The effect of protein conformational flexibility on the electronic properties of a chromophore

In this paper we address the question of how a protein environment can modulate the absorption spectrum of a chromophore during a molecular dynamics simulation. The effect of the protein is modeled as an external field acting on the unperturbed eigenstates of the chromophore. Using a first-principles method recently developed in our group, we calculated the perturbed electronic energies for each frame and the corresponding wavelength absorption during the simulation. We apply this method to a nanosencond timescale molecular dynamics simulation of the light-harvesting peridinin-chlorophyll-protein complex from Amphidinium carterae, where chlorophyll was selected among the chromophores of the complex for the calculation. The combination of this quantum-classical calculation with the analysis of the large amplitude motions of the protein makes it possible to point out the relationship between the conformational flexibility of the environment and the excitation wavelength of the chromophore. Results support the idea of the existence of a correlation between protein conformational flexibility and chlorophyll electronic transitions induced by light.     

Selective excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study

The effect of temperature on the activation of native fluctuation motions during molecular dynamics unfolding simulations of horse heart cytochrome c has been studied. Essential dynamics analysis has been used to analyze the preferred directions of motion along the unfolding trajectories obtained by high temperature simulations. The results of this study have evidenced a clear correlation between the directions of the deformation motions that occur in the first stage of the unfolding process and few specific essential motions characterizing the 300 K dynamics of the protein. In particular, one of those collective motions, involved in the fluctuation of a loop region, is specifically excited in the thermal denaturation process, becoming progressively dominant during the first 500 ps of the unfolding simulations. As further evidence, the essential dynamics sampling performed along this collective motion has shown a tendency of the protein to promptly unfold. According to these results, the mechanism of thermal induced denaturation process involves the selective excitation of one or few specific equilibrium collective motions.     

Molecular dynamics simulations of a pulmonary surfactant protein B peptide in a lipid monolayer

Pulmonary surfactant is a complex mixture of lipids and proteins that lines the air/liquid interface of the alveolar hypophase and confers mechanical stability to the alveoli during the breathing process. The desire to formulate synthetic mixtures for low-cost prophylactic and therapeutic applications has motivated the study of the specific roles and interactions of the different components. All-atom molecular dynamics simulations were carried out on a model system composed of a monolayer of palmitic acid (PA) and a surfactant protein B peptide, SP-B(1-25). A detailed structural characterization as a function of the lipid monolayer specific area revealed that the peptide remains inserted in the monolayer up to values of specific area corresponding to an untilted condensed phase of the the pure palmitic acid monolayer. The system remains stable by altering the conformational order of both the anionic lipid monolayer and the peptide secondary structure. Two elements appear to be key for the constitution of this phase: an electrostatic interaction between the cationic peptide residues with the anionic headgroups, and an exclusion of the aromatic residues on the hydrophobic end of the peptide from the hydrophilic and aqueous regions.     

Modulation of nuclear pore topology by transport modifiers

The nuclear pore complex (NPC) represents the only pathway for macromolecular communication between the nuclear and cytoplasmic compartments of the cell. Nucleocytoplasmic transport requires the interaction of transport receptors with phenylalanine-glycine (FG)-repeats that line the transport pathway through the NPC. Here we examine the effects of transport receptors and amphipathic alcohols on NPC topology using scanning force microscopy. We show that transport receptors that irreversibly bind FG-repeats increase NPC vertical aspect, whereas transport receptors that weakly interact with FG-repeats increase NPC diameter. Interestingly, small polar alcohols likewise increase NPC diameter. These opposing effects agree with the inhibition or enhancement of nuclear transport, respectively, previously ascribed to these agents.     

Expression of galP and glk in a Escherichia coli PTS mutant restores glucose transport and increases glycolytic flux to fermentation products

In Escherichia coli, the uptake and phosphorylation of glucose is carried out mainly by the phosphotransferase system (PTS). Despite the efficiency of glucose transport by PTS, the required consumption of 1 mol of phosphoenolpyruvate (PEP) for each mol of internalized glucose represents a drawback for some biotechnological applications where PEP is a precursor of the desired product. For this reason, there is considerable interest in the generation of strains that can transport glucose efficiently by a non-PTS mechanism. The purpose of this work was to study the effect of different gene expression levels, of galactose permease (GalP) and glucokinase (Glk), on glucose internalization and phosphorylation in a E. coli PTS(-) strain. The W3110 PTS(-), designated VH32, showed limited growth on glucose with a specific growth rate (mu) of 0.03 h(-1). A low copy plasmid family was constructed containing E. coli galP and glk genes, individually or combined, under the control of a trc-derived promoter set. This plasmid family was used to transform the VH32 strain, each plasmid having different levels of expression of galP and glk. Experiments in minimal medium with glucose showed that expression of only galP under the control of a wild-type trc promoter resulted in a mu of 0.55 h(-1), corresponding to 89% of the mu measured for W3110 (0.62 h(-1)). In contrast, no increase in specific growth rate (mu) was observed in VH32 with a plasmid expressing only glk from the same promoter. Strains transformed with part of the plasmid family, containing both galP and glk genes, showed a mu value similar to that of W3110. Fermentor experiments with the VH32 strain harboring plasmids pv1Glk1GalP, pv4Glk5GalP, and pv5Glk5GalP showed that specific acetate productivity was twofold higher than in W3110. Introduction of plasmid pLOI1594, coding for pyruvate decarboxylase and alcohol dehydrogenase from Zymomonas mobilis, to strain VH32 carrying one of the plasmids with galP and glk caused a twofold increase in ethanol productivity over strain W3110, also containing pLOI1594.     

