Effect of molecular confinement on internal enzyme dynamics: frequency domain fluorometry and molecular dynamics simulation studies

The tryptophanyl emission decay of the mesophilic beta-galactosidase from Aspergillus oryzae free in buffer and entrapped in agarose gel is investigated as a function of temperature and compared to that of the hyperthermophilic enzyme from Sulfolobus solfataricus. Both enzymes are tetrameric proteins with a large number of tryptophanyl residues, so the fluorescence emission can provide information on the conformational dynamics of the overall protein structure rather than that of the local environment. The tryptophanyl emission decays are best fitted by bimodal Lorentzian distributions. The long-lived component is ascribed to close, deeply buried tryptophanyl residues with reduced mobility; the short-lived one arises from tryptophanyl residues located in more flexible external regions of each subunit, some of which are involved in forming the catalytic site. The center of both lifetime distribution components at each temperature increases when going from the free in solution mesophilic enzyme to the gel-entrapped and hyperthermophilic enzyme, thus indicating that confinement of the mesophilic enzyme in the agarose gel limits the freedom of the polypeptide chain. A more complex dependence is observed for the distribution widths. Computer modeling techniques are used to recognize that the catalytic sites are similar for the mesophilic and hyperthermophilic beta-galactosidases. The effect due to gel entrapment is considered in dynamic simulations by imposing harmonic restraints to solvent-exposed atoms of the protein with the exclusion of those around the active site. The temperature dependence of the tryptophanyl fluorescence emission decay and the dynamic simulation confirm that more rigid structures, as in the case of the immobilized and/or hyperthermophilic enzyme, require higher temperatures to achieve the requisite conformational dynamics for an effective catalytic action and strongly suggest a link between conformational rigidity and enhanced thermal stability.     

Preliminary mutational analysis of the human kinin B2 receptor for nonpeptide antagonist ligands recognition

FR173657, LF16,0335, and LF16,0687 are nonpeptide antagonists, endowed with high affinity and selectivity for the human kinin B2 receptor. The kinin B2 receptor belongs to the family of G-protein-coupled receptors with seven transmembrane (TM) helices. In the present study, we aimed, through computer-assisted modeling and mutagenesis, to identify residues in the human B2 receptor (hB2R) amino acid sequence that are involved in nonpeptide antagonist binding in order to build up experimental data as a first step towards a molecular model of nonpeptide ligands binding site. Fourteen amino acid residues within the TM segments were mutated to alanine. The wild type and mutant receptors were stably expressed in Chinese hamster ovary (dhfr-) cells and tested for their ability to bind agonist ([3H]bradykinin) and peptide antagonist ([3H]MENI 1270) radioligands. The affinity of nonpeptide ligands was determined by heterologous competition experiments using the above radioligands. We found that some mutations in TM2 (W86A) and TM7 (Y295A, N297A) impair the binding affinity of the three nonpeptide antagonists. On the other hand, some mutated residues in TM3 (S1 17A) and TM6 (W256A) reduce the affinity of LF16,0335 and LF16,0687 only. Results are discussed in order to build up a hypothesis for the likely different interactions of various nonpeptide ligands with the B2 receptor.     

A solution NMR molecular model for the aspartate-ligated,cubane cluster containing ferredoxin from the hyperthermophilic archeaon Pyrococcus furiosus

A solution molecular model for the conformationally dynamically heterogeneous Pyrococcus furiosus ferredoxin with an intact disulfide bond has been constructed on the basis of reported (1)H NMR spectral parameters using distance geometry and simulated annealing protocols. Conventional long-mixing time NOESY and H-bonding constraints have been augmented by previously reported short-mixing time NOESY, steady-state NOE, and cluster paramagnetism-induced relaxation. The family of 15 structures with inconsequential violations exhibited low rms deviations for backbone atoms for the overwhelming majority of the residues, including the cluster ligating loop with the unprecedented ligated Asp14. Larger rms deviations were observed across the disulfide bond, but closer inspection revealed that the 15 structures can be factored into 10 substructures exhibiting an "S" or right-handed disulfide orientation and 5 exhibiting an "R" or left-handed disulfide orientation. The remainder of the structure is indistinguishable for the two disulfide orientations but confirms stabilizing extensions of secondary structural elements in the lengthening of the long helix and both the lengthening and incorporation of a third strand into the beta-sheet involving the termini, with these extensions interacting strongly in a modular fashion through the rings of Tyr46 and Trp2. These extensions of stabilizing interactions in Pyrococcus furiosus Fd, however, lead to strong destabilization of the disulfide bond and destabilization of the highly conserved first and last beta-turns in the sequence. It is concluded that the structural alternations in Pyrococcus Fd relative to other hyperthermostable Fds are not to increase thermostability but to place "stress" on the disulfide bond and render it more reducible. The possible physiological implications of this unique reducible disulfide bond are discussed.     

