Search results for "subtil"

Theoretical insights in enzyme catalysis

2004

In this tutorial review we show how the methods and techniques of computational chemistry have been applied to the understanding of the physical basis of the rate enhancement of chemical reactions by enzymes. This is to answer the question: Why is the activation free energy in enzyme catalysed reactions smaller than the activation free energy observed in solution? Two important points of view are presented: Transition State (TS) theories and Michaelis Complex (MC) theories. After reviewing some of the most popular computational methods employed, we analyse two particular enzymatic reactions: the conversion of chorismate to prephenate catalysed by Bacillus subtilis chorismate mutase, and a m…

QM/MM calculations of kinetic isotope effects in the chorismate mutase active site.

2003

Kinetic isotope effects have been computed for the Claisen rearrangement of chorismate to prephenate in aqueous solution and in the active site of chorismate mutase from B. subtilus. These included primary 13C and 18O and secondary 3H effects for substitutions at the bond-making and bond-breaking positions. The initial structures of the putative stationary points on the potential energy surface, required for the calculations of isotope effects using the CAMVIB/CAMISO programs, have been selected from hybrid QM/MM molecular dynamical simulations using the DYNAMO program. Refinement of the reactant complex and transition-state structures has been carried out by means of AM1/CHARMM24/TIP3P cal…

An

2020

Intracellular acid stress inhibits plant growth by unknown mechanisms and it occurs in acidic soils and as consequence of other stresses. In order to identify mechanisms of acid toxicity, we screened activation-tagging lines of Arabidopsis thaliana for tolerance to intracellular acidification induced by organic acids. A dominant mutant, sbt4.13-1D, was isolated twice and shown to over-express subtilase SBT4.13, a protease secreted into endoplasmic reticulum. Activity measurements and immuno-detection indicate that the mutant contains less plasma membrane H+-ATPase (PMA) than wild type, explaining the small size, electrical depolarization and decreased cytosolic pH of the mutant but not orga…

NUOVE STRATEGIE TERAPEUTICHE E DIAGNOSTICHE PER IL MANAGEMENT DEL RISCHIO CARDIO-METABOLICO IN PAZIENTI CON NAFLD CON O SENZA DIABETE MELLITO TIPO 2

Morphological determination of the phototrophic community composition of biological soil crusts in coastal sand dunes in northern Germany

2022

This dataset comprises the microbial community composition of biological soil crusts in north-German sand dunes. For this we obtained enrichment cultures of phototrophic microorganisms, by placing fragments of biocrusts of the same Petri dishes as used for sequencing, in Petri dishes with Bold Basal (1N BBM) agarized medium (Bischoff and Bold 1963). Cultures were grown under standard laboratory conditions: with a 12-hour alteration of light and dark phases and irradiation of 25 μmol photons m-2 s-1 at a temperature 20 ± 5 ºС. Microscopic study of these raw cultures began in the third week of cultivation. Morphological examinations were performed using Olympus BX53 light microscope with Noma…

Modification of the proteolytic fragmentation pattern upon oxidation of cysteines from ribulose 1,5-bisphosphate carboxylase/oxygenase.

2003

The proteolytic susceptibility of the native CO 2 -fixing photosynthetic enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39, Rubisco) has been shown to increase in vitro after oxidative treatments that affect cysteine thiols. A limited incubation of oxidized (pretreated with the disulfide cystamine) Rubisco from Chlamydomonas reinhardtii with subtilisin or proteinase K generated fragments of molecular mass about 53 kDa (band I in SDS-PAGE) and 47 kDa (band II) derived from the large subunit (55 kDa) of the enzyme. In contrast, proteolysis of the reduced Rubisco (pretreated with the free thiol cysteamine) produced only the 53 kDa band. The same fragmentation pattern was repr…

Cryptic Secondary Metabolites from the Sponge-Associated Fungus Aspergillus ochraceus

2019

The fungus Aspergillus ochraceus was isolated from the Mediterranean sponge Agelas oroides. The initial fermentation of the fungus on solid rice medium yielded 16 known compounds (4&ndash

Genetic and biochemical characterization by random and site-directed mutagenesis, repressors involved in stress response phenolic acids in Bacillus s…

2009

The aim of this work was to characterize the genetic and biochemical mechanisms involved in the PASR, the phenolic acid stress response induced by phenolic acids Bacillus subtilis. By genetics and molecular biology strategies, like reverse genetic, PCR or transposon random mutagenesis, gene deletion, complementation of strains, and gene expression, the main components of the PASR were identified and quantified. Site-directed and random mutagenesis of respectively the promoter of padC encoding the phenolic acid decaroxylase, and PadR, the repressor of the padC expression, allowed us to identify the site of binding of PadR with this promoter, as well as the amino-acid residues involved in the…

A supramolecular complex in the environmental stress signalling pathway of Bacillus subtilis

2003

SigmaB, an alternative sigma-factor of Bacillus subtilis, mediates the response of the cell to a variety of physical insults. Within the environmental stress signalling pathway RsbU, a protein phosphatase, is stimulated by its interaction with the protein kinase RsbT. In the absence of stress RsbT is expected to be trapped by an alternative binding partner, RsbS. Here, we have demonstrated that RsbS alone cannot act as an alternative partner for RsbT, but instead requires the presence of RsbR to create a high molecular mass RsbR:RsbS complex (approximately 1 MDa) able to capture RsbT. In this complex the phosphorylation state of RsbS, and not that of RsbR, controlled the binding to RsbT, wh…

Bax inhibitor-1 is likely a pH-sensitive calcium leak channel, not a H+/Ca2+ exchanger.

2014

The endoplasmic reticulum (ER) plays a key role in the synthesis, folding, and sorting of proteins, and disturbances of this delicate system can cause cell death. The ER also serves as the major intracellular calcium (Ca(2+)) store, and release of Ca(2+) from this store controls diverse cellular functions. At the interface of both these functions of the ER is Bax inhibitor-1 (BI-1), an evolutionarily conserved multifunctional protein that mediates Ca(2+) efflux from the ER and protects against ER stress. Several mechanisms have been proposed to explain how BI-1 might mediate Ca(2+) efflux from the ER. Chang et al. present structural evidence that a bacterial homolog of BI-1, BsYetJ, is a pH…