Intermolecular interactions and characterization of the novel factor Xa exosite involved in macromolecular recognition and inhibition: Crystal structure of human Gla-domainless factor Xa complexed with the anticoagulant protein NAPc2 from the hematophagous nematode Ancylostoma caninum

NAPc2, an anticoagulant protein from the hematophagous nematode Ancylostoma caninum evaluated in phase-II/IIa clinical trials, inhibits the extrinsic blood coagulation pathway by a two step mechanism, initially interacting with the hitherto uncharacterized factor Xa exosite involved in macromolecular recognition and subsequently inhibiting factor VIIa (K-i = 8.4 pM) of the factor VIIa/tissue factor complex. NAPc2 is highly flexible, becoming partially ordered and undergoing significant structural changes in the C terminus upon binding to the factor Xa exosite. In the crystal structure of the ternary factor Xa/NAPc2/selectide complex, the binding interface consists of an intermolecular antiparallel beta-sheet formed by the segment of the polypeptide chain consisting of residues 74-80 of NAPc2 with the residues 86-93 of factor Xa that is additional maintained by contacts between the short helical segment (residues 67-73) and a turn (residues 26-29) of NAPc2 with the short C-terminal helix of factor Xa (residues 233-243). This exosite is physiologically highly relevant for the recognition and inhibition of factor X/Xa by macromolecular substrates and provides a structural motif for the development of a new class of inhibitors for the treatment of deep vein thrombosis and angioplasty. (c) 2006 Elsevier Ltd. All rights reserved.

Monte Carlo investigations of intermolecular interactions in water-amide mixtures

Monte Carlo simulations of water-amides (amide=fonnamide-FOR, methylfonnamide-NMF and dimethylformamide-DMF) solutions have been carried out in the NpT ensemble at 308 K and 1 atm. The structure and excess enthalpy of the mixtures as a function of the composition have been investigated. The TIP4P model was used for simulating water and six-site models previously optimized in this laboratory were used for simulating the liquid amides. The intermolecular interaction energy was calculated using the classical 6-12 Lennard-Jones potential plus a Coulomb term. The interaction energy between solute and solvent has been partitioned what leads to a better understanding of the behavior of the enthalpy of mixture obtained for the three solutions experimentally. Radial distribution functions for the water-amides correlations permit to explore the intermolecular interactions between the molecules. The results show that three, two and one hydrogen bonds between the water and the amide molecules are formed in the FOR, NMF and DMF-water solutions, respectively. These H-bonds are, respectively, stronger for DMF-water, NMF-water and FOR-water. In the NMF-water solution, the interaction between the methyl group of the NMF and the oxygen of the water plays a role in the stabilization of the aqueous solution quite similar to that of an H-bond in the FOR-water solution. (c) 2005 Elsevier B.V. All rights reserved.

Intermolecular interactions of the malate synthase of Paracoccidioides spp

Background: The fungus Paracoccidioides spp is the agent of paracoccidioidomycosis (PCM), a pulmonary mycosis acquired by the inhalation of fungal propagules. Paracoccidioides malate synthase (PbMLS) is important in the infectious process of Paracoccidioides spp because the transcript is up-regulated during the transition from mycelium to yeast and in yeast cells during phagocytosis by murine macrophages. In addition, PbMLS acts as an adhesin in Paracoccidioides spp. The evidence for the multifunctionality of PbMLS indicates that it could interact with other proteins from the fungus and host. The objective of this study was to identify and analyze proteins that possibly bind to PbMLS (PbMLS-interacting proteins) because protein interactions are intrinsic to cell processes, and it might be possible to infer the function of a protein through the identification of its ligands. Results: The search for interactions was performed using an in vivo assay with a two-hybrid library constructed in S. cerevisiae; the transcripts were sequenced and identified. In addition, an in vitro assay using pull-down GST methodology with different protein extracts (yeast, mycelium, yeast-secreted proteins and macrophage) was performed, and the resulting interactions were identified by mass spectrometry (MS). Some of the protein interactions were confirmed by Far-Western blotting using specific antibodies, and the interaction of PbMLS with macrophages was validated by indirect immunofluorescence and confocal microscopy. In silico analysis using molecular modeling, dynamics and docking identified the amino acids that were involved in the interactions between PbMLS and PbMLS-interacting proteins. Finally, the interactions were visualized graphically using Osprey software. Conclusion: These observations indicate that PbMLS interacts with proteins that are in different functional categories, such as cellular transport, protein biosynthesis, modification and degradation of proteins and signal transduction. These data suggest that PbMLS could play different roles in the fungal cell. © 2013 de Oliveira et al.; licensee BioMed Central Ltd.

