Gene expression and molecular modeling of the HSP104 chaperone of Trypanosoma cruzi.

Heat shock protein (HSP) 104 is a highly conserved molecular chaperone that catalyzes protein unfolding, disaggregation and degradation under stress conditions. We characterized HSP104 gene structure and expression in Trypanosoma cruzi, a protozoan parasite that causes Chagas' disease. The T. cruzi HSP104 is an 869 amino-acid protein encoded by a single-copy gene that has the highest sequence similarity (76%) with that of T. brucei and the lowest (23%) with that of the human protein. HSP104 transcripts were detected at room temperature, and levels increased after incubation at 37° or 40°C. The HSP104 protein was found at low levels in non-heat-shocked cells, and accumulated continuously up to 24 h at elevated temperatures. We developed a predicted structural model of hexameric T. cruzi HSP104, which showed some conserved features.

A comparative proteomic analysis of Gluconacetobacter diazotrophicus PAL5 at exponential and stationary phases of cultures in the presence of high and low levels of inorganic nitrogen compound.

A proteomic view of G. diazotrophicus PAL5 at the exponential (E) and stationary phases (S) of cultures in the presence of low (L) and high levels (H) of combined nitrogen is presented. The proteomes analyzed on 2D-gels showed 131 proteins (42E+32S+29H+28L) differentially expressed by G. diazotrophicus, from which 46 were identified by combining mass spectrometry and bioinformatics tools. Proteins related to cofactor, energy and DNA metabolisms and cytoplasmic pH homeostasis were differentially expressed in E growth phase, under L and H conditions, in line with the high metabolic rate of the cells and the low pH of the media. Proteins most abundant in S-phase cells were stress associated and transporters plus transferases in agreement with the general phenomenon that binding protein-dependent systems are induced under nutrient limitation as part of hunger response. Cells grown in L condition produced nitrogen-fixation accessory proteins with roles in biosynthesis and stabilization of the nitrogenase complex plus proteins for protection of the nitrogenases from O(2)-induced inactivation. Proteins of the cell wall biogenesis apparatus were also expressed under nitrogen limitation and might function in the reshaping of the nitrogen-fixing G. diazotrophicus cells previously described. Genes whose protein products were detected in our analysis were mapped onto the chromosome and, based on the tendency of functionally related bacterial genes to cluster, we identified genes of particular pathways that could be organized in operons and are co-regulated. These results showed the great potential of proteomics to describe events in G. diazotrophicus cells by looking at proteins expressed under distinct growth conditions.

Structural biology of membrane-acting peptides: conformational plasticity of anticoccidial peptide PW2 probed by solution NMR.

The bottleneck for the complete understanding of the structure-function relationship of flexible membrane-acting peptides is its dynamics. At the same time, not only the structure but also the dynamics are the key points for their mechanism of action. Our model is PW2, a TRP-rich, cationic peptide selected from phage display libraries that shows anticoccidial activity against Eimeria acervulina. In this manuscript we used a combination of several NMR techniques to tackle these difficulties. The structural features of the membrane-acting peptide PW2 was studied in several membrane mimetic environments: we compared the structural features of PW2 in SDS and DPC micelles, that were reported earlier, with the structure properties in different lipid vesicles and the peptide free in water. We were able to unify the structural information obtained in each of these systems. The structural constraints of the peptide free in water were fundamental for the understanding of plasticity necessary for the membrane interaction. Our data suggested that the WWR sequence is the region responsible for anchoring the peptide to the interfaces, and that this same region displays some degree of conformational order in solution. For PW2, we found that affinity is related to the aromatic region, by anchoring the peptide to the membrane, and specificity is related to the N- and C-termini, which are able to accommodate in the membrane due to its plasticity.

LexA-DNA bond strength by single molecule force spectroscopy.

