Publications

 

2012-2007 (Full list on Google Scholar)

 

2014

[1] Nascimento AS, Muniz JR, Aparício R, Golubev AM, Polikarpov I. Insights Into Structure and Function of Fungal beta-mannosidases from Glycoside Hydrolase Family 2 Based on Multiple Crystal Structures of T. harzianum Enzyme.  FEBS J. 2014 Jun 26. doi: 10.1111/febs.12894. [Epub ahead of print]

[2]Mello BL, Polikarpov I. Family 1 carbohydrate binding-modules enhance saccharification rates. AMB Express. 2014 Apr 25;4:36.

[3] Tamaki FK, Textor LC, Polikarpov I, Marana SR. Sets of Covariant Residues Modulate the Activity and Thermal Stability of GH1 β-Glucosidases. PLoS One. 2014 May 7;9(5):e96627.

[4]  Chandel AK, Antunes FA, Anjos V, Bell MJ, Rodrigues LN, Polikarpov I, de Azevedo ER, Bernardinelli OD, Rosa CA, Pagnocca FC, da Silva SS. Multi-scale structural and chemical analysis of sugarcane bagasse in the process of sequential acid-base pretreatment and ethanol production by Scheffersomyces shehatae and Saccharomyces cerevisiae. Biotechnol Biofuels. 2014 Apr 16;7(1):63. [Epub ahead of print]

[5] Bendo L, Casanova M, Figueira AC, Polikarpov I, Zucolotto V. Nanostructured sensors containing immobilized nuclear receptors for thyroid hormone detection. J Biomed Nanotechnol. 2014 May;10(5):744-50.

[6] Camilo CM, Polikarpov I. High-throughput cloning, expression and purification of glycoside hydrolases using Ligation-Independent Cloning (LIC). Protein Expr Purif. 2014 Jul;99:35-42.

[7] Segato F, Berto GL, Ares de Araújo E, Muniz JR, Polikarpov I. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Aspergillus terreus endo-β-1,4-glucanase from glycoside hydrolase family 12. Acta Crystallogr F Struct Biol Commun. 2014 Feb;70(Pt 2):267-70.

[8] Evangelista DE, Schutzer de Godoy A, Fonseca Pereira de Paula F, Henrique-Silva F, Polikarpov I. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the pectin methylesterase from the sugar cane weevil Sphenophorus levis. Acta Crystallogr F Struct Biol Commun. 2014 Mar;70(Pt 3):331-4.

[9] Horta MA, Vicentini R, Delabona Pda S, Laborda P, Crucello A, Freitas S, Kuroshu RM, Polikarpov I, Pradella JG, Souza AP. Transcriptome profile of Trichoderma harzianum IOC-3844 induced by sugarcane bagasse. PLoS One. 2014 Feb 18;9(2):e88689.

[10] Souza PC, Puhl AC, Martínez L, Aparício R, Nascimento AS, Figueira AC, Nguyen P, Webb P, Skaf MS, Polikarpov I. Identification of a new hormone-binding site on the surface of thyroid hormone receptor. Mol Endocrinol. 2014 Apr;28(4):534-45.

[11] Lima MA, Gomez LD, Steele-King CG, Simister R, Bernardinelli OD, Carvalho MA, Rezende CA, Labate CA, Deazevedo ER, McQueen-Mason SJ, Polikarpov I. Evaluating the composition and processing potential of novel sources of Brazilian biomass for sustainable biorenewables production. Biotechnol Biofuels. 2014 Jan 18;7(1):10.

[12] Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JR, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ. Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Nature. 2014 Jun 19;509(7505):422-6.

[13] Wichelecki DJ, Froese DS, Kopec J, Muniz JR, Yue WW, Gerlt JA. Enzymatic and structural characterization of rTSγ provides insights into the function of rTSβ. Biochemistry. 2014 Apr 29;53(16):2732-8.

