Search results for "Models"
showing 10 items of 8211 documents
Design and Synthesis of 4-Substituted Indolo[3,2-e][1,2,3]triazolo[1,5-a]pyrimidine Derivatives with Antitumor Activity
2008
New derivatives of the indolo[3,2- e][1,2,3]triazolo[1,5- a]pyrimidine system, substituted in the 4 position, were designed as novel antitumor agents because of their theoretical capability to form stable complexes with DNA fragments. The calculated free energies of binding were found in the range -12.76 --> -39.68 Kcal/mol. The docking studies revealed a common binding mode with the chromophore intercalated between GC base pairs, whereas the side chain lies along the minor groove. Compounds, selected on the basis of the docking studies and suitably synthesized, showed antiproliferative activity against each type of tumor cell line investigated, generally in the low micromolar range. The mo…
Structures of yeast peroxisomal Δ(3),Δ(2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks f…
2015
Δ3,Δ2-Enoyl-CoA isomerases (ECIs) catalyze the shift of a double bond from 3Z- or 3E-enoyl-CoA to 2E-enoyl-CoA. ECIs are members of the crotonase superfamily. The crotonase framework is used by many enzymes to catalyze a wide range of reactions on acyl-CoA thioesters. The thioester O atom is bound in a conserved oxyanion hole. Here, the mode of binding of acyl-CoA substrate analogues to peroxisomalSaccharomyces cerevisiaeECI (ScECI2) is described. The best defined part of the bound acyl-CoA molecules is the 3′,5′-diphosphate-adenosine moiety, which interacts with residues of loop 1 and loop 2, whereas the pantetheine part is the least well defined. The catalytic base, Glu158, is hydrogen-bo…
Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predi…
1997
We have developed an automatic approach for homology modeling using restrained molecular dynamics and simulated annealing procedures, together with conformational search algorithms available in the molecular mechanics program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168). The accuracy of the method is validated by "predicting" structures of two homeodomain proteins with known three-dimensional structures, and then applied to predict the three-dimensional structure of the homeodomain of the murine Msx-1 transcription factor. Regions of the unknown protein structure that are highly homologous to the known template structure are constrained by "homology distance constraints,"…
Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon
2021
18 páginas, 7 figuras, 2 tablas
Nano-materials for use in sensing of salmonella infections: Recent advances
2016
Salmonella infectious diseases spreading every day through food have become a life-threatening problem for millions of people and growing menace to society. Health expert's estimate that the yearly cost of all the food borne diseases is approximately $5-6 billion. Traditional methodologies for salmonella analysis provide high reliability and very low limits of detection. Among them immunoassays and Nucleic acid-based assays provide results within 24h, but they are expensive, tedious and time consuming. So, there is an urgent need for development of rapid, robust and cost-effective alternative technologies for real-time monitoring of salmonella. Several biosensors have been designed and comm…
Reversed Enantioselectivity of Diisopropyl Fluorophosphatase against Organophosphorus Nerve Agents by Rational Design
2009
Diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris is an efficient and robust biocatalyst for the hydrolysis of a range of highly toxic organophosphorus compounds including the nerve agents sarin, soman, and cyclosarin. In contrast to the substrate diisopropyl fluorophosphate (DFP) the nerve agents possess an asymmetric phosphorus atom, which leads to pairs of enantiomers that display markedly different toxicities. Wild-type DFPase prefers the less toxic stereoisomers of the substrates which leads to slower detoxification despite rapid hydrolysis. Enzyme engineering efforts based on rational design yielded two quadruple enzyme mutants with reversed enantioselectivity and overall en…
Small-angle X-ray scattering reveals compact domain-domain interactions in the N-terminal region of filamin C
2014
Filamins are multi-domain, actin cross-linking, and scaffolding proteins. In addition to the actin cross-linking function, filamins have a role in mechanosensor signaling. The mechanosensor function is mediated by domain-domain interaction in the C-terminal region of filamins. Recently, we have shown that there is a three-domain interaction module in the Nterminal region of filamins, where the neighboring domains stabilize the structure of the middle domain and thereby regulate its interaction with ligands. In this study, we have used small-angle X-ray scattering as a tool to screen for potential domain-domain interactions in the N-terminal region. We found evidence of four domain-domain in…
Magneto-optical nanomaterials: a SPIO–phthalocyanine scaffold built step-by-step towards bimodal imaging
2013
A SPIO-phthalocyanine nanohybrid is developed as a bimodal contrast agent for Optical and Magnetic Resonance Imaging. The organic coating was covalently attached onto SPIO in a step-by-step approach. Each coated-SPIO was thoroughly characterized. The hydrodynamic size of the SPIO-Pc is ca. 60 nm with a coverage of ca. 690 Pc/SPIO.
Use of a reduced Schiff-Base ligand to prepare novel chloro-bridged chains of rare Cu(II) trinuclear complexes with mixed azido/oxo and chloro/oxo br…
2010
Two mixed bridged one-dimensional (1D) polynuclear complexes, [Cu(3)L(2)(mu(1,1)-N(3))(2)(mu-Cl)Cl](n) (1) and {[Cu(3)L(2)(mu-Cl)(3)Cl].0.46CH(3)OH}(n) (2), have been synthesized using the tridentate reduced Schiff-base ligand HL (2-[(2-dimethylamino-ethylamino)-methyl]-phenol). The complexes have been characterized by X-ray structural analyses and variable-temperature magnetic susceptibility measurements. In both complexes the basic trinuclear angular units are joined together by weak chloro bridges to form a 1D chain. The trinuclear structure of 1 is composed of two terminal square planar [Cu(L)(mu(1,1)-N(3))] units connected by a central Cu(II) atom through bridging nitrogen atoms of end…
Syntheses, structures, and magnetic properties of diphenoxo-bridged Cu(II)Ln(III) and Ni(II)(low-spin)Ln(III) compounds derived from a compartmental …
2010
Syntheses, characterization, and magnetic properties of a series of diphenoxo-bridged discrete dinuclear M(II)Ln(III) complexes (M = Cu or Ni, Ln = Ce-Yb) derived from the compartmental Schiff base ligand, H(2)L, obtained on condensation of 3-ethoxysalicylaldehyde with trans-1,2-diaminocyclohexane, are described. Single crystal X-ray structures of eight Cu(II)Ln(III) compounds (Ln = Ce (1), Pr (2), Nd (3), Sm (4), Tb (7), Ho (9), Er (10), and Yb (12)) and three Ni(II)Ln(III) (Ln = Ce (13), Sm (16), and Gd (18)) compounds have been determined. Considering the previously reported structure of the Cu(II)Gd(III) (6) compound (Eur. J. Inorg. Chem. 2005, 1500), a total of twelve structures are di…