The SOS system of Escherichia coli is coordinated by two proteins: LexA, a repressor protein of several unlinked genes, and the coprotease RecA. As known to date LexA controls 31 genes with slightly different DNA binding motifs allowing for a variable degree of repression from one gene to the other. Besides the SOS system LexA plays an important role in the regulation of transcription. The protein regulates transcription by using particular motifs to bind DNA, the helix-turn-helix motif. Here, we employed AFM-based single molecule force spectroscopy to characterize the interaction of LexA protein with two different DNA motifs: recA and yebG. We measured the dissociation rates to be 0.045 s(-1) for recA and 0.13 s(-1) for yebG, respectively, which is in accordance with the predicted higher affinity between LexA-recA compared to LexA-yebG. The widths of the binding potentials were determined to be 5.4 +/- 1 angstroms and 4.9 +/- 0.5 angstroms, respectively. This short-ranged potential is characteristic for a stiff hydrogen-bonding network between protein and DNA. The unbinding occurs in a breakup rather than a gradual sliding.

Correlation between conformation and antibody binding: NMR structure of cross-reactive peptides from T. cruzi, human and L. braziliensis.

The structure of peptides corresponding to the C-terminal residues from Trypanosoma cruzi (R13), human (H13) and Leishmania braziliensis (A13) ribosomal proteins were determined using nuclear magnetic resonance. Although there is only one amino acid difference between them, the peptides present distinct structures in solution: R13 adopts a random coil conformation while H13 and A13 form a bend. Interaction of these peptides with polyclonal antibodies from chronic Chagas' disease patients and a monoclonal antibody raised against T. cruzi ribosomal P2beta protein was probed by transferred NOE. The results show that the flexibility of R13 is fundamental for the binding to the antibody.

Structural studies of oligonucleotides containing G-quadruplex motifs using AFM.

G-quadruplex DNAs are cyclic arrays of four guanine bases binding by Hoogsteen hydrogen bonds, found in the telomeric regions of chromosomes and in transcriptional regulatory regions of several important oncogenes. Here, we used high resolution atomic force microscopy (AFM) to observe a specific guanine (G) tetrad mediated complex formation of oligonucleotides containing a G-quadruplex motifs (G-ODN) combined with a palindromic sequence under physiological extracellular conditions. These oligonucleotides have been investigated in correlation to their immunostimulatory effects. We observed structural dependence on ion concentration and G-ODN concentration, where high concentration self-assembled DNA networks were formed.

New stochastic strategy to analyze helix folding.

We propose an alternative stochastic strategy to search secondary structures based on the generalized simulated annealing (GSA) algorithm, by using conformational preferences based on the Ramachandran map. We optimize the search for polypeptide conformational space and apply to peptides considered to be good alpha-helix promoters above a critical number of residues. Our strategy to obtain conformational energies consist in coupling a classical force field (THOR package) with the GSA procedure, biasing the Phi x Psi backbone angles to the allowed regions in the Ramachandran map. For polyalanines we obtained stable alpha-helix structures when the number of residues were equal or exceeded 13 amino acids residues. We also observed that the energy gap between the global minimum and the first local minimum tends to increase with the polypeptide size. These conformations were generated by performing 2880 stochastic molecular optimizations with a continuum medium approach. When compared with molecular dynamics or Monte Carlo methods, GSA can be considered the fastest.

Multifractality, Levinthal paradox, and energy hypersurface.

Multifractal properties in the potential energy hypersurface of polypeptides and proteins are investigated. Characteristic multifractal behavior for different molecular systems is obtained from the f(alpha) spectra. The analysis shows that the dimension of the phase space of the problem influences the accessibility to different parts of the potential energy hypersurface. Also, we show that it is necessary to take into account the H-bond formation between amino acids in the conformational-folding search. The present findings indicate that the f(alpha) function describes some structural properties of a protein. The behavior of the f(alpha) spectra gives an alternative explanation about the Levinthal paradox. Furthermore, the anomalous temperature dependence of the Raman spin-lattice relaxation rates can be related to the perturbations in the secondary structures.

Hydration of T-antigen Gal beta(1-3)GalNAc and the isomer Gal beta(1-3)GlcNAc by molecular dynamics simulations.

