PubMed Health⌕ Search

Biomedical subjects

Paulo M Bisch

Publications and source records attributed to Paulo M Bisch.

10 recordsLinked to original sources

Probing the interaction between vesicular stomatitis virus and phosphatidylserine.

The entry of enveloped animal viruses into their host cells always depends on membrane fusion triggered by conformational changes in viral envelope glycoproteins. Vesicular stomatitis virus (VSV) infection is mediated by virus spike glycoprotein G, which induces membrane fusion between the viral envelope and the endosomal membrane at the acidic environment of this compartment. In this work, we evaluated VSV interactions with membranes of different phospholipid compositions, at neutral and acidic pH, using atomic force microscopy (AFM) operating in the force spectroscopy mode, isothermal calorimetry (ITC) and molecular dynamics simulation. We found that the binding forces differed dramatically depending on the membrane phospholipid composition, revealing a high specificity of G protein binding to membranes containing phosphatidylserine (PS). In a previous work, we showed that the sequence corresponding amino acid 164 of VSV G protein was as efficient as the virus in catalyzing membrane fusion at pH 6.0. Here, we used this sequence to explore VSV-PS interaction using ITC. We found that peptide binding to membranes was exothermic, suggesting the participation of electrostatic interactions. Peptide-membrane interaction at pH 7.5 was shown to be specific to PS and dependent on the presence of His residues in the fusion peptide. The application of the simplified continuum Gouy-Chapman theory to our system predicted a pH of 5.0 at membrane surface, suggesting that the His residues should be protonated when located close to the membrane. Molecular dynamics simulations suggested that the peptide interacts with the lipid bilayer through its N-terminal residues, especially Val(145) and His(148).

Amino Acids↗

A kinetic mechanism for Drosophila bicoid cooperative binding.

The Bicoid (Bcd) protein is a concentration-dependent transcriptional activator in the embryo of Drosophila melanogaster. Bcd regulates the expression of the maternal and zygotic gene hunchback (hb) that shows a step-like-function expression pattern, in the anterior half of the egg. The regulatory region of hb contains six major binding sites for the Bcd protein, named A1, A2, A3 (strong sites), and X1, X2, X3 (weak sites). Cooperativity between Bcd molecules binding to the hb enhancer element has been characterized as an important mechanism for the step-like shape of hb anterior expression domain. The objective of the present report is to analyse the mechanism of this cooperative binding based on a reaction network model. Using this method we have analysed experimental results from the literature describing how the Bcd protein binds to hb enhancer elements containing the A1 or X1 site alone or these two sites together at wild type distance. This approach allows us to estimate the kinetic constants of protein-protein and protein-DNA interactions. Moreover our results suggest that binding of a Bcd dimer to the hb enhancer element is more stable than binding of a monomer. We propose a cooperative kinetic mechanism for binding of Bcd to the hb enhancer element: First, a monomer binds to the site with a relatively low affinity; after that, another monomer binds to the first one with higher affinity, generating a dimer bound to the site. This yet unreported monomer-monomer cooperative mechanism takes place for occupancy of either one-site or two-site enhancer elements. In addition, we find cooperativity between neighbor sites, as previously reported in the literature.

Animals↗

Gene characterization and predicted protein structure of the mitochondrial chaperonin HSP10 of Trypanosoma cruzi.

Heat shock protein (HSP) 10 is a member of the highly conserved group of molecular chaperons, which are necessary for efficient folding of many proteins in normal and stress conditions and have been implicated in several human diseases. We have characterized the HSP10 genes of Trypanosoma cruzi, the causative agent of Chagas' disease. After sequence analysis of clones obtained from the T. cruzi Genome Initiative, we show that the T. cruzi HSP10 coding region is 300 bp long, encoding a polypeptide of 100 amino acids with highest sequence identity (83%) to HSP10 of Trypanosoma brucei and lowest (28%) to HSP10 of Escherichia coli. The T. cruzi HSP10 genes are arranged in 3 tandemly repeated copies, which give rise to a major mRNA of 1.0 kb that remains unaltered during heat shock; a smaller mRNA species is induced at 37 degrees C by alternate polyadenylation. Finally, the presence of a conserved 5-amino acid residue deletion in trypanosomatid HSP10s led us to generate a molecular model of the T. cruzi HSP10 structure. The oligomeric assembly of this model shows some peculiar characteristics that may have functional significance.