[14] Zubcevic L, Bavro VN, Muniz JR, Schmidt MR, Wang S, De Zorzi R, Venien-Bryan C, Sansom MS, Nichols CG, Tucker SJ. Control of KirBac3.1 potassium channel gating at the interface between cytoplasmic domains. J Biol Chem. 2014 Jan 3;289(1):143-51.

 

2013

[1] da Silva FM, dos Santos JC, Campos JL, Mafud AC, Polikarpov I, Figueira AC, Nascimento AS. Structure-based identification of novel PPAR gamma ligands. Bioorg Med Chem Lett. 2013 Nov 1;23(21):5795-802.

[2] Lima MA, Oliveira-Neto M, Kadowaki MA, Rosseto FR, Prates ET, Squina FM, Leme AF, Skaf MS, Polikarpov I. Aspergillus niger β-glucosidase has a cellulase-like tadpole molecular shape: insights into glycoside hydrolase family 3 (GH3) β-glucosidase structure and function. J Biol Chem. 2013 Nov 15;288(46):32991-3005.

[3] de Araújo EA, Tomazini A Jr, Kadowaki MA, Murakami MT, Polikarpov I. Crystallization and preliminary X-ray diffraction analysis of a new xyloglucanase from Xanthomonas campestris pv. campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jun;69(Pt 6):676-8.

[4] Bernardes A, Souza PC, Muniz JR, Ricci CG, Ayers SD, Parekh NM, Godoy AS, Trivella DB, Reinach P, Webb P, Skaf MS, Polikarpov I. Molecular mechanism of peroxisome proliferator-activated receptor α activation by WY14643: a new mode of ligand recognition and receptor stabilization. J Mol Biol. 2013 Aug 23;425(16):2878-93.

[5] Dos Reis CV, Bernardes A, Polikarpov I. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Bifidobacterium adolescentis xylose isomerase. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 May 1;69(Pt 5):588-91.

[6] Lima MA, Lavorente GB, da Silva HK, Bragatto J, Rezende CA, Bernardinelli OD, Deazevedo ER, Gomez LD, McQueen-Mason SJ, Labate CA, Polikarpov I. Effects of pretreatment on morphology, chemical composition and enzymatic digestibility of eucalyptus bark: a potentially valuable source of fermentable sugars for biofuel production – part 1. Biotechnol Biofuels. 2013 May 9;6(1):75.

[7] Coletta VC, Rezende CA, da Conceição FR, Polikarpov I, Guimarães FE. Mapping the lignin distribution in pretreated sugarcane bagasse by confocal and fluorescence lifetime imaging microscopy. Biotechnol Biofuels. 2013 Apr 1;6(1):43.

[8] Prates ÉT, Stankovic I, Silveira RL, Liberato MV, Henrique-Silva F, Pereira N Jr, Polikarpov I, Skaf MS. X-ray structure and molecular dynamics simulations of endoglucanase 3 from Trichoderma harzianum: structural organization and substrate recognition by endoglucanases that lack cellulose binding module. PLoS One. 2013;8(3):e59069.

[9] Sant’anna RO, Braga CA, Polikarpov I, Ventura S, Lima LM, Foguel D. Inhibition of human transthyretin aggregation by non-steroidal anti-inflammatory compounds: a structural and thermodynamic analysis. Int J Mol Sci. 2013 Mar 6;14(3):5284-311.

[10] Rosseto FR, Puhl AC, Andrade MO, Polikarpov I. Crystallization and preliminary diffraction analysis of the catalytic domain of major extracellular endoglucanase from Xanthomonas campestris pv. campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Feb 1;69(Pt 2):137-40.

[11] Textor LC, Colussi F, Silveira RL, Serpa V, de Mello BL, Muniz JR, Squina FM, Pereira N Jr, Skaf MS, Polikarpov I. Joint X-ray crystallographic and molecular dynamics study of cellobiohydrolase I from Trichoderma harzianum: deciphering the structural features of cellobiohydrolase catalytic activity. FEBS J. 2013 Jan;280(1):56-69.

[12] Vaz de Lima LA, Nascimento AS. MolShaCS: a free and open source tool for ligand similarity identification based on Gaussian descriptors. Eur J Med Chem. 2013 Jan;59:296-303.