We present a 250 ps molecular dynamics simulation of the T-antigen Gal beta(1-3)GalNAc and its isomer Gal beta(1-3)GlcNAc in the classic Gibbs Ensemble, Number of particles, Pressure and Temperature (NPT) with explicit representation of 432 water molecules. We computed the radial distribution function, equilibrium conformation, intramolecular and intermolecular hydrogen bonds, and water residence time to characterize the hydration pattern of these sugars, which are not very different and exhibit hydrophilic behavior. Based on hydration dynamics, it was concluded that these sugars should be classified as negative hydrated. Formation of an intramolecular hydrogen bond between the ring oxygen atom O5 of the first unit and the OH4' group of glycoside of the second unit might influence interaction with the antigenic receptor and could explain the main difference of affinities between them.

Molecular dynamics simulation of alpha-melanocyte stimulating hormone in a water-membrane model interface.

The conformation of the tridecapeptide alpha-melanocyte stimulating hormone in the presence of a double water-membrane interface was studied by molecular dynamics simulation, using the computational package THOR. In this program the solvent is represented by a continuous medium with dielectric constant epsilon, and the interface between different media is simulated by a surface of discontinuity of the dielectric constant. The electrostatic image method was used to write down the terms, added to the force field, that describe the polarisation effects induced in the interface by the atomic charges. The program was further improved by the introduction of a second surface, parallel to the first one, to mimic the membrane. A conformational search using the software Prelude was employed to find an initial geometry for the peptide in water. The molecular dynamics simulation performed during 10 ns showed that the peptide structure is flexible in water, without stabilisation of any preferential conformation. In the presence of the model membrane, the peptide moved to the medium representing the interior of the membrane. Inside the low dielectric constant medium, the structure of the peptide showed a turn in the central sequence of amino acids and a packed conformation remained stabilised during more than 7.0 ns of simulation.

Atomic force microscopy study of tooth surfaces.

Atomic force microscopy (AFM) was used to study tooth surfaces in order to compare the pattern of particle distribution in the outermost layer of the tooth surfaces. Human teeth and teeth from a rodent (Golden hamster), from a fish (piranha), and from a grazing mollusk (chiton) with distinct feeding habits were analyzed in terms of particle arrangement, packing, and size distribution. Scanning electron microscopy and transmission electron microscopy were used for comparison. It was found that AFM gives high-contrast, high-resolution images and is an important tool as a source of complementary and/or new structural information. All teeth were cleaned and some were etched with acidic solutions before analysis. It was observed that human enamel (permanent teeth) presents particles tightly packed in the outer surface, whereas enamel from the hamster (continuously growing teeth) shows particles of less dense packing. The piranha teeth have a thin cuticle covering the long apatite crystals of the underlying enameloid. This cuticle has a rough surface of particles that have a globular appearance after the brief acidic treatment. The similar appearance of the in vivo naturally etched tooth surface suggests that the pattern of globule distribution may be due to the presence of an organic material. Elemental analysis of this cuticle indicated that calcium, phosphorus, and iron are the main components of the structure while electron microdiffraction of pulverized cuticle particles showed a pattern consistent with hydroxyapatite. The chiton mineralized tooth cusp had a smooth surface in an unabraded region and a very rough structure with the magnetite crystals (already known to make part of the structure) protruding from the surface. It was concluded that the structures analyzed are optimized for efficiency in feeding mechanism and life span of the teeth.

Effect of ionic strength and outer surface charge on the mechanical stability of the erythrocyte membrane: a linear hydrodynamic analysis.

A linear hydrodynamic analysis in normal modes has been developed for a membrane model that simulated the erythrocytes membrane. The characteristic dispersion equation was obtained by solving the linearized dynamic equations. Values of the parameters related to the erythrocyte membrane were used to obtain the critical stability curves as a function of cell surface electric charge and suspending phase ionic strength. According to this model, the mechanical stability of the membrane increases with the decrease of the negative charge value on the outer membrane surface. The conclusion is that the transmembrane-potential and surface-charge changes that follow the reduction in ionic strength were responsible for the stability increase observed in previously reported experiments on heated erythrocytes.