Habitat use, reproductive traits and social interactions in a stream-dweller treefrog endemic to the Brazilian Cerrado

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Male and female interactions during courtship of the Neotropical damselfly Mnesarete pudica (Odonata: Calopterygidae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Darunavir: A Critical Review of Its Properties, Use and Drug Interactions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Dominance and Subordination Interactions Among Nestmates in Pre and Post-Emergence Phases of the Basal Eusocial Wasp Mischocyttarus (Monogynoecus) montei (Hymenoptera, Vespidae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Regular and chaotic interactions of two BPS dyons at low energy

We identify and analyze quasiperiodic and chaotic motion patterns in the time evolution of a classical, non-Abelian Bogomol'nyi-Prasad-Sommerfield (BPS) dyon pair at low energies. This system is amenable to the geodesic approximation which restricts the underlying SU(2) Yang-Mills-Higgs dynamics to an eight-dimensional phase space. We numerically calculate a representative set of long-time solutions to the corresponding Hamilton equations and analyze quasiperiodic and chaotic phase space regions by means of Poincare surfaces of section, high-resolution power spectra and Lyapunov exponents. Our results provide clear evidence for both quasiperiodic and chaotic behavior and characterize it quantitatively. Indications for intermittency are also discussed.

Subtractive renormalization of one-pion-exchange and contact interactions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

On energy transfer between vibrating systems under linear and nonlinear interactions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The membranotropic activity of N-terminal peptides from the pore-forming proteins sticholysin I and II is modulated by hydrophobic and electrostatic interactions as well as lipid composition

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Charge-orbital ordering and phase separation in the two-orbital model for manganites: Roles of Jahn-Teller phononic and Coulombic interactions

The main properties of realistic models for manganites are studied using analytic mean-field approximations and computational numerical methods, focusing on the two-orbital model with electrons interacting through Jahn-Teller (JT) phonons and/or Coulombic repulsions. Analyzing the model including both interactions by the combination of the mean-field approximation and the exact diagonalization method, it is argued that the spin-charge-orbital structure in the insulating phase of the purely JT-phononic model with a large Hund couphng J(H) is not qualitatively changed by the inclusion of the Coulomb interactions. As an important application of the present mean-held approximation, the CE-type antiferromagnetic state, the charge-stacked structure along the z axis, and (3x(2) - r(2))/(3y(2) - r(2))-type orbital ordering are successfully reproduced based on the JT-phononic model with large JH for the half-doped manganite, in agreement with recent Monte Carlo simulation results. Topological arguments and the relevance of the Heisenberg exchange among localized t(2g) spins explains why the inclusion of the nearest-neighbor Coulomb interaction does not destroy the charge stacking structure. It is also verified that the phase-separation tendency is observed both in purely JT-phononic (large JH) and purely Coulombic models in the vicinity of the hole undoped region, as long as realistic hopping matrices are used. This highlights the qualitative similarities of both approaches and the relevance of mixed-phase tendencies in the context of manganites. In addition, the rich and complex phase diagram of the two-orbital Coulombic model in one dimension is presented. Our results provide robust evidence that Coulombic and JT-phononic approaches to manganites are not qualitatively different ways to carry out theoretical calculations, but they share a variety of common features.

Ligand Exchange Inducing Efficient Incorporation of CisPt Derivatives into Ureasil-PPO Hybrid and Their Interactions with the Multifunctional Hybrid Network

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)