[13] Ferguson FM, Fedorov O, Chaikuad A, Philpott M, Muniz JR, Felletar I, von Delft F, Heightman T, Knapp S, Abell C, Ciulli A. Targeting low-druggability bromodomains: fragment based screening and inhibitor design against the BAZ2B bromodomain. J Med Chem. 2013 Dec 27;56(24):10183-7.

[14] Zubcevic L, Bavro VN, Muniz JR, Schmidt MR, Wang S, De Zorzi R, Venien-Bryan C, Sansom MS, Nichols CG, Tucker SJ. Control of KirBac3.1 potassium channel gating at the interface between cytoplasmic domains. J Biol Chem. 2014 Jan 3;289(1):143-51.

[15] Muniz JR, Guo K, Kershaw NJ, Ayinampudi V, von Delft F, Babon JJ, Bullock AN. Molecular architecture of the ankyrin SOCS box family of Cul5-dependent E3 ubiquitin ligases. J Mol Biol. 2013 Sep 9;425(17):3166-77.

[16] Shafqat N, Muniz JR, Pilka ES, Papagrigoriou E, von Delft F, Oppermann U, Yue WW. Insight into S-adenosylmethionine biosynthesis from the crystal structures of the human methionine adenosyltransferase catalytic and regulatory subunits. Biochem J. 2013 May 15;452(1):27-36.

 

2012

 

[1] F.A.H. Batista, D.B.B. Trivella, A. Bernardes, J. Gratieri, P.S.L. Oliveira, A.C.M. Figueira, P. Webb, I. Polikarpov, Structural Insights into Human Peroxisome Proliferator Activated Receptor Delta (PPAR-Delta) Selective Ligand Binding, Plos One 7 (2012).

 

[2] A. Bernardes, F.A.H. Batista, M.d.O. Neto, A.C.M. Figueira, P. Webb, D. Saidemberg, M.S. Palma, I. Polikarpov, Low-Resolution Molecular Models Reveal the Oligomeric State of the PPAR and the Conformational Organization of Its Domains in Solution, Plos One 7 (2012).

 

[3] F. Colussi, W. Garcia, F.R. Rosseto, B.L. Soares de Mello, M. de Oliveira Neto, I. Polikarpov, Effect of pH and temperature on the global compactness, structure, and activity of cellobiohydrolase Cel7A from Trichoderma harzianum, European Biophysics Journal with Biophysics Letters 41 (2012).

[4] M.C. Lemos, W.R. Correr, L.R. da Silva de Avo, C.M. Ramos Germano, C. Kurachi, I. Polikarpov, D.G. Melo, Fluorescence spectroscopy as a tool to detect and evaluate glucocorticoid-induced skin atrophy, Lasers in Medical Science 27 (2012).

[5] M.V. Liberato, W.C. Generoso, W. Malago, Jr., F. Henrique-Silva, I. Polikarpov, Crystallization and preliminary X-ray diffraction analysis of endoglucanase III from Trichoderma harzianum, Acta Crystallographica Section F-Structural Biology and Crystallization Communications 68 (2012).

[6] M.V. Liberato, A.S. Nascimento, S.D. Ayers, J.Z. Lin, A. Cvoro, R.L. Silveira, L. Martinez, P.C.T. Souza, D. Saidemberg, T. Deng, A.A. Amato, M. Togashi, W.A. Hsueh, K. Phillips, M.S. Palma, F.A.R. Neves, M.S. Skaf, P. Webb, I. Polikarpov, Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (PPAR) gamma Activators and Pan-PPAR Partial Agonists, Plos One 7 (2012).

[7] P. Maziero, M. de Oliveira Neto, D. Machado, T. Batista, C.C. Schmitt Cavalheiro, M.G. Neumann, A.F. Craievich, G.J. de Moraes Rocha, I. Polikarpov, A.R. Goncalves, Structural features of lignin obtained at different alkaline oxidation conditions from sugarcane bagasse, Industrial Crops and Products 35 (2012).

