Publications

2012

  • Structural Analysis of Pla Protein from the biological warfare agent Yersinia pestis: Docking and Molecular Dynamics of Interactions with the Mammalian Plasminogen System.
  • Journal of Biomolecular Structure and Dynamics.

    Ruback, E; Lobo, LA; França, TCC; Pascutti, PG

  • Molecular dynamics simulations of peptide inhibitors complexed with Trypanosoma cruzi trypanothione reductase.
  • Chemical Biology & Drug Design.

    Pita, SSR; Batista, PR; Albuquerque, MG; Pascutti, PG

  • Hybrid QM/MM molecular dynamics study of benzocaine in a membrane environment: how does a quantum mechanical treatment of both anesthetic and lipids affect their interaction.
  • Journal of Chemical Theory and Computation.

    Bernardi, RC; Pascutti, PG

  • GSAFold: A new application of GSA to protein structure prediction.
  • Proteins: Structure, Function, and Bioinformatics.

    Melo, MCR; Bernardi, RC; Fernandes, TVA; Pascutti, PG

  • The role of helices 5 and 6 on the human β1-adrenoceptor activation mechanism.
  • Molecular Simulation.

    Hoelz, LVB; Ribeiro, AAST; Bernardi, RC; Horta, BAC; Albuquerque, MG; Silva, JFM; Pascutti, PG; Alencastro, RB

     

    2011

  • Molecular dynamics simulations and QM/MM studies of the reactivation by 2-PAM of tabun inhibited human acethylcolinesterase.
  • Journal of the Brazilian Chemical Society

    Gonçalves, AS; França, TCC; Figueroa-Villar, JD; Pascutti, PG

  • Structural analysis of the N-terminal fragment of the antiangiogenic protein endostatin: A molecular dynamics study.
  • Proteins: Structure, Function, and Bioinformatics.

    Torres, PHM; Limaverde, GSCS; Pascutti, PG

  • Computational Perspectives into Plasmepsins Structure Function Relationship: Implications to Inhibitors Design.
  • Journal of Tropical Medicine.

    Gil, AL; Valiente, PA; Pascutti, PG; Pons, T

  • Dynamical behaviour of the human β1-adrenoceptor under agonist binding.
  • Molecular Simulation.

    Hoelz, LVB; Bernardi, RC; Horta, BAC; Araújo, JQ; Albuquerque, MG; Silva, JFM; Pascutti, PG; Alencastro, RB

  • Alvos Terapêuticos na Doença de Chagas: a Tripanotiona Redutase como Foco.
  • Revista Virtual de Química.

    Pita, SSR; Pascutti, PG;

  • Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding.
  • Journal of Physical Chemistry.

    Gomes, DEB; Lins, RD; Pascutti, PG; Chenghong, L; Soares, TA

  • Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening.
  • Journal of Chemical Theory and Computation

    Batista, PR; Pandey, G; Pascutti, PG; Bisch, PM; Perahia, D; Robert, CH

  • High temperatures enhance cooperative motions between CBM and catalytic domains of a thermostable cellulase: mechanism insights from essential dynamics.
  • Physical Chemistry Chemical Physics.

    Batista, PR; de Souza Costa, MG; Pascutti, PG; Bisch, PM; de Souza, W

     

    2010

  • Conformational Analysis of Toxogonine, TMB-4 and HI-6 using PM6 and RM1 methods.
  • Journal of the Brazilian Chemical Society.

    Gonçalves, AS; França, TCC; Figueroa-Villar, JD; Pascutti, PG

  • The Ionic Lock Activation Mechanism of the Human β1-adrenoceptor.
  • Drugs of the Future.

    Hoelz, LVB; Bernardi, RC; Albuquerque, MG; Silva, JFM; Pascutti, PG; Alencastro, RB

  • Design, docking studies and molecular dynamics of new potential selective inhibitors of Plasmodium falciparum serine hydroxymethyltransferase.
  • Molecular Simulation.

