Modélisation de protéines par homologie

Résumé

thumb|Modélisation de protéines par homologie La modélisation de protéines par homologie, également connue sous le nom de modélisation comparative des protéines, se réfère à la construction d’un modèle d’une protéine « cible », dont la résolution est de niveau atomique, à partir de sa séquence d’acides aminés et d'une structure expérimentale tridimensionnelle d’une protéine homologue connexe (le « modèle »). La modélisation par homologie repose sur l’identification d’une ou plusieurs structures protéiques connues susceptibles de ressembler à la structure de la séquence d’acides aminés recherchée et sur la production d’un alignement qui mappe des résidus (un acide aminé à l’intérieur d’une chaîne peptidique) dans la séquence d’acides aminés recherchée à des résidus dans la séquence d’acides aminés modèle. Cela repose sur l'intuition que la forme d'une protéine dépend de sa composition chimique, et notamment des interactions entre les différents champs de force générés par les atomes d

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https://fr.wikipedia.org/wiki/Mod%C3%A9lisation_de_prot%C3%A9ines_par_homologie

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La prédiction de la structure des protéines est l'inférence de la structure tridimensionnelle des protéines à partir de leur séquences d'acides aminés, c'est-à-dire la prédiction de leur pliage et d

redresse=1.36|vignette|Représentation d'une protéine, ici deux sous-unités d'une molécule d'hémoglobine. On observe les représentées en couleur, ainsi que deux des quatre molécules d'hème, qui sont l

La bioinformatique (ou bio-informatique), est un champ de recherche multidisciplinaire de la biotechnologie où travaillent de concert biologistes, médecins, informaticiens, mathématiciens, physicien

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P4-ATPases (flippases) translocate specific phospholipids such as phosphatidylserine from the exoplasmic leaflet of the cell membrane to the cytosolic leaflet, upholding an essential membrane asymmetry. The mechanism of flipping this giant substrate has remained an enigma. We have investigated the importance of amino acid residues in transmembrane segment M4 of mammalian P4-ATPase ATP8A2 by mutagenesis. In the related ion pumps Na+, K+-ATPase and Ca2+-ATPase, M4 moves during the enzyme cycle, carrying along the ion bound to a glutamate. In ATP8A2, the corresponding residue is an isoleucine, which recently was found mutated in patients with cerebellar ataxia, mental retardation, and dysequilibrium syndrome. Our analyses of the lipid substrate concentration dependence of the overall and partial reactions of the enzyme cycle in mutants indicate that, during the transport across the membrane, the phosphatidylserine head group passes near isoleucine-364 (I364) and that I364 is critical to the release of the transported lipid into the cytosolic leaflet. Another M4 residue, N359, is involved in recognition of the lipid substrate on the exoplasmic side. Our functional studies are supported by structural homology modeling and molecular dynamics simulations, suggesting that I364 and adjacent hydrophobic residues function as a hydrophobic gate that separates the entry and exit sites of the lipid and directs sequential formation and annihilation of water-filled cavities, thereby enabling transport of the hydrophilic phospholipid head group in a groove outlined by the transmembrane segments M1, M2, M4, and M6, with the hydrocarbon chains following passively, still in the membrane lipid phase.

Natl Acad Sciences2014

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Crystallization of gas-selective nanoporous graphene by competitive etching and growth: a modeling study

Kumar Varoon Agrawal, Soumajit Dutta, Mojtaba Rezaei

A robust synthesis methodology for crystallizing nanoporous single-layer graphene hosting a high density of size-selective nanopores is urgently needed to realize the true potential of two-dimensional membranes for gas separation. Currently, there are no controllable etching techniques for single-layer graphene that are self-limiting, and that can generate size-selective nanopores at a high pore-density. In this work, we simulate a unique chemical vapor deposition based crystallization of graphene on Cu(111), in the presence of an etchant, to generate a high density (>10(13) cm(-2)) of sub-nanometer-sized, elongated nanopores in graphene. An equilibrium between the growth rate and the etching rate is obtained, and beyond a critical time, the total number of the carbon atoms and the edge carbon atoms do not change. Using an optimal first-order etching chemistry, a log-mean pore-size of 5.0 +/- 1.7 (number of missing carbon atoms), and a pore-density of 3 x 10(13) cm(-2) was achieved. A high throughput calculation route for estimating gas selectivity from ensembles of thousands of nanopores was developed. The optimized result yielded H-2/CO2, H-2/N-2 and H-2/CH4 selectivities larger than 200, attributing to elongated pores generated by the competitive etching and growth. The approach of competitive etching during the crystal growth is quite generic and can be applied to a number of two-dimensional materials.

2019

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Proof of concept of a dual-band circularly-polarized RF MEMS beam-switching reflectarray

Caner Güçlü, Julien Perruisseau-Carrier

In this communication we propose the concept of a circularly polarized reflectarray (RA) antenna capable of independent beam-switching in both K and Ka bands. The RA unit cell comprises one microstrip ring per each operation frequency. Each ring is integrated with six equally spaced series RF micro electro-mechanical systems (RF MEMS) switches, which allows implementing the sequential rotation principle formerly used in circularly-polarized RA for single-frequency operation. A detailed design is proposed, considering the best relative arrangement of the rings corresponding to each frequency, the accurate modeling of the RF MEMS switches, and the full-wave simulation of the full array. The designed RA is implemented on a 4-inch quartz wafer and comprises 109 K-band and 124 Ka-band split-rings. Two prototypes representing two frozen states of the reconfigurable antenna are fabricated and measured. The designed RA can +/- 120 degrees provide progressive phase difference in both operation bands exhibiting beam switching to +/- 35 degrees and +/- 24 degrees off the broad-side in K and Ka bands respectively. The performance of the designed antenna is verified by the agreement of the measured and simulated radiation patterns.

Institute of Electrical and Electronics Engineers2012

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