[8] A.C. Puhl, A. Bernardes, R.L. Silveira, J. Yuan, J.L.O. Campos, D.M. Saidemberg, M.S. Palma, A. Cvoro, S.D. Ayers, P. Webb, P.S. Reinach, M.S. Skaf, I. Polikarpov, Mode of Peroxisome Proliferator-Activated Receptor gamma Activation by Luteolin, Molecular Pharmacology 81 (2012) 788-799.

[9] A.C. Puhl, A. Bernardes, R.L. Silveira, J. Yuan, J.L.O. Campos, D.M. Saidemberg, M.S. Palma, A. Cvoro, S.D. Ayers, P. Webb, P.S. Reinach, M.S. Skaf, I. Polikarpov, Mode of Peroxisome Proliferator-Activated Receptor gamma Activation by Luteolin, Molecular Pharmacology 81 (2012).

[10] C.R. Santos, J.H. Paiva, M.L. Sforca, J.L. Neves, R.Z. Navarro, J. Cota, P.K. Akao, Z.B. Hoffmam, A.N. Meza, J.H. Smetana, M.L. Nogueira, I. Polikarpov, J. Xavier-Neto, F.M. Squina, R.J. Ward, R. Ruller, A.C. Zeri, M.T. Murakami, Dissecting structure-function-stability relationships of a thermostable GH5-CBM3 cellulase from Bacillus subtilis 168, Biochemical Journal 441 (2012).

 

2011

 

[1] L. Bleicher, E.T. Prates, T.C.F. Gomes, R.L. Silveira, A.S. Nascimento, A.L. Rojas, A. Golubev, L. Martinez, M.S. Skaf, I. Polikarpov, Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations, Journal of Physical Chemistry B 115 (2011).

[2] F. Colussi, V. Serpa, P.d.S. Delabona, L.R. Manzine, M.L. Voltatodio, R. Alves, B.L. Mello, N. Pereira, Jr., C.S. Farinas, A.M. Golubev, M.A. Morim Santos, I. Polikarpov, Purification, and Biochemical and Biophysical Characterization of Cellobiohydrolase I from Trichoderma harzianum IOC 3844, Journal of Microbiology and Biotechnology 21 (2011).

[3] K.C. dos Santos, M.F.G.F. da Silva, J.B. Fernandes, P.C. Vieira, I. Polikarpov, V. Zucolotto, M.R. Forim, Development and validation of a fast RP-HPLC method to determine the analogue of the thyroid hormone, 3,5,3 ‘-triiodothyroacetic acid (TRIAC), in polymeric nanoparticles, Analytical Methods 3 (2011).

[4] A.C.M. Figueira, D.M. Saidemberg, P.C.T. Souza, L. Martinez, T.S. Scanlan, J.D. Baxter, M.S. Skaf, M.S. Palma, P. Webb, I. Polikarpov, Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange, Molecular Endocrinology 25 (2011).

[5] R.N. Maeda, V.I. Serpa, V.A. Lima Rocha, R.A. Alves Mesquita, L.M. Melo Santa Anna, A.M. de Castro, C.E. Driemeier, N. Pereira, Jr., I. Polikarpov, Enzymatic hydrolysis of pretreated sugar cane bagasse using Penicillium funiculosum and Trichoderma harzianum cellulases, Process Biochemistry 46 (2011).

[6] L. Martinez, A.C.M. Figueira, P. Webb, I. Polikarpov, M.S. Skaf, Mapping the Intramolecular Vibrational Energy Flow in Proteins Reveals Functionally Important Residues, Journal of Physical Chemistry Letters 2 (2011).

[7] C.A. Rezende, M.A. de Lima, P. Maziero, E.R. deAzevedo, W. Garcia, I. Polikarpov, Chemical and morphological characterization of sugarcane bagasse submitted to a delignification process for enhanced enzymatic digestibility, Biotechnology for Biofuels 4 (2011).