Synthesis of building blocks of human milk oligosaccharides. Fucosylated derivatives of the lacto- and neolacto-series

The synthesis of protected fucosylated derivatives of a Galβ(1→3)GlcNAc and of lactosamine Galβ(1→4)GlcNAc building blocks contained in human milk oligosaccharides is described. Both chemical and enzymatic methods have been exploited for selective protection of the disaccharide. Fucosylation of the appropriate derivatives allowed an easy and relatively short access to different products from common precursors.     

Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction)

Background  

PCR amplification of bacterial 16S rRNA genes provides the most comprehensive and flexible means of sampling bacterial communities. Sequence analysis of these cloned fragments can provide a qualitative and quantitative insight of the microbial population under scrutiny although this approach is not suited to large-scale screenings. Other methods, such as denaturing gradient gel electrophoresis, heteroduplex or terminal restriction fragment analysis are rapid and therefore amenable to field-scale experiments. A very recent addition to these analytical tools is represented by microarray technology.     

Do hemoglobin and hemocyanin impair schistosoma killing by no?

Nitric oxide (NO) possesses antiparasitic effects on both Protozoa and Metazoa in definitive and intermediate hosts as well as in vectors. Here, we postulate that hemoglobin and hemocyanin may impair Schistosoma killing by NO in the definitive and intermediate hosts. Interestingly, hemoglobin, myoglobin, and neuroglobin may protect Plasmodium and Trypanosoma from the antiparasitic effects of NO.     

The synthesis of the tripodal phosphine CH3C{CH2P(m-CF3C6H4)2}3 and its rhodium coordination chemistry

The new tripodal phosphine CH₃C{CH₂P(m-CF₃C₆H₄)₂}₃, CF₃PPP, was prepared by reacting CH₃C(CH₂Br)₃ with Li⁺P(m-CF₃C₆H₄)₂⁻, the latter being best obtained by adding Li⁺NⁱPr₂⁻ to PH(m-CF₃C₆H₄)₂. The rhodium complexes [RhCl(CO)(CF₃PPP)], [Rh(LL)(CF₃PPP)](CF₃SO₃) (LL = 2 CO or NBD), [RhX₃(CF₃PPP)], [RhX(MeCN)₃(CF₃PPP)](CF₃SO₃)₂ (X = H and Cl), [RhCl₂(MeCN)(CF₃PPP)](CF₃SO₃) and [Rh(MeCN)₃(CF₃PPP)](CF₃SO₃)₃ were prepared and characterized. The X-ray crystal structure of [Rh(NBD)(CF₃PPP)](CF₃SO₃) is reported. The lower oxygen sensitivity of the CF₃PPP rhodium(I) complexes, relative to the corresponding species with the parent ligand CH₃C(CH₂PPh₂)₃, is attributed to the higher effective nuclear charge on the metal centers caused by the presence of the six CF₃ substituents on the terdentate phosphine. A similar effect may be responsible for the easier hydrolysis of the CF₃PPP-containing, cationic rhodium(III) complexes relative to the corresponding compounds of the parent ligand.     

Costs and benefits of breeding in human-altered landscapes for the Eagle Owl Bubo bubo

We studied a population of 23–25 Eagle Owl Bubo bubo pairs between 1994 and 2000 in a 1330-km² study plot in the central-eastern Italian Alps. Compared to random sites, territories were located at lower elevation and closer to intensively cultivated-urbanized valley floors. Early laying was associated with low elevation and negatively affected productivity. Diet was dominated by rats, hedgehogs and dormice ( n  = 978 prey items), all of them typical of low-elevation habitats. Higher productivity was associated with a higher proportion of rats in the diet of individual pairs. Low availability of rats resulted in a more diverse diet, in turn associated with low productivity. Territories were occupied every year in a non-random fashion, and those most occupied were characterized by higher productivity and higher occurrence of the favoured prey types in the diet, suggesting they were of superior quality. Eagle Owls also paid a cost associated with nesting near human-altered habitats: the main cause of mortality reported to local authorities was electrocution. This is an increasing cause of death for many European populations and may be a cause for conservation concern. Human persecution is also an important cause of mortality in some parts of the European range. Apart from such costs, the study population appeared to have adapted well to the proximity of humans: estimates of density and productivity were comparable to those recorded elsewhere in Europe. The pattern found in our population also held at higher spatial scales: data from 17 European populations showed density to be highest in low-elevation, human-altered landscapes.