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Serrão VHB, Fernandes ADF, Basso LGM, Scortecci JF, Crusca Júnior E, Cornélio ML, de Souza BM, Palma MS, de Oliveira Neto M, Thiemann OH. The Specific Elongation Factor to Selenocysteine Incorporation in Escherichia coli: Unique tRNA Sec Recognition and its Interactions. J Mol Biol 2021; 433:167279. [PMID: 34624294 DOI: 10.1016/j.jmb.2021.167279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
Several molecular mechanisms are involved in the genetic code interpretation during translation, as codon degeneration for the incorporation of rare amino acids. One mechanism that stands out is selenocysteine (Sec), which requires a specific biosynthesis and incorporation pathway. In Bacteria, the Sec biosynthesis pathway has unique features compared with the eukaryote pathway as Ser to Sec conversion mechanism is accomplished by a homodecameric enzyme (selenocysteine synthase, SelA) followed by the action of an elongation factor (SelB) responsible for delivering the mature Sec-tRNASec into the ribosome by the interaction with the Selenocysteine Insertion Sequence (SECIS). Besides this mechanism being already described, the sequential events for Sec-tRNASec and SECIS specific recognition remain unclear. In this study, we determined the order of events of the interactions between the proteins and RNAs involved in Sec incorporation. Dissociation constants between SelB and the native as well as unacylated-tRNASec variants demonstrated that the acceptor stem and variable arm are essential for SelB recognition. Moreover, our data support the sequence of molecular events where GTP-activated SelB strongly interacts with SelA.tRNASec. Subsequently, SelB.GTP.tRNASec recognizes the mRNA SECIS to deliver the tRNASec to the ribosome. SelB in complex with its specific RNAs were examined using Hydrogen/Deuterium exchange mapping that allowed the determination of the molecular envelopes and its secondary structural variations during the complex assembly. Our results demonstrate the ordering of events in Sec incorporation and contribute to the full comprehension of the tRNASec role in the Sec amino acid biosynthesis, as well as extending the knowledge of synthetic biology and the expansion of the genetic code.
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Affiliation(s)
- Vitor Hugo Balasco Serrão
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil; Department of Chemistry and Biochemistry, University California - Santa Cruz, 1156 High St., Santa Cruz, CA 95060, United States
| | - Adriano de Freitas Fernandes
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil
| | - Luis Guilherme Mansor Basso
- Physical Sciences Laboratory, State University of Northern Rio de Janeiro Darcy Ribeiro - UENF, Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil; Faculty of Science, Philosophy and Letters, University of Sao Paulo, CEP 14040-901 Ribeirão Preto, SP, Brazil
| | - Jéssica Fernandes Scortecci
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Science Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Edson Crusca Júnior
- Department of Physical Chemistry, Chemistry Institute of the São Paulo State University - UNESP, CEP 14800-900 Araraquara, SP, Brazil
| | - Marinônio Lopes Cornélio
- Physics Department, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University - UNESP, São Jose do Rio Preto, SP, Brazil
| | - Bibiana Monson de Souza
- Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University - UNESP, Rio Claro, SP, Brazil
| | - Mário Sérgio Palma
- Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University - UNESP, Rio Claro, SP, Brazil
| | - Mario de Oliveira Neto
- Bioscience Institute of Universidade Estadual Paulista, Rubião Jr., Botucatu, SP CEP 18618-000, Brazil
| | - Otavio Henrique Thiemann
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil; Department of Genetics and Evolution, Federal University of São Carlos - UFSCar, 13565-905 São Carlos, SP, Brazil.
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2
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Erthal LCS, Marques AF, Almeida FCL, Melo GLM, Carvalho CM, Palmieri LC, Cabral KMS, Fontes GN, Lima LMTR. Regulation of the assembly and amyloid aggregation of murine amylin by zinc. Biophys Chem 2016; 218:58-70. [PMID: 27693831 DOI: 10.1016/j.bpc.2016.09.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 09/10/2016] [Accepted: 09/17/2016] [Indexed: 11/17/2022]
Abstract
The secretory granule of the pancreatic β-cells is a zinc-rich environment copopulated with the hormones amylin and insulin. The human amylin is shown to interact with zinc ions with major contribution from the single histidine residue, which is absent in amylin from other species such as cat, rhesus and rodents. We report here the interaction of murine amylin with zinc ions in vitro. The self-assembly of murine amylin is tightly regulated by zinc and pH. Ion mobility mass spectrometry revealed zinc interaction with monomers and oligomers. Nuclear magnetic resonance confirms the binding of zinc to murine amylin. The aggregation process of murine amylin into amyloid fibrils is accelerated by zinc. Collectively these data suggest a general role of zinc in the modulation of amylin variants oligomerization and amyloid fibril formation.