[8] P.C.T. Souza, G.B. Barra, L.F.R. Velasco, I.C.J. Ribeiro, L.A. Simeoni, M. Togashi, P. Webb, F.A.R. Neves, M.S. Skaf, L. Martinez, I. Polikarpov, Helix 12 Dynamics and Thyroid Hormone Receptor Activity: Experimental and Molecular Dynamics Studies of Ile280 Mutants, Journal of Molecular Biology 412 (2011).

[9] L.C. Textor, J.C. Santos, N. Hidalgo Cuadrado, M.G. Roig, G.G. Zhadan, V.L. Shnyrov, I. Polikarpov, Purification, crystallization and preliminary crystallographic analysis of peroxidase from the palm tree Chamaerops excelsa, Acta Crystallographica Section F-Structural Biology and Crystallization Communications 67 (2011).

[10] D.B.B. Trivella, M.I. Sairre, D. Foguel, L.M.T.R. Lima, I. Polikarpov, The binding of synthetic triiodo L-thyronine analogs to human transthyretin: Molecular basis of cooperative and non-cooperative ligand recognition, Journal of Structural Biology 173 (2011).

 

2010

 

[1] F.A.H. Batista, L.S. Goto, W. Garcia, D.I. de Moraes, M. de Oliveira Neto, I. Polikarpov, M.R. Cominetti, H.S. Selistre-de-Araujo, L.M. Beltramini, A.P. Ulian Araujo, Camptosemin, a tetrameric lectin of Camptosema ellipticum: structural and functional analysis, European Biophysics Journal with Biophysics Letters 39 (2010).

[2] F. Colussi, L.C. Textor, V. Serpa, R.N. Maeda, N. Pereira, Jr., I. Polikarpov, Purification, crystallization and preliminary crystallographic analysis of the catalytic domain of the extracellular cellulase CBHI from Trichoderma harzianum, Acta Crystallographica Section F-Structural Biology and Crystallization Communications 66 (2010).

[3] A.S. de Araujo, L. Martinez, R.d.P. Nicoluci, M.S. Skaf, I. Polikarpov, Structural modeling of high-affinity thyroid receptor-ligand complexes, European Biophysics Journal with Biophysics Letters 39 (2010).

[4] H. Fischer, M. de Oliveira Neto, H.B. Napolitano, I. Polikarpov, A.F. Craievich, Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale, Journal of Applied Crystallography 43 (2010).

[5] L.M.T.R. Lima, V.d.A. Silva, L.d.C. Palmieri, M.C.B.R. Oliveira, D. Foguel, I. Polikarpov, Identification of a novel ligand binding motif in the transthyretin channel, Bioorganic & Medicinal Chemistry 18 (2010).

[6] L. Martinez, P.C.T. Souza, W. Garcia, F.A.H. Batista, R.V. Portugal, A.S. Nascimento, M. Nakahira, L.M.T.R. Lima, I. Polikarpov, M.S. Skaf, On the Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors, Journal of Physical Chemistry B 114 (2010).

[7] A.C. Migliorini Figueira, I. Polikarpov, D. Veprintsev, G.M. Santos, Dissecting the Relation between a Nuclear Receptor and GATA: Binding Affinity Studies of Thyroid Hormone Receptor and GATA2 on TSH beta Promoter, Plos One 5 (2010).

[8] A.C. Migliorini Figueira, L.M.T.R. Lima, L.H.F. Lima, A.T. Ranzani, G.d.S. Mule, I. Polikarpov, Recognition by the Thyroid Hormone Receptor of Canonical DNA Response Elements, Biochemistry 49 (2010).

[9] L.d.C. Palmieri, L.M.T.R. Lima, J.B.B. Freire, L. Bleicher, I. Polikarpov, F.C.L. Almeida, D. Foguel, Novel Zn2+-binding Sites in Human Transthyretin IMPLICATIONS FOR AMYLOIDOGENESIS AND RETINOL-BINDING PROTEIN RECOGNITION, Journal of Biological Chemistry 285 (2010).

