Search results for "binding"
showing 10 items of 3896 documents
Evolution of the leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster.
2004
ABSTRACT In Buchnera aphidicola strains associated with the aphid subfamilies Thelaxinae, Lachninae, Pterocommatinae, and Aphidinae, the four leucine genes ( leuA , - B , - C , and - D ) are located on a plasmid. However, these genes are located on the main chromosome in B. aphidicola strains associated with the subfamilies Pemphiginae and Chaitophorinae. The sequence of the chromosomal fragment containing the leucine cluster and flanking genes has different positions in the chromosome in B. aphidicola strains associated with three tribes of the subfamily Pemphiginae and one tribe of the subfamily Chaitophorinae. Due to the extreme gene order conservation of the B. aphidicola genomes, the v…
Comparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reaction.
2006
Chalcone isomerase catalyzes the transformation of chalcones to flavanones. We present a computational study of the rate-limiting chemical step, an intramolecular Michael addition of a 2'-oxyanion to the alpha,beta-double bound. By using quantum mechanical/molecular mechanical hybrid methods we traced the free-energy profiles associated with the reaction of two different substrates (chalcone and 6'-deoxychalcone) in two different conformations of the active site that are described in the different crystallographic structures available. We have obtained significant differences (about 4 kcal/mol) in the free-energy barriers calculated for the two active sites. According to our results, the ac…
Enzymatic effects on reactant and transition states. The case of chalcone isomerase.
2007
Chalcone isomerase catalyzes the transformation of chalcone to naringerin as a part of flavonoid biosynthetic pathways. The global reaction takes place through a conformational change of the substrate followed by chemical reaction, being thus an excellent example to analyze current theories about enzyme catalysis. We here present a detailed theoretical study of the enzymatic action on the conformational pre-equilibria and on the chemical steps for two different substrates of this enzyme. Free-energy profiles are obtained in terms of potentials of mean force using hybrid quantum mechanics/molecular mechanics potentials. The role of the enzyme becomes clear when compared to the counterpart eq…
CtsR is the master regulator of stress response gene expression in Oenococcus oeni.
2005
ABSTRACT Although many stress response genes have been characterized in Oenococcus oeni , little is known about the regulation of stress response in this malolactic bacterium. The expression of eubacterial stress genes is controlled both positively and negatively at the transcriptional level. Overall, negative regulation of heat shock genes appears to be more widespread among gram-positive bacteria. We recently identified an ortholog of the ctsR gene in O. oeni . In Bacillus subtilis , CtsR negatively regulates expression of the clp genes, which belong to the class III family of heat shock genes. The ctsR gene of O. oeni is cotranscribed with the downstream clpC gene. Sequence analysis of t…
Sequestration of organomettalic compounds by synthetic and naturally occuring polycarboxylate ligands. Binding of monomethylmercury(II) by polyacryli…
2007
The sequestering capacity of synthetic and naturally occurring polycarboxylate ligands towards mono- methylmercury(II) was evaluated by stability quantitative data on the interaction of CH3Hgþ with different molecular weight synthetic polyacrylates (2 and 20 kDa average M.wt) and alginate (70– 100 kDa) extracted from brown algae Macrocystis pyrifera. The influence of ionic medium was evaluated by measurements on the CH3Hgþ-polyacrylate systems in NaNO3 medium at different ionic strengths (0.10, 0.25, 0.50 and 0.75mol Lÿ1), and a Debye–Hu¨ ckel type equation was used for the dependence of complex formation constants on ionic strength. Measurements on the CH3Hgþ - alginate system were carried…
Albumin binding and hydrophobic character of promazine and chlorpromazine metabolites.
1972
1. The binding of didesmethylpromazine, promazine N-oxide, 2-hydroxypromazine, promazine sulfoxide, monodesmethylpromazine sulfoxide, didesmethylchlorpromazine, chlorpromazine N-oxide, and chlorpromazine sulfoxide to bovine serum albumin was determined by means of sephadex gel filtration. 2. The albumin binding of these substances was characterized by the following parameters: the percentage α of free substance, the percentage β of bound substance, the binding constants K1, k+ and m, the number of binding sites per albumin molecule, and the free binding energy ΔFo. 3. The partition coefficients between n-octanol and buffer solution, pH 7.40, were measured for the above mentioned metabolites…
Retention of aroma compounds in starch matrices: competitions between aroma compounds toward amylose and amylopectin
2002
International audience; The retention of three aroma compounds-isoamyl acetate, ethyl hexanoate, and linalool--from starch-containing model food matrices was measured by headspace analysis, under equilibrium conditions. We studied systems containing standard or waxy corn starch with one or two aroma compounds. The three studied aroma compounds interact differently: ethyl hexanoate and linalool form complexes with amylose, and isoamyl acetate cannot. However, in systems containing one aroma compound, we observed with both starches a significant retention of the three molecules. These results indicate that amylopectin could play a role in the retention of aroma. In systems containing two arom…
High-performance and ion-exchange chromatography and chromatofocusing of the human uterine progesterone receptor: its application to the identificati…
1984
Two independent lines of evidence were used to identify the human uterine progesterone receptor. First, three differently tritiated progestogens (Org 2058, R 5020, progesterone) were used for reversible labelling of the receptor. Secondly, the highly potent affinity label 21-[3H]dehydro Org 2058 was used to label covalently the steroid-specific binding site of the receptor. The labelled cytosols were chromatographed on a Mono Q high-performance anion-exchange column in the absence or presence of a high molar excess of the respective unlabelled competitor steroids. In the case of 21-[3H]dehydro Org 2058, Org 2058 was used as the unlabelled competitor. After elution with a NaCl gradient, the …
The spectra of mixed $^3$He-$^4$He droplets
2005
The diffusion Monte Carlo technique is used to calculate and analyze the excitation spectrum of $^3$He atoms bound to a cluster of $^4$He atoms, by using a previously determined optimum filling of single-fermion orbits with well defined orbital angular momentum $L$, spin $S$ and parity quantum numbers. The study concentrates on the energies and shapes of the three kinds of states for which the fermionic part of the wave function is a single Slater determinant: maximum $L$ or maximum $S$ states within a given orbit, and fully polarized clusters. The picture that emerges is that of systems with strong shell effects whose binding and excitation energies are essentially determined over configur…
Coupled-cluster theory for atoms and molecules in strong magnetic fields
2015
An implementation of coupled-cluster (CC) theory to treat atoms and molecules in finite magnetic fields is presented. The main challenges for the implementation stem from the magnetic-field dependence in the Hamiltonian, or, more precisely, the appearance of the angular momentum operator, due to which the wave function becomes complex and which introduces a gauge-origin dependence. For this reason, an implementation of a complex CC code is required together with the use of gauge-including atomic orbitals to ensure gauge-origin independence. Results of coupled-cluster singles-doubles-perturbative-triples (CCSD(T)) calculations are presented for atoms and molecules with a focus on the depende…