Prof. Guilherme Menegon Arantes

Instituto de Química – USP – Sala 0915, Bloco 9 inferior
Fone: 11-30913848         Email: garantes (at) iq.usp.br

Tese de livre docência: Bioquímica e biofísica computacionais: Simulações da reatividade e da estrutura de biomoléculas.

Tese de doutorado: Sobre as proteínas tirosina-fosfatases. Reatividade intrínseca de ésteres de fosfato e simulação computacional dos mecanismos de reação enzimática.

Currículos e IDs: Lattes, Google Scholar, ResearchGate, ORCID, ResearcherID .

Publicações representativas:

• Benchmark of approximate quantum chemical and machine learning potentials for biochemical proton transfer reactions, Arantes GM, Rezac J, J. Chem. Theory Comput., 2025;
• Supercomputação na era da inteligência artificial, Arantes GM, Jornal da USP, 12/Março/2025;
• Redox-activated proton transfer through a redundant network in the Qo site of cytochrome bc1, Arantes GM, J. Chem. Inf. Model., 65, 2660-2669, 2025;
• Flexibility and hydration of the Qo site determine multiple pathways for proton transfer in cytochrome bc1, Camilo SG, Arantes GM, J. Chem. Inf. Model., 65, 6184-6197, 2025;
• Dissecting reaction mechanisms and catalytic contributions in flavoprotein fumarate reductases, Curtolo F, Arantes GM, J. Chem. Inf. Model., 63, 3510-3520, 2023;
• Mechanism of rotenone binding to respiratory complex I depends on ligand flexibility, Pereira CS, Teixeira MH, Russell DA, Hirst J, Arantes GM, Sci. Rep., 13:6738, 2023;
• Molecular properties and tautomeric equilibria of isolated flavins, Curtolo F, Arantes GM. J. Comp. Chem., 43, 1561-1572, 2022, DOI: 10.1002/jcc.26957;
• Cryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy. Chung I, Wright JJ, Bridges HR, Ivanov BS, Biner O, Pereira CS,  Arantes GM,  Hirst J, Nat. Comm., 13, 2758, 2022;
• Interactions of truncated menaquinones in lipid monolayers and bilayers, Van Cleave C, Koehn
  JT, Pereira CS, Haase AA, Peters BJ, Koehn JT, Croslow SW, McLaughlin KG, Werst KR, Goach AL, Crick DC, Arantes GM, Crans DC. Int. J. Mol. Sci., 22, 9755, 2021;
• Highly dynamic polynuclear metal cluster revealed in a single metallothionein molecule, Yuan G, Curtolo F, Deng Y,Wu T, Tian F, Ma Q, Liu Y, Zuo J, Arantes GM, Zheng P. Research, vol. 2021, 9756945, 2021;
• Tunneling and nonadiabatic effects on a proton-coupled electron transfer model for the Qo site in cytochrome bc1, Camilo SG, Curtolo F, Galasi, VV, Arantes GM. J. Chem. Inf. Model., 61, 1840-1849, 2021;
• Mechanisms for flavin mediated oxidation: Hydride or hydrogen-atom transfer? Curtolo F e Arantes GM. J. Chem. Inf. Model., 60, 6282-6287, 2020;
• Combining free energy simulations and NMR chemical-shift perturbation to identify transient cation-pi contacts in proteins. Reis AAO, Sayegh RSR, Marana SR, Arantes GM. J. Chem. Inf. Model., 60, 890-897, 2020;
• Modelling the hydrolysis of iron-sulfur clusters. Teixeira MH, Curtolo F, Camilo SG, Field MJ, Zheng P, Li H, Arantes GM. J. Chem. Inf. Model., 60, 653-660, 2020;
• Balanced internal hydration discriminates substrate binding to respiratory complex I. Teixeira MH, Arantes GM. BBA Bioenergetics, 1860, 541-548, 2019;
• Effects of lipid composition on membrane distribution and permeability of natural quinones. Teixeira MH, Arantes GM. RSC Adv., 9, 16892-16899, 2019. Parâmetros do campo de força;
  