[10] D.B.B. Trivella, L. Bleicher, L.d.C. Palmieri, H.J. Wiggers, C.A. Montanari, J.W. Kelly, L.M.T.R. Lima, D. Foguel, I. Polikarpov, Conformational differences between the wild type and V30M mutant transthyretin modulate its binding to genistein: Implications to tetramer stability and ligand-binding, Journal of Structural Biology 170 (2010).

[11] L. Watanabe, P.R. de Moura, L. Bleicher, A.S. Nascimento, L.S. Zamorano, J.J. Calvete, L. Sanz, A. Perez, S. Bursakov, M.G. Roig, V.L. Shnyrov, I. Polikarpov, Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia), Journal of Structural Biology 169 (2010).

[12] A.S. Nascimento, Structural requirement for PPARgamma binding revealed by a meta analysis of holo-crystal structures, Biochimie 92 (2010) 499-506.

 

2009

 

[1] S.T. Cunha Lima, N.-H. Nguyen, M. Togashi, J.W. Apriletti, P. Nguyen, I. Polikarpov, T.S. Scanlan, J.D. Baxter, P. Webb, Differential effects of TR ligands on hormone dissociation rates: Evidence for multiple ligand entry/exit pathways, Journal of Steroid Biochemistry and Molecular Biology 117 (2009).

[2] P.R. de Moura, L. Watanabe, L. Bleicher, D. Colau, L. Dumoutier, M.M. Lemaire, J.-C. Renauld, I. Polikarpov, Crystal structure of a soluble decoy receptor IL-22BP bound to interleukin-22, Febs Letters 583 (2009).

[3] B.G. Guimaraes, L. Sanfelici, R.T. Neuenschwander, F. Rodrigues, W.C. Grizolli, M.A. Raulik, J.R. Piton, B.C. Meyer, A.S. Nascimento, I. Polikarpov, The MX2 macromolecular crystallography beamline: a wiggler X-ray source at the LNLS, Journal of Synchrotron Radiation 16 (2009).

[4] B. Guimaraes, L. Sanfelici, R. Neuenschwander, F. Rodrigues, W. Grizolli, M. Raulik, J. Piton, B. Meyer, A. Nascimento, I. Polikarpov, The MX2 macromolecular crystallography beamline: a wiggler X-ray source at the LNLS, Journal of Synchrotron Radiation 16 (2009) 69-75.

[5] S. Krauchenco, N.H. Martins, M. Sanches, I. Polikarpov, Effectiveness of commercial inhibitors against subtype F HIV-1 protease, Journal of Enzyme Inhibition and Medicinal Chemistry 24 (2009).

[6] L.M.T.R. Lima, C.F. Becker, G.M. Giesel, A.F. Marques, M.T. Cargnelutti, M. de Oliveira Neto, R.Q. Monteiro, H. Verli, I. Polikarpov, Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases, Biochimica Et Biophysica Acta-Proteins and Proteomics 1794 (2009).

[7] L. Martinez, A.S. Nascimento, F.M. Nunes, K. Phillips, R. Aparicio, S.M.G. Dias, A.C.M. Figueira, J.H. Lin, P. Nguyen, J.W. Apriletti, F.A.R. Neves, J.D. Baxter, P. Webb, M.S. Skaf, I. Polikarpov, Gaining ligand selectivity in thyroid hormone receptors via entropy, Proceedings of the National Academy of Sciences of the United States of America 106 (2009).

[8] N.F. Valadares, L.B. Salum, I. Polikarpov, A.D. Andricopulo, R.C. Garratt, Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies, Journal of Chemical Information and Modeling 49 (2009).

[9] L. Watanabe, P.R. de Moura, A.S. Nascimento, D. Colau, L. Dumoutier, J.-C. Renauld, I. Polikarpov, Crystallization and preliminary X-ray diffraction analysis of human IL-22 bound to its soluble decoy receptor IL-22BP, Acta Crystallographica Section F-Structural Biology and Crystallization Communications 65 (2009).

 

2008

 

[1] L. Bleicher, P.R. de Moura, L. Watanabe, D. Colau, L. Dumoutier, J.-C. Renauld, I. Polikarpov, Crystal structure of the IL-22/IL-22R1 complex and its implications for the IL-22 signaling mechanism, Febs Letters 582 (2008).