Amino Acid Sequence↗

Analyzing different parameters of steered molecular dynamics for small membrane interacting molecules.

The aim of this report is two-fold: First, to show the applicability of the Steered Molecular Dynamics (SMD) methodology for analyzing non-specific interactions governing the membrane affinity process of small biological molecules. Second, to point out a correlation between the system response and certain combinations of the SMD parameters (spring-elastic-constant and pulling-group). For these purposes, a simplified membrane model was used, modeled as a non-polar region limited by two polar aqueous media in a continuous dielectric representation. Polarization-induced effects at both interfaces were taken into account by the "electrostatic images" method. To perform SMD simulations a harmonic external force, representing a spring acting on a selected atom, forces the molecule to "break" its interaction with the surrounding environment by extracting it out of the membrane. With this approach, small molecules and peptides, with known affinity for the membrane environment, were studied: the zwitterionic tryptophan residue and a pentapeptide AcWLKLL. The SMD parameters, spring-elastic-constant and pulling-group, were varied and combined in order to analyze the systems responses in each case. It was observed that, the spring stiffness was crucial to reveal specific events that occur during the molecule behavior; hence, it was directly responsible for the sensitivity of this methodology. The pulling-group selected highly influenced on the reaction pathway, a fact that it was not observed with other parameters; consequently, force profiles are like the "fingerprints" of these induced pathways. The potential profile for the tryptophan was recovered from the SMD simulations being in good agreement with that estimated by an approximation method. With this rather simple model approach, SMD methodology has proven to be suitable for revealing the main interactions that govern the membrane affinity processes of small molecules and peptides.

Cell Membrane↗

Chemical treatment of mica for atomic force microscopy can affect biological sample conformation.

An important aspect in the preparation of substrate materials to use in atomic force microscopy lies in the question of interactions introduced by treatments designed to immobilize the sample over the substrate. Here we used a mica substrate that was chemically modified with cationic nickel to immobilize actin filaments (F-actin). Chemical modification could be followed quantitatively by measuring the interaction force between the scanning tip and the mica surface. This approach allowed us to observe polymeric F-actin in a structure that resembles an actin gel. It also improved sample throughput and conferred sample stability as well as repeatability from run to run.

Actin Cytoskeleton↗

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair.

We present an analysis of the electrostatic properties in the catalytic site of papain (EC 3.4.22.2), an archetype enzyme of the C1 cysteine proteinase family, and we investigate their possible role in the formation, stabilization and regulation of the Cys25((-))...His159((+)) catalytic ion pair. The electrostatic properties were computed using a reassociation method based in multicentered multipolar expansions obtained from ab initio quantum calculations of overlapping protein fragments. Solvent effects were introduced by coupling the use of multicentered multipolar expansions to two continuum boundary element methods to solve the Poisson and the linearized Poisson-Boltzmann equations. The electrostatic profile found in the proton transfer region of papain showed that this enzyme has a well-defined electrostatic environment to favor the formation and stabilization of the catalytic ion pair. The papain catalytic site electrostatic profile can be considered as an electrostatic fingerprint of the papain family with the following characteristics: (i) the presence of a net electric field highly aligned in the (Cys25)-SG-->(His159)-ND1 direction; (ii) the electrostatic profile has a saddle-point character; (iii) it is basically a local environmental effect. Furthermore, our analysis describes a possible regulatory mechanism (the E(SG-->ND1) attenuation effect) controlling the ion pair reactivity and permits to infer the Asp57 acidic residue as the most probable candidate to act as the electrostatic modulator.

Amino Acids↗

Nonspecific interaction forces at water-membrane interface by forced molecular dynamics simulations.