• Mutations close to a hub residue affect the distant active site of a GH1 β-glucosidase. Souza VP, Ikegami CM, Arantes GM, Marana SR. PlosOne, 13, e0198696, 2018;
• Escape of a small molecule from inside T4 lysozyme by multiple pathways.  Nunes-Alves A, Zuckerman DM, Arantes GM. Biophys. J., 114, 1058-1066, 2018;
• Mechanical unfolding of macromolecules coupled to bond dissociation. Nunes-Alves A, Arantes GM. J. Chem. Theory Comput., 14, 282-290, 2018;
• Conformational flexibility of the complete catalytic domain of Cdc25B phosphatases. Sayegh RSR, Tamaki FK, Marana SR, Salinas RK e Arantes GM. Proteins, 84, 1567-1575, 2016;
• Protein thermal denaturation is modulated by central residues in the protein structure network. Souza VP, Ikegami CM, Arantes GM, Marana SR. FEBS Journal, 283,1124-1138, 2016;
• Ferric-thiolate bond dissociation studied with electronic structure calculations. Arantes GM e Field MJ. J. Phys. Chem. A, 119, 10084-10090, 2015;
• Partition, orientation and mobility of ubiquinones in a lipid bilayer. Galassi VV e Arantes GM. BBA Bioenergetics, 1847, 1560-1573, 2015. Parâmetros do campo de força.
• Force-induced chemical reactions on the metal centre in a single metalloprotein molecule. Zheng P, Arantes GM, Field MJ e Li H. Nat. Commun., 6:7569, 2015;
• Ligand-receptor affinities computed by an adapted linear interaction model for continuum electrostatics and by protein conformational averaging. Nunes-Alves A, Arantes GM. J. Chem. Inf. Model., 54, 2309-2319, 2014;
• Theoretical modeling of low energy electronic transitions in reduced cobaloximes.  Bhattacharjee A, Chavarot-Kerlidou M, Dempsey JL, Gray HB, Fujita E, Fontecave M, Artero V, Arantes GM e Field MJ. ChemPhysChem, 15, 2951-2958, 2014;
• Homolytic cleavage of Fe-S bonds in rubredoxin under mechanical stress. Arantes GM, Bhattacharjee A, Field MJ. Angew. Chem. Int. Ed., 52, 8144-8146, 2013;
• A component of the Xanthomonadaceae type IV secretion system combines a VirB7 motif with a N0 domain found in outer membrane transport proteins.  Souza DP, Andrade MO, Alvarez-Martinez CE, Arantes GM, Farah CS, Salinas RK. PLOS Pathogens, 7, e1002031, 2011;
• Flexibility and inhibitor binding in Cdc25 phosphatases. Arantes GM. Proteins, 78, 3017-3032, 2010;
• Approximate multiconfigurational treatment of spin-coupled metal complexes. Arantes GM, Taylor PR. J. Chem. Theory Comp., 6, 1981-1989, 2010;
• The catalytic acid in the dephosphorylation of the Cdk2-pTpY/CycA protein complex by Cdc25B phosphatase. Arantes GM. J. Phys. Chem. B., 112, 15244–15247, 2008;
• A microscopic view of substitution reactions solvated by ionic liquids. Arantes GM, Ribeiro MCC. J. Chem. Phys., 128, 114503, 2008;
• A computational perspective on enzymatic catalysis. Arantes GM. Quim. Nova, 31, 377-383 , 2008;
• Free-energy profiles for catalysis by a dual-specificity phosphatase. Arantes GM. Biochemical Journal, 399, 343-350, 2006;
• Specific parametrisation of a hybrid potential to simulate reactions in Phosphatases. Arantes GM, Loos M. Phys. Chem. Chem. Phys., 8, 347-353, 2006;
• Thiolysis and alcoholysis of phosphate tri and monoesteres with aryl and alkyl leaving groups. An ab initio study in the gas-phase, Arantes GM, Chaimovich H. J. Phys. Chem. A, 109, 5625-5635, 2005;
• Parameterisation of the electronegativity equalisation method based on the charge model 1, Menegon G, Shimizu K, Farah JPS, Dias LG, Chaimovich H. Phys. Chem. Chem. Phys., 4, 5933-5936, 2002;
• Ab initio study on the thiolysis of trimethyl phosphate ester in the gas-phase, Menegon G, Loos M, Chaimovich H. J. Phys. Chem. A, 106(39), 9078-9084, 2002;