[2] L. Bleicher, R. Aparicio, F.M. Nunes, L. Martinez, S.M. Gomes Dias, A.C. Migliorini Figueira, M.A. Morim Santos, W.H. Venturelli, R. da Silva, P.M. Donate, F.A.R. Neves, L.A. Simeoni, J.D. Baxter, P. Webb, M.S. Skaf, I. Polikarpov, Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms, Bmc Structural Biology 8 (2008).

[3] W. Garcia, A.C.M. Figueira, M.d.O. Neto, C.A. de Guzzi, H.H. Buzza, R.V. Portugal, M.R. Calgaro, I. Polikarpov, Probing conformational changes in orphan nuclear receptor: The NGFI-B intermediate is a partially unfolded dimer, Biophysical Chemistry 137 (2008).

[4] W. Garcia, N.C. Rodrigues, M. de Oliveira Neto, A.P. Ulian de Araujo, I. Polikarpov, M. Tanaka, T. Tanaka, R.C. Garratt, The stability and aggregation properties of the GTPase domain from human SEPT4, Biochimica Et Biophysica Acta-Proteins and Proteomics 1784 (2008).

[5] A.M. Golubev, A.L. Rojas, A.S. Nascimento, L. Bleicher, A.A. Kulminskaya, E.V. Eneyskaya, I. Polikarpov, Crystallization and Preliminary Crystallographic Analysis of Laminarinase from Rhodothermus marinus: A Case of Pseudomerohedral Twinning, Protein and Peptide Letters 15 (2008).

[6] K.-Y. Kim, A.S. Nascimento, A.M. Golubev, I. Polikarpov, C.-S. Kim, S.-I. Kang, S.-I. Kim, Catalytic mechanism of inulinase from Arthrobacter sp S37, Biochemical and Biophysical Research Communications 371 (2008).

[7] P. Kuser, F. Cupri, L. Bleicher, I. Polikarpov, Crystal structure of yeast hexokinase PI in complex with glucose: A classical “induced fit” example revised, Proteins-Structure Function and Bioinformatics 72 (2008).

[8] L. Martinez, I. Polikarpov, M.S. Skaf, Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered molecular dynamics approach, Journal of Physical Chemistry B 112 (2008).

[9] A.S. Nascimento, S. Krauchenco, A.M. Golubev, A. Gustchina, A. Wlodawer, I. Polikarpov, Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A, Journal of Molecular Biology 382 (2008).

[10] M.D.O. Neto, J.R. Ferreira, Jr., D. Colau, H. Fischer, A.S. Nascimento, A.F. Craievich, L. Dumoutier, J.-C. Renauld, I. Polikarpov, Interleukin-22 forms dimers that are recognized by two interleukin-22R1 receptor chains, Biophysical Journal 94 (2008).

[11] L.B. Salum, I. Polikarpov, A.D. Andricopulo, Structure-Based Approach for the Study of Estrogen Receptor Binding Affinity and Subtype Selectivity, Journal of Chemical Information and Modeling 48 (2008).

[12] M.T. Sonoda, L. Martinez, P. Webb, M.S. Skaf, I. Polikarpov, Ligand dissociation from estrogen receptor is mediated by receptor dimerization: Evidence from molecular dynamics simulations, Molecular Endocrinology 22 (2008).

[13] N.F. Valadares, I. Polikarpov, R.C. Garratt, Ligand induced interaction of thyroid hormone receptor beta with its coregulators, Journal of Steroid Biochemistry and Molecular Biology 112 (2008).

[14] L.S. Zamorano, D.G. Pina, J.B. Arellano, S.A. Bursakov, A.P. Zhadan, J.J. Calvete, L. Sanz, P.R. Nielsen, E. Villar, O. Gavel, M.G. Roig, L. Watanabe, I. Polikarpov, V.L. Shnyrov, Thermodynamic characterization of the palm tree Roystonea regia peroxidase stability, Biochimie 90 (2008).

