Fig. 1 shows the simplified Nafion fragment in our simulation. Both intra- and inter-molecular interactions were involved in this study. Intermolecular interactions include the van der Waals and the electrostatic potentials. Intramolecular interactions consist of bond, angle and dihedral potentials. The force constants used above were determined from the DREIDING force field. The SPC/E model was employed for water molecules. The three-site OPLS potential model was utilized for the intermolecular potential in methanol. Each proton which migrates inside the electrolyte is assumed to combine with one water molecule to form the hydronium (H3O+). The force parameters for the hydronium were taken from Burykin et al [5]. The atomistic simulation was carried out on the software DLPOLY. First, a 500 ps NPT ensemble was performed to make the system reach a proper configuration. This step was followed by another 500 ps NVT simulation. All molecular simulations were performed at a temperature of 323K with three-dimensional periodic boundary conditions. The intermolecular interactions were truncated at 10 Å and the equations of motion were solved using the Verlet scheme with a time step of 1 fs. Fig. 2 shows the calculated density of the simulation system for different methanol concentrations at 323K. It can be seen that the density decreases with the methanol uptakes. The volume of the system increases as the methanol concentration increases, which means that the membrane swelling with methanol uptakes. The radial distribution functions (RDFs) of the ether-like oxygen (O2) toward water and methanol molecules for different methanol concentrations at 323K are shown in Fig. 3. From this figure, we find that methanol molecules can reside in the vicinity of the hydrophobic part of the side chain while water can not. Fig. 4 shows the RDFs between the oxygen atom of the sulfonic acid groups (O3) and solvents for different methanol concentrations at 323K. As shown in Fig. 4, both water and methanol have a tendency to cluster near the sulfonic acid groups, but water molecules prefer to associate with the sulfonic acid groups in comparison with methanol molecules. The mean square displacements (MSDs) of water and methanol molecules for different methanol concentrations at 323K are displayed in Fig. 5. It is shown that MSD curves have a linear tendency, which means both water and methanol molecules are diffusing in the system during the simulation. As the methanol concentration increases, the slope of MSD curve increases for methanol and decreases for water. This indicates higher methanol content constrains the mobility of water molecules but enhances the mobility of methanol molecules that cross the electrolyte. In summary, molecular simulations of the Nafion membrane swollen in different methanol concentrations (0, 11.23, 21.40, 46.92 wt%) at 323K have been carried out. Both methanol migration mechanism and hydronium diffusion phenomenon have been visualized by monitoring the trajectories of the specific species in the system. MSDs are used to evaluate the mobility and shows that the higher the methanol concentration, the greater the tendency of methanol crossover.

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Handa, M., K. Titani, K. Takio, and Z. M. Ruggeri. "CHARACTERIZATION OF THE VON WILLEBRAND FACTOR-BINDING DOMAIN OF PLATELET MEMBRANE GLYCOPROTEIN Ib." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642925.

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We have previously obtained immunochemical evidence that the von Willebrand factor (vWF)-binding domain of the platelet membrane glycoprotein (GP) Ib is located near the amino terminus of the a subunit (Journal of Biological Chemistry 261: 12579-12585, 1986). We have now determined the complete amino acid sequence of the 45 kDa tryptic fragment of glycocalicin that contains this domain. Purified glycocalicin was subjected to limited digestion with trypsin and the proteolytic fragments were separated by size-exclusion high-pressure liquid chromatography. Two fragments of 45 kDa and 84 kDa, respectively, were obtained under nonreducing conditions. After reduction and S-carboxymethylation, the 84 kDa fragment was unchanged, while the 45 kDa fragment yielded two new fragments, one of 35 kDa and the other of 7 kDa. This finding proves the existence of a trypsin cleavage site within a disulfide loop. Two primary sets of overlapping fragments were obtained by cleavage of the carboxymethylated protein at methionyl and lysyl bonds following treatment with cyanogen bromide and Achromobacter protease I, respectively. Additional fragments were obtained by treatment of glycocalicin with Staphylococcus aureus V8 protease and Serratia marcescens protease. Analysis of all these fragments provided data that allowed determination of the sequence of the amino terminal 299 residues of the GP Ib a-chain. This includes the 45 kDa tryptic fragment containing the vWF-binding domain. This 299-residue sequence, corresponding approximately to two thirds of the α-chain polypeptide, is largely hydrophobic and contains only two N-linked and one O-linked carbohydrate chains. A hydrophilic region exists between residues 215-299, with a cluster of ten negatively charged residues at 269-287. This area is likely to attract positively charged molecules. The hydrophilic, highly glycosylated (at Ser/Thr residues) region corresponding to the previously described "macroglycopeptide" begins at residue 292. The determined sequence of glycocalicin contains a region with seven repeats, indicative of gene duplication, and is highly homologous to human leucine-rich α2-glycoprotein.

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