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Affiliation(s)
- Luiza C S Erthal
- School of Pharmacy, Federal University of Rio de Janeiro - UFRJ, CCS, Bss24, Ilha do Fundão, 21941-590 Rio de Janeiro, Brazil
| | - Adriana F Marques
- School of Pharmacy, Federal University of Rio de Janeiro - UFRJ, CCS, Bss24, Ilha do Fundão, 21941-590 Rio de Janeiro, Brazil
| | - Fábio C L Almeida
- School of Pharmacy, Federal University of Rio de Janeiro - UFRJ, CCS, Bss24, Ilha do Fundão, 21941-590 Rio de Janeiro, Brazil
| | - Gustavo L M Melo
- School of Pharmacy, Federal University of Rio de Janeiro - UFRJ, CCS, Bss24, Ilha do Fundão, 21941-590 Rio de Janeiro, Brazil
| | - Camila M Carvalho
- School of Pharmacy, Federal University of Rio de Janeiro - UFRJ, CCS, Bss24, Ilha do Fundão, 21941-590 Rio de Janeiro, Brazil
| | - Leonardo C Palmieri
- School of Pharmacy, Federal University of Rio de Janeiro - UFRJ, CCS, Bss24, Ilha do Fundão, 21941-590 Rio de Janeiro, Brazil
| | - Katia M S Cabral
- School of Pharmacy, Federal University of Rio de Janeiro - UFRJ, CCS, Bss24, Ilha do Fundão, 21941-590 Rio de Janeiro, Brazil
| | - Giselle N Fontes
- Laboratory for Macromolecules (LAMAC-DIMAV), Brazilian National Institute of Metrology, Quality and Technology - INMETRO, Av. N. Sa. das Graças, 50 - Xerém, Duque de Caxias-RJ, 25250-020 Rio de Janeiro, Brazil
| | - Luís Maurício T R Lima
- School of Pharmacy, Federal University of Rio de Janeiro - UFRJ, CCS, Bss24, Ilha do Fundão, 21941-590 Rio de Janeiro, Brazil; Laboratory for Macromolecules (LAMAC-DIMAV), Brazilian National Institute of Metrology, Quality and Technology - INMETRO, Av. N. Sa. das Graças, 50 - Xerém, Duque de Caxias-RJ, 25250-020 Rio de Janeiro, Brazil; National Institute of Science and Technology for Structural Biology and Bioimaging (INBEB-INCT), Federal University of Rio de Janeiro, Rio de Janeiro 21941-590, Brazil.
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3
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Lixa C, Marques AF, Cortines JR, Neves BC, Oliveira DM, Anobom CD, Lima LMT, Pinheiro AS. Refolding, purification, and preliminary structural characterization of the DNA-binding domain of the quorum sensing receptor RhlR from Pseudomonas aeruginosa. Protein Expr Purif 2016; 121:31-40. [DOI: 10.1016/j.pep.2016.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/18/2015] [Accepted: 01/08/2016] [Indexed: 12/22/2022]
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4
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Allosteric regulation of the Plasmodium falciparum cysteine protease falcipain-2 by heme. Arch Biochem Biophys 2015; 573:92-9. [PMID: 25791019 DOI: 10.1016/j.abb.2015.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/22/2015] [Accepted: 03/09/2015] [Indexed: 11/20/2022]
Abstract
During the erythrocytic cycle of Plasmodium falciparum malaria parasites break down host hemoglobin, resulting in the release of free heme (ferriprotoporphyrin IX). Heme is a generator of free radicals that cause oxidative stress, but it is detoxified by crystallization into hemozoin inside the food vacuole. We evaluated the interaction of heme and heme analogues with falcipain-2, a P. falciparum food vacuole cysteine protease that plays a key role in hemoglobin digestion. Heme bound to falcipain-2 with a 1:1 stoichiometry, and heme inhibited falcipain-2 activity against both human hemoglobin and chromogenic peptide substrates through a noncompetitive-like mechanism. A series of porphyrin analogues was screened for inhibition of falcipain-2, demonstrating a minor contribution of iron to heme-falcipain-2 interaction, and revealing dependence on both propionic and vinyl groups for inhibition of falcipain-2 by heme. Docking and molecular dynamics simulation unveiled a novel, inducible heme-binding moiety in falcipain-2 adjacent to the catalytic site. Kinetic data suggested that the noncompetitive-like inhibition was substrate inhibition induced by heme. Collectively these data suggest that binding of heme to falcipain-2 may limit the accumulation of free heme in the parasite food vacuole, providing a means of heme detoxification in addition to crystallization into hemozoin.