 

2007

 

[1] A.L.B. Ambrosio, S.M.G. Dias, I. Polikarpov, R.B. Zurier, S.H. Burstein, R.C. Garratt, Ajulemic acid, a synthetic nonpsychoactive cannabinoid acid, bound to the ligand binding domain of the human peroxisome proliferator-activated receptor gamma, Journal of Biological Chemistry 282 (2007) 18625-18633.

[2] M.R. Calgaro, M.d.O. Neto, A.C.M. Figueira, M.A.M. Santos, R.V. Portugal, C.A. Guzzi, D.M. Saidemberg, L. Bleicher, J. Vernal, P. Fernandez, H. Terenzi, M.S. Palma, I. Polikarpov, Orphan nuclear receptor NGFI-B forms dimers with nonclassical interface, Protein Science 16 (2007).

[3] F.L. Leite, M.d.O. Neto, L.G. Paterno, M.R.M. Ballestero, I. Polikarpov, Y.P. Mascarenhas, P.S.P. Herrmann, L.H.C. Mattoso, O.N. Oliveira, Jr., Nanoscale conformational ordering in polyanilines investigated by SAXS and AFM, Journal of Colloid and Interface Science 316 (2007).

[4] H.C. Matozo, M.A.M. Santos, M.d.O. Neto, L. Bleicher, L.M.T.R. Lima, R. Iuliano, A. Fusco, I. Polikarpov, Low-resolution structure and fluorescence anisotropy analysis of protein tyrosine phosphatase eta catalytic domain, Biophysical Journal 92 (2007).

[5] A.C. Migliorini Figueira, M. de Oliveira Neto, A. Bernardes, S.M. Gomes Dias, A.F. Craievich, J.D. Baxter, P. Webb, I. Polikarpov, Low-resolution structures of thyroid hormone receptor dimers and tetramers in solution, Biochemistry 46 (2007).

[6] A.S. Nascimento, D.L. Catalano-Dupuy, A. Bernardes, M.d.O. Neto, M.A.M. Santos, E.A. Ceccarelli, I. Polikarpov, Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP(+) reductase and its complex with NADP(+), Bmc Structural Biology 7 (2007).

[7] L.B. Salum, I. Polikarpov, A.D. Andricopulo, Quantitative structure-activity relationships for a series of selective estrogen receptor-beta modulators, Sar and Qsar in Environmental Research 18 (2007).

[8] L.d.B. Salum, I. Polikarpov, A.D. Andricopulo, Structural and chemical basis for enhanced affinity and potency for a large series of estrogen receptor ligands: 2D and 3D QSAR studies, Journal of Molecular Graphics & Modelling 26 (2007).

[9] M. Sanches, S. Krauchenco, N.H. Martins, A. Gustchina, A. Wlodawer, I. Polikarpov, Structural characterization of B and non-B subtypes of HIV-protease: Insights into the natural susceptibility to drug resistance development, Journal of Molecular Biology 369 (2007).

[10] K.F. Santos, M.T. Murakami, A.C.O. Cintra, M.H. Toyama, S. Marangoni, V.P. Forrer, J.R. Brandao Neto, I. Polikarpov, R.K. Arni, Crystallization and preliminary X-ray crystallographic analysis of the heterodimeric crotoxin complex and the isolated subunits crotapotin and phospholipase A(2), Acta Crystallographica Section F-Structural Biology and Crystallization Communications 63 (2007).

[11] N.F. Valadares, M.S. Castilho, I. Polikarpov, R.C. Garratt, 2D QSAR studies on thyroid hormone receptor ligands, Bioorganic & Medicinal Chemistry 15 (2007).

[12] L. Watanabe, A.S. Nascimento, L.S. Zamorano, V.L. Shnyrov, I. Polikarpov, Purification, crystallization and preliminary X-ray diffraction analysis of royal palm tree (Roystonea regia) peroxidase, Acta Crystallographica Section F-Structural Biology and Crystallization Communications 63 (2007).

 

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