Nonspecific interactions are the main driving forces for the behavior of molecules with great affinity for biologic membranes. To investigate not only the molecular details of these interactions but to estimate their magnitude as well, the theoretical method of Forced Molecular Dynamics Simulations, based on the Atomic Force Spectroscopy experimental technique, was applied. In this approach, an additional one-dimensional elastic force, representing the cantilever probe, was incorporated to the force field of a Molecular Dynamics computational program. This force represents a spring fixed on one end to a selected atom of the molecule; the other end of the spring is displaced at constant velocity to pull the molecule out of the membrane. The force experimented by the molecule due to the spring, is proportional to the spring elongation relative to its equilibrium position. This value is registered during the entire simulation, and its maximum value will determine the molecule-membrane interaction force. Nonexplicit medium simulations were carried out. Polar and apolar media were considered according to their polarizability degree and a specific dielectric constant value was assigned. In this approach, the membrane was considered as the apolar region limited by two flat surfaces with a polar aqueous medium. The potential energy discontinuity at the interfaces was smoothed by considering the polarization-induced effects using the image method. The results of this methodology are presented using a small system, a single Alanine amino acid model, which enables extended simulations in a microsecond time scale. The confinement of this amino acid at the interface reduces its degrees of freedom and forces it to adopt one of the six defined conformations. A correlation between these stable structures at the water-membrane interface and the interaction force value was determined.

Alanine↗

Mutational analysis and molecular modeling of the binding of Staphylococcus aureus enterotoxin C2 to a murine T cell receptor Vbeta10 chain.

We investigated the role of the beta chain HV4 region in the binding of a Vbeta10 T cell receptor to superantigen S. aureus enterotoxin C2 (SEC2)/MHC class II complexes. Residues 6971 of the Cw3/1.1 TCR Vbeta10 chain, derived from an H-2K(d)-restricted cytotoxic clone, were individually changed to alanine using site-directed mutagenesis, and mutated TCR beta chains were transfected along with the wild-type TCR alpha chain into a TCR alpha(-)beta(-) T hybridoma. SEC2/MHC recognition was measured by IL-2 production. Alanine substitutions in the HV4beta region, either did not affect (Ser69 and Lys71), or increased the recognition of SEC2/HLA-DR1 complex (Asp70), arguing against a general and direct role for the HV4beta region in superantigenrecognition. A theoretical-computational model of the SEC2/TCR Vbeta10 chain complex was constructed and predicted the presence of a unique salt bridge between Vbeta Asp30 and SEC2 Lys103. A perfect correlation was found between the likely presence of this salt bridge and the capacity of the HV4beta and previously obtained CDR1beta alanine mutants to induce an equal or greater response than the wild-type TCR.

Animals↗

Stochastic molecular dynamics of peanut lectin PNA complex with T-antigen disaccharide.

The stochastic boundary molecular dynamics simulation method was applied to investigate the structure of a complex comprised of a tetrameric peanut lectin and the tumour-associated disaccharide, Galbeta1-3GalNAc (T-antigen). Only a small region encompassing the active site was explicitly included in the calculations, but the electrical contribution of most outer atoms was taken into account by adding to the effective potential a term coming from an electrostatic potential grid that was pre-calculated and used to approximate the electrostatic energy and the force at any point in the interacting site. Results of simulating the intermolecular hydrogen bond network agree fairly well with X-ray experiments. An estimation of the direct and water-mediated interaction mean lifetimes and mean water residence times around the T-antigen oxygen atoms was computed over 400 ps. Monitoring the behaviour of water molecules within the active site revealed that there is a constant exchange of water with the bulk, especially in the proximity of ASN41, ASN127 and GLU129. The temporal evolution of the glycosidic linkage was also investigated and compared with simulations of T-antigen in solution. These studies of peanut lectins-sugar complexes clearly emphasize the importance of bound water molecules in generating carbohydrate specificity.

Antigens, Tumor-Associated, Carbohydrate↗

Interaction between chondroitin-6-sulfate and Entamoeba histolytica as revealed by force spectroscopy.

We have observed by atomic force microscopy (AFM) the amoeba surface and probed the interaction force between Entamoeba histolytica and chondroitin-6-sulphate (C6S). We have used several substrates to adhere trophozoites. The best reproducibility in sample preparation was obtained with fibronectin-coated coverslips and when the cells were fixed with paraformaldehyde. The images obtained with the AFM showed that the trophozoite exhibits an irregular surface. Pseudopods and waving adhesion plaques could be observed. Force spectroscopy analysis showed that the trophozoite surface strongly interacts with C6S-functionalized tips. During cantilever retraction, attractive force peaks were observed at distances up to 1.3 microm above the trophozoite surface. Statistical analysis of the force distributions collected for five samples shown a reproducible 2.2 nN mean adhesion force. We observed a reduction of the adhesion force and of the interaction distance after addition of galactose to the buffer solution suggesting that the observed interaction is also Gal/GalNAc-lectin-mediated.

Animals↗