    Silva, ML; Gonçalves, AS; Batista, PR; Figueroa-Villar, JD; Pascutti, PG; França, TCC

  • The Role of Nonbonded Interactions in the Conformational Dynamics of Organophosphorous Hydrolase Adsorbed onto Functionalized Mesoporous Silica Surfaces.
  • Journal of Physical Chemistry. B

    Gomes, DEB; Lins, RD; Pascutti, PG; Chenghong, L; Soares, TAG

  • Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis application to the HIV-1 protease.
  • Physical Chemistry Chemical Physics.

    Batista, PR; Robert, CH; Maréchal, JD; Hamida-Rebai, MB; Pascutti, PG; Bisch, PM; Perahia, D

  • Self-affine analysis of protein energy.
  • Physica. A

    Figueirêdo, PH; Moret, MA; Pascutti, PG; Nogueira Jr., E; Coutinho, S

  • How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics.
  • BMC Genomics.

    Costa, MGS; Batista, PR; Shida, CS; Robert, CH; Bisch, PM; Pascutti, PG

  • Conformational selection, dynamic restriction and the hydrophobic effect coupled to stabilization of the BIR3 domain of the human X-linked inhibitor of apoptosis protein by the tetrapeptide AVPI
  • Biophysical Chemistry.

    Souza, TLF; Sanches, D; Gonçalves, RB; Pita, SSR; Pascutti, PG; Bianconi, ML; Almeida, FCL; Silva, JL; Oliveira, AC

  • New parameterization approaches of the LIE method to improve free energy calculations of PlmII-Inhibitors complexes.
  • Journal of Computational Chemistry.

    Valiente, PA; Gil, AL; Batista, PR; Caffarena, ER; Pons, T; Pascutti, PG

  • Understanding the HIV-1 protease nelfinavir resistance mutation D30N in subtypes B and C through molecular dynamics simulations.
  • Journal of Molecular Graphics & Modelling.

    Soares, RO; Batista, PR; Costa, MGS; Dardenne, LE; Pascutti, PG; Soares, MA

  • Solvation of anionic water-soluble porphyrins: A computational study.
  • International Journal of Quantum Chemistry.

    Guizado, TRC; Louro, SRW; Pascutti, PG; Anteneodo, C

     

    2009

  • Dissociation of molecular aggregates under high hydrostatic pressure: the influence of water structure on Benzene cluster solubility.
  • Journal of the Brazilian Chemical Society.

    Gonçalves, AS; Caffarena, ER; Pascutti, PG

  • Molecular Dynamics Study of Biomembrane-Local Anesthetics Interactions.
  • Molecular Physics.

    Bernardi, RC; Gomes, DEB; Taft, CA; Ota, AT; Pascutti, PG

  • Self-similarity and protein compactness.
  • Physical Review. E

    Moret, MA; Santana, MC; Zebende, GF; Pascutti, PG

    Highly Cited Papers

    Prof. Pedro Pascutti publications have been cited over 300 times (ISI) as of June 2012. The most highly cited publications are listed below:

     

    Research Categories

    • Molecular Dynamics Videos to Teach Biochemistry

      Is under development at our lab a new way to teach biochemistry using videos from molecular simulations. These videos can help high-school and undergrad students to better understand biochemical process, such as an enzymatic reaction.

    • Anesthetics and Ion Channels

      Detailing the action mechanisms of anesthetics, both local (LA) and general (GA), have been the purpose of several studies, since this is not well established. The anesthetics interactions with ion channels and membrane lipids are essential to understand its effect. Experiments had showed that the TREK-1, a K2P channel, is of paramount importance for these anesthetic effects. Most of the channel sensitivity to local and GA is attributed to its intracellular C-terminal moiety, which works as a sensor domain required for integration of the anesthetic action into channel activity. We have investigated by MD simulations the anesthetic effect, specificaly its interaction with the biological membrane and the TREK-1 channel. Overall, the MD study reveals a direct coupling of the TREK-1 C-terminus to the intracellular membrane surface. Also, negatively charged lipids and intracellular acidosis could increase such interaction. In our simulations with the general anesthetic isoflurane, we show that the channels opening must be an indirect reaction of the membrane swelling. Regarding the local anesthetics, our MD simulations combined with free-energy and QM/MM calculations, indicate that charged forms of LA interacts most with the lipid/water interface and that uncharged LA can interchange between both bilayer faces.

