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De-epoxidation of Violaxanthin after Reconstitution into Different Carotenoid Binding Sites of Light-harvesting Complex II

2001

In higher plants, the de-epoxidation of violaxanthin (Vx) to antheraxanthin and zeaxanthin is required for the pH-dependent dissipation of excess light energy as heat and by that process plays an important role in the protection against photo-oxidative damage. The de-epoxidation reaction was investigated in an in vitro system using reconstituted light-harvesting complex II (LHCII) and a thylakoid raw extract enriched in the enzyme Vx de-epoxidase. Reconstitution of LHCII with varying carotenoids was performed to replace lutein and/or neoxanthin, which are bound to the native complex, by Vx. Recombinant LHCII containing either 2 lutein and 1 Vx or 1.6 Vx and 1.1 neoxanthin or 2.8 Vx per mono…

Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations.

2007

Decapping is a central step in eukaryotic mRNA turnover and in gene expression regulation. The human scavenger decapping enzyme, DcpS, catalyses cap hydrolysis following mRNA degradation. DcpS is a dimeric enzyme, with two active sites. Crystal structures suggest that DcpS must undergo significant conformational changes upon ligand binding, but the mechanism of this transition is unknown. Here, we report two long timescale (20 ns) molecular dynamics simulations of the apo-form of DcpS. The dimer is observed to undergo a strikingly cooperative motion, with one active site closing while the other opens. The amplitude of the conformational change is 6–21 A and the apparent timescale is 4–13 ns…

Photoaffinity cross-linking of F1ATPase from the thermophilic bacterium PS3 by 3′-arylazido-β-alanyl-2-azido ATP

1989

AbstractThe photoactivatable bifunctional 3′-arylazido-β-alanyl-2-azido ATP (2,3′-DiN3ATP) has been applied to study the localization of the nucleotide-binding sites of coupling factor 1 (F1ATPase, TF1) from the thermophilic bacterium PS3 by photoaffinity cross-linking. UV irradiation of TF1 in the presence of 2,3′-DiN3ATP results in the nucleotide-dependent formation of various higher molecular mass cross-links formed by two, three or even four α- and/or β-subunits. The differences observed upon photoaffinity cross-linking by the bifunctional 2-azido ATP or 8-azido ATP analog are discussed. They are probably due to the varied maximal distance between both azido groups, or to the different …

Incorporation of Membrane Proteins in Solid-Supported Lipid Layers

1995

Citrate Sensing by the C 4 -Dicarboxylate/Citrate Sensor Kinase DcuS of Escherichia coli : Binding Site and Conversion of DcuS to a C 4 -Dicarboxylat…

2007

ABSTRACT The histidine protein kinase DcuS of Escherichia coli senses C 4 -dicarboxylates and citrate by a periplasmic domain. The closely related sensor kinase CitA binds citrate, but no C 4 -dicarboxylates, by a homologous periplasmic domain. CitA is known to bind the three carboxylate and the hydroxyl groups of citrate by sites C1, C2, C3, and H. DcuS requires the same sites for C 4 -dicarboxylate sensing, but only C2 and C3 are highly conserved. It is shown here that sensing of citrate by DcuS required the same sites. Binding of citrate to DcuS, therefore, was similar to binding of C 4 -dicarboxylates but different from that of citrate binding in CitA. DcuS could be converted to a C 4 -…

Photoaffinity labeling of the coupling factor 1 from the thermophilic bacterum PS3 by 8-azido ATP

1984

AbstractTo localize the nucleotide binding sites of the F1ATPase (TF1) from the thermophilic bacterium PS3 we have used 14C-labeled 8-azido ATP (8-N3ATP) as photoaffmity label. 8-N3ATP is hydrolyzed by the F,ATPase in the absence of ultraviolet light. Irradiation by ultraviolet light of the enzyme in the presence of 8-N3ATP results in reduction of ATPase activity and in preferential nucleotide specific labeling of the α subunits (0.8–0.9 mol 8-N3ATP/TF1,α:β = 4:1). Inactivation and labeling do not depend on the presence of Mg2+. Both effects decrease upon addition of various nucleotide di- or triphosphates.

Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Dynamics in the …

2020

<p>We here investigate the mechanism of SARS-CoV-2 3CL protease inhibition by one of the most promising families of inhibitors, those containing an aldehyde group as warhead. These compounds are covalent inhibitors that inactivate the protease forming a stable hemithioacetal complex. Inhibitor 11a is a potent inhibitor that has been already tested in vitro and in animals. Using a combination of classical and QM/MM simulations we determined the binding mode of the inhibitor into the active site and the preferred rotameric state of the catalytic histidine. In the noncovalent complex the aldehyde group is accommodated into the oxyanion hole formed by the NH main chain groups of residues …

Chiral synthetic pseudopeptidic derivatives as triplet excited state quenchers

2009

The behavior of 6 pseudopeptidic models, synthesized by connecting different protected amino acids (Trp, Tyr, Phe, and Lys) with various diamino spacers, as quenchers of the triplet excited state of tiaprofenic acid (and its methyl ester), has been investigated. A series of quenching constants have been determined, which depend on the nature of the quencher and on the stereochemistry of the excited drug. A significant degree of stereodifferentiation has been found for the peptidomimetic synthesized with Phe and Tyr linked by a piperazine bridge. The obtained results support the utility of laser flash photolysis (LFP) as a tool to investigate the interactions between photoexcited drugs and s…

Impact of amino acids 22-27 of Rho-subfamily GTPases on glucosylation by the large clostridial cytotoxins TcsL-1522, TcdB-1470 and TcdB-8864

1999

Here we report data describing some principles of the interaction between small GTP-binding proteins and large Clostridial cytotoxins (LCTs). Our investigation was based on the differential glucosylation of Rac1 versus RhoA by LCTs TcsL-1522, TcdB-1470 and TcdB-8864. Chimeric RhoA/Rac1 proteins and GTPases mutated at defined regions or single amino acids were used as substrates. Starting with chimeric Rac/Rho proteins we demonstrated that proteins containing the N-terminal 73 amino acids of Rac1 (but not those of RhoA) were efficiently glucosylated. Within this stretch, three regions differ significantly in Rac1 and RhoA. Regions containing amino acids 41-45 and 50-54 had no effect on toxin…

The skeletal isomerization of but-1-ene catalyzed by theta-1 zeolite

2001

The complete mechanism for the skeletal isomerization of but-1-ene catalyzed by theta-1 zeolite was investigated theoretically by means of DFT calculations, and the influence of the local geometry of the active site and of electrostatic effects on the geometries of the species involved and on activation and reaction energies were analyzed. It was found that whereas the geometry and stability of alkoxide intermediates are strongly influenced by the local geometry of the active site, the ionic transition states are mainly stabilized by electrostatic effects. Both aspects result in a lowering of the activation energies of the elementary steps that form the mechanism and therefore in enhanced r…