Interaction of chlorpromazine with phospholipid membranes. An EPR study of membrane surface potential effects.

The interaction of chlorpromazine (CPZ) with artificial membranes (egg-yolk phosphatidylcholine liposomes) has been studied. Measurements of the surface electric potential, which is modified in the presence of the ionized form of the drug, were obtained by electron paramagnetic resonance spectroscopy (EPR) using a positively charged amphiphilic spin-probe. This probe partitions between the aqueous and lipidic phases depending on the surface potential and on the structural state of the membrane. The surface potential was measured as a function of drug concentration in the range where the spectral line-shapes are not affected by the incorporation of the drug. From these experimental results and through an appropriate formalism we obtain information on the binding of the drug to the lipid bilayer and on the ionization of the drug in the lipidic phase.

Molecular dynamics at a cytoplasm/membrane interface of a signal sequence from an E. coli maltoporin.

We used a recently developed software that mimics a cytoplasm/membrane environment, with an interface separating two continuous media of different dielectric constants (1). This software has been designed to allow modelling of different kinds of molecules of biological interest such as proteins and drugs, in each of the isolated continuous media, as well as in their interactions with membrane-like structures, making use of the dielectric discontinuity represented by the interface. In the present study we have applied this program ("THOR") to model a polypeptide sequence corresponding to a 50% active mutant of the signal sequence of the lamB gene product of E. coli, known as maltoporin or lambda receptor (2). The peptide was first submitted to optimization of its molecular geometry followed by molecular dynamics in water (epsilon = 80) until thermalization was achieved. The conformation evolved from a rather extended random conformation to increasingly folded structures. The presence of the dielectric discontinuity induced the movement of the molecule's center of mass from water towards the interface. The entry of the peptide into the lower dielectric constant medium (epsilon = 2) through the interface was paralleled by a decrease in the total potential energy, indicating the affinity of the peptide for the lipid-mimetic phase.

Oscillations and multiple steady states in active membrane transport models.

The dynamic behavior of some non-linear extensions of the six-state alternating access model for active membrane transport is investigated. We use stoichio-metric network analysis to study the stability of steady states. The bifurcation analysis has been done through standard numerical methods. For the usual six-state model we have proved that there is only one steady state, which is globally asymptotically stable. When we added an autocatalytic step we found self-oscillations. For the competition between a monomer cycle and a dimer cycle, with steps of dimer formation, we have also found self-oscillations. We have also studied models involving the formation of a complex with other molecules. The addition of two steps for formation of a complex of the monomer with another molecule does not alter either the number or the stability of steady states of the basic six-state model. The model which combines the formation of a complex with an autocatalytic step shows both self-oscillations and multiple steady states. The results lead us to conclude that oscillations could be produced by active membrane transport systems if the transport cycle contains a sufficiently large number of steps (six in the present case) and is coupled to at least one autocatalytic reaction,. Oscillations are also predicted when the monomer cycle is coupled to a dimer cycle. In fact, the autocatalytic reaction can be seen as a simplification of the model involving competition between monomer and dimer cycles, which seems to be a more realistic description of biological systems. A self-regulation mechanism of the pumps, related to the multiple stationary states, is expected only for a combined effect of autocatalysis and formation of complexes with other molecules. Within the six-state model this model also leads to oscillation.

Autocatalytic cooperativity and self-regulation of ATPase pumps in membrane active transport.

We investigate the effect of autocatalysis on the conformational changes of membrane pumps during active transport driven by ATP. The translocation process is described by means of an alternating access model. The usual kinetic scheme is extended by introducing autocatalytic steps and allowing for dynamic formation of enzyme complexes. The usual features of cooperative models are recovered, i.e., sigmoid shapes of flux versus concentration curves. We show also that two autocatalytic steps lead to a mechanism of inhibition by the substrate as experimentally observed for some ATPase pumps. In addition, when the formation of enzyme complexes is allowed, the model exhibits a multiple stationary states regime, which can be related to a self-regulation mechanism of the active transport in biological systems.