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    • Cellulose and 2nd Generation Biofuels

      The imminent lack of fuel instigated by the upcoming end of the world’s oil reserves has increased the interest in new energy sources. Biofuels are an alternative largely used in Brazil, where gasoline and ethanol consumption are about the same. However, to the ethanol production, just the sugarcane juice is employed and a large amount of biomass is not efficiently used. This colossal amount of resources, specially the cellulose fibers, is the basis to the production of the so called second generation biofuels. Nevertheless, the crystalline structure of the cellulose fibers is a big challenge, since enzymes do not efficiently degrade this kind of structure, however they do efficiently break down imperfect fibers. Structural studies had shown the importance of a hydrogen bond web to stabilize these fibers. In this work, we are studying the behavior of this fiber using molecular modeling tools, in order to develop a technic to break down these hydrogen bonds, which should lead to the production of single chains or even a less structured fiber. In this work, QM/MM MD simulations of a fully hydrated cellulose fiber segment were carried out to observe the influence of the hydration in the fiber stability. The structure obtained using these simulations were used as input in a DFT study of a small portion of the fiber. These QM simulations were carried out to study the energy and frequency of the inter-chain hydrogen bond. Our simulations are showing a very stable frequency value to these bonds and we could use it to break these H-bonds using QM/MM calculations, to produce a resonance phenomenon.

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    • Protein Folding

      The rate of experimental determination of protein structures is still very slow when compared with the rate of accumulation data of the amino acids sequences. This makes protein folding a central problem for the development of post genome biology. Nowadays, the determination of protein structures is achieved through two main experimental techniques: X-ray Crystallography and Nuclear Magnetic Resonance (NMR). However, due to limitations in these techniques, several methods of in silico prediction of protein folding were developed in the last few years. We focused on a combination of two computational methods, Generalized Simulated Annealing (GSA) - based in the generalized thermodynamics proposed by Tsallis - and Molecular Dynamics (MD), to investigate the protein folding problem. Initially, we used the GSA methodology on an idealized model, based in polialanine polymers, to find the optimal GSA parameters. After these adjustments, we studied the GSA performance in complex structures. Furthermore, we used the MD method to refine the low energy final structures of each model proposed with the GSA method. The first realistic model studied was the mastoparan-X, a peptide extracted from wasp venom that is very important for the study of new antibiotics. The results showed that the optimization of the extended mastoparan-X structure with the GSA method and subsequent refinement with Molecular Dynamics was an excellent strategy for protein folding studies.

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    • Software Development

      Computational Biology has expanded our reach into biological systems. It has done so by increasing our ability to explore and simulate multiple cells, metabolic or signaling routes or even single molecules. All done with the help of computers and especially designed software. In our group, the aim has been to develop computational methods to predict protein structures and the binding of ligands to proteins.
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    • Neurotoxic Agent Tabun

      The elucidation of the reactivation routes of human acetylcholinesterase (HuAChE) inhibited by organophosphorous compounds is of crucial importance to the development of efficient antidotes against poisoning by chemical warfare agents. In order to contribute to a better understanding of the reactivation mechanism, we applied, in this work, classical molecular dynamics (MD) simulations to study the interactions between pralidoxime (2 PAM), one known o xime used as antidote, and the active site's amino acids of HuAChE inhibited by the neurotoxic agent tabun (GA). Further, quantum mechanical/molecular mechanical (QM/MM) hybrid methods were used to propose a reactivation mechanism for the inhibited enzyme. It is important to notice that before the QM/MM studies; it was necessary to compile a computational package to merge two programs, MOPAC with RM1 semi-empirical method and the GROMACS version 3.3.3 package.