Characterization of tryptophan environments in glutamate dehydrogenases from temperature-dependent phosphorescence

Tryptophan room temperature phosphorescence in solution was detected in glutamic dehydrogenase from bovine liver and Escherichia coli with lifetimes of 1.2 and 0.65 s, respectively. Although these enzymes possess three and five tryptophanyl residues per polypeptide chain, respectively, the temperature dependence of the phosphorescence quantum yield estimates that the room temperature emission is due, in either case, to a single residue. Long triplet-state lifetimes and very small rates of O2 quenching indicate that these tryptophanyl side chains are embedded in a highly inflexible internal region of the macromolecule. Aided by sequence homology with dehydrogenases of known structure and theoretical predictions of secondary structure [Wootton, J.C. (1974) Nature (London) 252, 542-546; Brett, M., Chambers, G.K., Holder, A. A., Fincham, J.R.S., & Wootton, J.C. (1976) J. Mol. Biol. 106, 1-22], the phosphorescing tryptophans have been tentatively placed in the catalytic coenzyme binding domain of each enzyme. The particular sensitivity of the triplet-state lifetime in probing local changes in conformation provides a strong indication that within the time window of phosphorescence measurements the six subunits in the hexameric enzymes are equivalent. Furthermore, while in the bovine enzyme this parameter is markedly affected by the interaction with ligands which have a functional role, the constancy of the phosphorescence lifetime at various degrees of polymerization suggests that the association process is not accompanied by important conformational changes in the macromolecule.     

Eye factors and lens-forming transformations of outer cornea in Xenopus laevis larvae

Outer cornea of lensectomized Xenopus laevis tadpoles at state 50 (according to Nieuwkoop, P.D. and Faber, J., ('56) Normal Table of Xenopus laevis, Daudin, North-Holland, Amsterdam, pp. 1-243) was removed 3, 7 and 10 days after lensectomy and implanted between the outer and the inner cornea of larvae of the same species at stage 51-52. In these conditions, the implanted outer cornea remained isolated from the retinal factor of the vitreous chamber, although it received the nutritional factors normally reaching the outer cornea. Results show that lens-forming transformation process of the outer cornea is arrested, and lens-forming structures undergo regression at speed which increases with increasing precocity of the stage of lens-forming transformation undergone by the implanted cornea. These data suggest that the process of lens-forming transformation is not a single-step process, but a sequence of interactions extending over a long period of time requiring the continuous presence of the retinal factor in the vitreous chamber until complete differentiation of the lens is achieved.     

Heterogeneity of protein conformation in solution from the lifetime of tryptophan phosphorescence

The decay of Trp phosphorescence of proteins in fluid solutions was shown to provide a sensitive tool for probing the conformational homogeneity of these macromolecules in the millisecond to second time scale. Upon examination of 15 single Trp emitting proteins multiexponential decays were observed in 12 cases, a demonstration that the presence of slowly interconverting conformers in solution is more the norm rather than an exception. The amplitude of preexponential terms, from which the conformer equilibrium is derived, was found to be a sensitive function of solvent composition (buffer, pH, ionic strength and glycerol cosolvent), temperature, and complex formation with substrates and cofactors. In many cases, raising the temperature, a point is reached at which the decay becomes practically monoexponential, meaning that conformer interconversion rates have become commensurate with the triplet lifetime. Estimation of activation free energy barriers to interconversion shows that the large values of DeltaG* are rather similar among polypeptides and that the protein substates involved are sufficiently long-lived to display individual binding/catalytic properties.     

Experimental and simulative dissociation of dimeric Cu,Zn superoxide dismutase doubly mutated at the intersubunit surface

The equilibrium properties of dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase mutant bearing two negative charges in the amino acid clusters at the association interface has been studied, experimentally and computationally, and compared to those of the native enzyme. Pressure-dependent dissociation is observed for the mutant, as observed by the fluorescence shift of the unique tryptophan residue located at the intersubunit surface. The spectral shift occurs slowly, reaching a plateau after 15-20 min, and is fully reversible. Measurement of the degree of dissociation allows us to calculate the standard volume variation upon association and the dissociation constant at atmospheric pressure. On the other hand the native protein is undissociable at any pressure. In the simulative approach, the dissociation free energy has been calculated through the blue moon calculation method for the case of a multidimensional reaction coordinate, corrected for the rotational contribution within the semiclassical approximation for a free rigid-body rotor. The scheme permits to define a definite path for the rupture of the dimer and to calculate the effective force involved in the process. The calculated free energy difference is close to the experimental one, and the value obtained for the mutant is well below that obtained for the native protein, indicating that the theoretical reaction scheme is able to reproduce the experimental trend. Moreover, we find that, when the separation distance increases, the protein structure of the monomer is stable in line with the fast recovery of the original fluorescence properties after decompression, which excludes the presence of partly unfolded intermediates during the dimer-monomer transition.     

Pyrazolo[1,5-a]quinazoline scaffold as 5-deaza analogue of pyrazolo[5,1-c][1,2,4]benzotriazine system: synthesis of new derivatives,biological activity on GABAA receptor subtype and molecular dynamic study

To investigate the binding affinity of GABA_A receptor subtype, new pyrazolo [1,5-a]quinazolines were designed, synthesized, and in vitro evaluated. These compounds, 5-deaza analogues of pyrazolo[5,1-c][1,2,4]benzotriazine derivatives which were already studied in our research group, permit us to evaluate the relevance of the nitrogen or the oxygen atom at 5-position of the tricyclic scaffold. Molecular dynamic study was done on a set of the new and known ligands to rationalize and to explain the lack of affinity on the 4- or 5-substituted new derivative. In fact, from biological results, it can be found that the only 5-unsubstituted new derivative, compound 15, has receptor recognition (K_i?=?834.7?nM).     

Precise Gene Editing Preserves Hematopoietic Stem Cell Function following Transient p53-Mediated DNA Damage Response

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Achillea ligustica: composition and antimicrobial activity of essential oils from the leaves, flowers and some pure constituents

The composition of the essential oils obtained from the leaves and the flowers of Achillea ligustica (Asteraceae) growing in Sicily has been studied. The main constituents of the leaves were 4-terpineol (19.3%), carvone (8.9%), γ-terpinene (7.2%) and β-phellandrene (6.8%). 4-terpineol (12.0%), carvone (10.0%), and β-phellandrene (5.4%), along with linalool (20.4%) and cedrol (4.3%) were detected in the flower’s oil. Furthermore, the antimicrobial activity of the essential oils and of some of the main constituents were assayed on bacteria and fungi. In memory of Prof. Ivano Morelli (1940–2005)     

Seasonal variation of the chemical constituents of the essential oil of Santolina etrusca from Italy

The seasonal variation of the essential oil, in terms of both yield and composition, of a population of Santolina etrusca (Asteraceae) is reported in detail for different aerial parts, including sterile branches, fertile branches, and capitula. The yields generally increased from November to June, and then decreased in August and September. The main constituents of the sterile branches were 1,8-cineole and viridiflorol. The oil from fertile branches was characterized by myrcene as principal compound, whereas the essential oil obtained from the capitula contained germacrene D as the main constituent. Several compounds, as identified by GC and GC/MS, were found to prevail during the cold season.