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Fattori J, Indolfo NDC, Campos JCLDO, Videira NB, Bridi AV, Doratioto TR, Assis MAD, Figueira ACM. Investigation of Interactions between DNA and Nuclear Receptors: A Review of the Most Used Methods. NUCLEAR RECEPTOR RESEARCH 2014. [DOI: 10.11131/2014/101090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Juliana Fattori
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Nathalia de Carvalho Indolfo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | | | - Natália Bernardi Videira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Aline Villanova Bridi
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Tábata Renée Doratioto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Michelle Alexandrino de Assis
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
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Silva JL, Oliveira AC, Vieira TCRG, de Oliveira GAP, Suarez MC, Foguel D. High-Pressure Chemical Biology and Biotechnology. Chem Rev 2014; 114:7239-67. [DOI: 10.1021/cr400204z] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jerson L. Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Andrea C. Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Tuane C. R. G. Vieira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Guilherme A. P. de Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Marisa C. Suarez
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Debora Foguel
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
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7
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Marques AF, Esser D, Rosenthal PJ, Kassack MU, Lima LMTR. Falcipain-2 inhibition by suramin and suramin analogues. Bioorg Med Chem 2013; 21:3667-73. [PMID: 23680445 DOI: 10.1016/j.bmc.2013.04.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/09/2013] [Accepted: 04/17/2013] [Indexed: 10/26/2022]
Abstract
Falcipain-2 is a cysteine protease of the malaria parasite Plasmodium falciparum that plays a key role in the hydrolysis of hemoglobin, a process that is required by intraerythrocytic parasites to obtain amino acids. In this work we show that the polysulfonated napthylurea suramin is capable of binding to falcipain-2, inhibiting its catalytic activity at nanomolar concentrations against both synthetic substrates and the natural substrate hemoglobin. Kinetic measurements suggest that the inhibition occurs through an noncompetitive allosteric mechanism, eliciting substrate inhibition. Smaller suramin analogues and those with substituted methyl groups also showed inhibition within the nanomolar range. Our results identify the suramin family as a potential starting point for the design of falcipain-2 inhibitor antimalarials that act through a novel inhibition mechanism.
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Affiliation(s)
- Adriana Fonseca Marques
- Laboratory for Pharmaceutical Biotechnology, School of Pharmacy, Federal University of Rio de Janeiro, CCS, Bss34, Ilha do Fundão, 21941-590 Rio de Janeiro, RJ, Brazil
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8
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Manzine LR, Serrão VHB, Lima LMTDRE, de Souza MM, Bettini J, Portugal RV, van Heel M, Thiemann OH. Assembly stoichiometry of bacterial selenocysteine synthase and SelC (tRNAsec). FEBS Lett 2013; 587:906-11. [DOI: 10.1016/j.febslet.2013.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/09/2013] [Accepted: 02/06/2013] [Indexed: 11/24/2022]
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9
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Macedo B, Millen TA, Braga CACA, Gomes MPB, Ferreira PS, Kraineva J, Winter R, Silva JL, Cordeiro Y. Nonspecific Prion Protein–Nucleic Acid Interactions Lead to Different Aggregates and Cytotoxic Species. Biochemistry 2012; 51:5402-13. [DOI: 10.1021/bi300440e] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruno Macedo
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, RJ 21941-590,
Rio de Janeiro, Brazil
| | - Thiago A. Millen
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Carolina A. C. A. Braga
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Mariana P. B. Gomes
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, RJ 21941-590,
Rio de Janeiro, Brazil
| | - Priscila S. Ferreira
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Julia Kraineva
- Faculty of Chemistry,
Physical
Chemistry I, Dortmund University, Dortmund,
Germany
| | - Roland Winter
- Faculty of Chemistry,
Physical
Chemistry I, Dortmund University, Dortmund,
Germany
| | - Jerson L. Silva
- Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro,
Brazil
| | - Yraima Cordeiro
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, RJ 21941-590,
Rio de Janeiro, Brazil
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10
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Sinha SK, Bandyopadhyay S. Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations. J Chem Phys 2012; 135:135101. [PMID: 21992339 DOI: 10.1063/1.3634004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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11