The role of acute wall recoil and late restenosis: results of the OCBAS trial (Optimal Coronary Balloon Angioplasty with Provisional Stenting versus Primary Stent)

Early deterioration of minimal luminal diameter immediately after PTCA, has been associated with an increase of late restenosis. Lesions with no early loss after PTCA have a low restenosis rate. Coronary stents reduce restenosis in lesions exhibiting early wall recoil. The purpose of the OCBAS study was to compare two strategies during coronary interventions; provision vs. elective stenting. 116 patients with good PTCA results were randomized to stent (n = 57) or to optimal PTCA (n = 59). After randomization in PTCA group, 13.5% of the patients crossed over to stent due to early loss (provisional stenting). Baseline demographic and angiographic characteristics were similar in both groups of patients. At 7.6 months, 96.6% of the entire population had a follow-up angiographic study; 98.2% in the stent and 94.9% in the PTCA group. Immediate and follow-up angiographic data showed that acute gain was significantly higher in the stent than in the PTCA group (1.95 vs. 1.5 mm; P < 0.03). However, late loss was significantly higher in the stent than the PTCA groups (0.63 +/- 0.59 vs. 0.26 +/- 0.44, respectively; P = 0.01). Hence, net gain with both techniques was similar (1.32 +/- 0.3 vs. 1.24 +/- 0.29 mm for the stent and PTCA groups respectively; P = NS). Angiographic restenosis rate at follow-up (19.2% in stent vs. 16.4% in PTCA; P = NS) and TVR (17.5 in stent vs. 13.5% in PTCA; P = NS) were also similar. Furthermore, event-free survival was 80.8% in the stent versus 83.1% in the PTCA group (P = NS). Overall costs (hospital and follow-up) were US$591,740 in the stent versus US$398,480 in the PTCA group (P < 0.02). The strategy of the PTCA with delay angiogram and provisional stent if early loss occurs, had similar restenosis rate and TVR than universal use of bare stents.     

Effects of betamethasone,sulindac and quinacrine drugs on the inflammatory neoangiogenesis response induced by polyurethane sponge implanted in mouse

In this study, we showed the effect of the betamethasone, sulindac and quinacrine alone or combined, on the inflammatory angiogenesis promoted by polyurethane sponge on mice. The main finding reported here is that the formation of new blood vessels was strongly inhibited by low concentration of betamethasone, sulindac or quinacrine, whether alone or in combination. It is known that steroidal anti-inflammatory drugs inhibit the enzymes required for the production of prostaglandins through a nuclear glucocorticoid receptor (GR) mediated mechanism. This mechanism may occur in endothelial cells as well. Considering that activity of cyclo-oxigenases 1 and 2 is inhibited by sulindac, and that these enzymes are located in the stromal tissue, we propose that the anti-angiogenic effect of these agents may occur via inhibition of both COX isoforms. On the other hand, quinacrine inhibited PLA2 activity, and we propose here that the anti-angiogenic effect occurs via inhibition of the enzyme PLA2. The potentiated effect of the association of betamethasone, sulindac and quinacrine may have some therapeutic benefit in the control of pathological angiogenesis. Further studies are required to validate these propositions.     

Stenurus globicephalae Baylis et Daubney, 1925 (Nematoda: Pseudaliidae) from a false killer whale,Pseudorca crassidens (Cetacea: Delphinidae), stranded on the coast of Uruguay

Stenurus globicephalae Baylis et Daubney, 1925 (Nematoda: Pseudaliidae) was found in the cranial air sinuses of a false killer whale, Pseudorca crassidens (Owen), stranded on the coast of Uruguay in 1999. Although this species has been reported once in P. crassidens from the North Atlantic, this is the first record for South America. A total of 920 specimens were obtained, of which 663 were females (body length: 4.34 +/- 0.45 cm) and 257 were males (2.99 +/- 0.18 cm). Morphometric details are presented for S. globicephalae in this host, which do not show significant differences from those parasitizing Globicephala melas (Traill), but are distinct from those parasitizing Peponocephala electra (Gray). The host's skull revealed loss of osseous mass with the disappearance of the left zygomatic arch, and the left jaw had three osseous fenestrations in the region related to the organ of acoustic reception. These lesions support the hypothesis that this infection, known as stenurosis, was related to the stranding.     

Polymorphism in allergens

Allergens are antigens that elicit an IgE-mediated immune response; they originate from diverse sources such as pollens, mites, molds, mammal exudates, insects and food. Allergenic molecules can contain several antigenic determinants, termed epitopes. Allergenic proteins have been discovered with polymorphisms, i.e., a mixture of similar molecules with minor variations in their amino acid sequences. These are called isoallergens or allergenic variants depending on the degree of similarity. Polymorphism may be defined by the presence of several alleles of the same gene or as families of related genes. Polymorphisms can have an important effect on the epitopes recognized by T lymphocytes, monoclonal antibodies and IgE of allergic patients. Individual polymorphisms can affect the basal level of allergenicity as well as the cross-reactivity with other allergens. The use of isoforms with low or total absence of IgE binding capacity but with high capacity to stimulate T cell response has been suggested as an alternative to the conventional immunotherapy for allergic diseases. Standardization of allergenic compounds can be affected by the differing proportions of isoforms in allergenic sources from different regions.