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Vieira TCRG, Reynaldo DP, Gomes MPB, Almeida MS, Cordeiro Y, Silva JL. Heparin Binding by Murine Recombinant Prion Protein Leads to Transient Aggregation and Formation of RNA-Resistant Species. J Am Chem Soc 2010; 133:334-44. [DOI: 10.1021/ja106725p] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tuane C. R. G. Vieira
- Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro 21491-902
| | - Daniel P. Reynaldo
- Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro 21491-902
| | - Mariana P. B. Gomes
- Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro 21491-902
| | - Marcius S. Almeida
- Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro 21491-902
| | - Yraima Cordeiro
- Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro 21491-902
| | - Jerson L. Silva
- Instituto de Bioquímica Médica, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro 21491-902
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Figueira ACM, Polikarpov I, Veprintsev D, Santos GM. Dissecting the Relation between a nuclear receptor and GATA: binding affinity studies of thyroid hormone receptor and GATA2 on TSHβ promoter. PLoS One 2010; 5:e12628. [PMID: 20838640 PMCID: PMC2935386 DOI: 10.1371/journal.pone.0012628] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 08/16/2010] [Indexed: 01/08/2023] Open
Abstract
Background Much is known about how genes regulated by nuclear receptors (NRs) are switched on in the presence of a ligand. However, the molecular mechanism for gene down-regulation by liganded NRs remains a conundrum. The interaction between two zinc-finger transcription factors, Nuclear Receptor and GATA, was described almost a decade ago as a strategy adopted by the cell to up- or down-regulate gene expression. More recently, cell-based assays have shown that the Zn-finger region of GATA2 (GATA2-Zf) has an important role in down-regulation of the thyrotropin gene (TSHβ) by liganded thyroid hormone receptor (TR). Methodology/Principal Findings In an effort to better understand the mechanism that drives TSHβ down-regulation by a liganded TR and GATA2, we have carried out equilibrium binding assays using fluorescence anisotropy to study the interaction of recombinant TR and GATA2-Zf with regulatory elements present in the TSHβ promoter. Surprisingly, we observed that ligand (T3) weakens TR binding to a negative regulatory element (NRE) present in the TSHβ promoter. We also show that TR may interact with GATA2-Zf in the absence of ligand, but T3 is crucial for increasing the affinity of this complex for different GATA response elements (GATA-REs). Importantly, these results indicate that TR complex formation enhances DNA binding of the TR-GATA2 in a ligand-dependent manner. Conclusions Our findings extend previous results obtained in vivo, further improving our understanding of how liganded nuclear receptors down-regulate gene transcription, with the cooperative binding of transcription factors to DNA forming the core of this process.
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Affiliation(s)
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Dmitry Veprintsev
- Biomolecular Research Laboratory, Paul Scherrer Institut, Villigen PSI, Switzerland
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Figueira ACM, Lima LMTR, Lima LHF, Ranzani AT, Mule GDS, Polikarpov I. Recognition by the thyroid hormone receptor of canonical DNA response elements. Biochemistry 2010; 49:893-904. [PMID: 20025240 DOI: 10.1021/bi901282s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To shed more light on the molecular requirements for recognition of thyroid response elements (TREs) by thyroid receptors (TRs), we compared the specific aspects of DNA TRE recognition by different TR constructs. Using fluorescence anisotropy, we performed a detailed and hierarchical study of TR-TRE binding. This was done by comparing the binding affinities of three different TR constructs for four different TRE DNA elements, including palindromic sequences and direct repeats (F2, PAL, DR-1, and DR-4) as well as their interactions with nonspecific DNA sequences. The effect of MgCl(2) on suppressing of nonselective DNA binding to TR was also investigated. Furthermore, we determined the dissociation constants of the hTRbeta DBD (DNA binding domain) and hTRbeta DBD-LBD (DNA binding and ligand binding domains) for specific TREs. We found that a minimum DNA recognition peptide derived from DBD (H1TR) is sufficient for recognition and interaction with TREs, whereas scrambled DNA sequences were unrecognized. Additionally, we determined that the TR DBD binds to F2, PAL, and DR-4 with high affinity and similar K(d) values. The TR DBD-LBD recognizes all the tested TREs but binds preferentially to F2, with even higher affinity. Finally, our results demonstrate the important role played by LBDs in modulating TR-DNA binding.
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Affiliation(s)
- Ana Carolina Migliorini Figueira
- Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, Av. Trabalhador Saocarlense, 400, Sao Carlos, SP, Brazil 13560-970
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Lima LMT, Silva VDA, Palmieri LDC, Oliveira MCB, Foguel D, Polikarpov I. Identification of a novel ligand binding motif in the transthyretin channel. Bioorg Med Chem 2010; 18:100-10. [DOI: 10.1016/j.bmc.2009.11.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 11/05/2009] [Accepted: 11/06/2009] [Indexed: 10/20/2022]
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15
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Romano SA, Cordeiro Y, Lima LMTR, Lopes MH, Silva JL, Foguel D, Linden R. Reciprocal remodeling upon binding of the prion protein to its signaling partner hop/STIl. FASEB J 2009; 23:4308-16. [DOI: 10.1096/fj.09-138974] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Sebastián A. Romano
- Instituto de Biofísica Carlos Chagas Filho Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Yraima Cordeiro
- Faculdade de Farmácia Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | | | | | - Jerson L. Silva
- Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Débora Foguel
- Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Rafael Linden
- Instituto de Biofísica Carlos Chagas Filho Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
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16
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Ishimaru D, Ano Bom APD, Lima LMTR, Quesado PA, Oyama MFC, de Moura Gallo CV, Cordeiro Y, Silva JL. Cognate DNA stabilizes the tumor suppressor p53 and prevents misfolding and aggregation. Biochemistry 2009; 48:6126-35. [PMID: 19505151 DOI: 10.1021/bi9003028] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The tumor suppressor protein p53 is a nuclear protein that serves as an important transcription factor. The region responsible for sequence-specific DNA interaction is located in its core domain (p53C). Although full-length p53 binds to DNA as a tetramer, p53C binds as a monomer since it lacks the oligomerization domain. It has been previously demonstrated that two core domains have a dimerization interface and undergo conformational change when bound to DNA. Here we demonstrate that the interaction with a consensus DNA sequence provides the core domain of p53 with enhanced conformational stability at physiological salt concentrations (0.15 M). This stability could be either increased or abolished at low (0.01 M) or high (0.3 M) salt concentrations, respectively. In addition, interaction with the cognate sequence prevents aggregation of p53C into an amyloid-like structure, whereas binding to a nonconsensus DNA sequence has no effect on p53C stability, even at low ionic strength. Strikingly, sequence-specific DNA binding also resulted in a large stabilization of full-length p53, whereas nonspecific sequence binding led to no stabilization. The effects of cognate DNA could be mimicked by high concentrations of osmolytes such as glycerol, which implies that the stabilization is caused by the exclusion of water. Taken together, our results show an enhancement in protein stability driven by specific DNA recognition. When cognate DNA was added to misfolded protein obtained after a pressurization cycle, the original conformation was mostly recovered. Our results may aid the development of therapeutic approaches to prevent misfolded species of p53.
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Affiliation(s)
- Daniella Ishimaru
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil
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17
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Enhanced prion protein stability coupled to DNA recognition and milieu acidification. Biophys Chem 2009; 141:135-9. [DOI: 10.1016/j.bpc.2008.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Revised: 12/23/2008] [Accepted: 12/23/2008] [Indexed: 11/19/2022]
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18
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Silva JL, Foguel D. Hydration, cavities and volume in protein folding, aggregation and amyloid assembly. Phys Biol 2009; 6:015002. [DOI: 10.1088/1478-3975/6/1/015002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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Matozo HC, Santos MAM, de Oliveira Neto M, Bleicher L, Lima LMTR, Iuliano R, Fusco A, Polikarpov I. Low-resolution structure and fluorescence anisotropy analysis of protein tyrosine phosphatase eta catalytic domain. Biophys J 2007; 92:4424-32. [PMID: 17400699 PMCID: PMC1877755 DOI: 10.1529/biophysj.106.094961] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rat protein tyrosine phosphatase eta, rPTPeta, is a class I "classical" transmembrane RPTP, with an intracellular portion composed of a unique catalytic region. The rPTPeta and the human homolog DEP-1 are downregulated in rat and human neoplastic cells, respectively. However, the malignant phenotype is reverted after exogenous reconstitution of rPTPeta, suggesting that its function restoration could be an important tool for gene therapy of human cancers. Using small-angle x-ray scattering (SAXS) and biophysical techniques, we characterized the intracellular catalytic domain of rat protein tyrosine phosphatase eta (rPTPetaCD) in solution. The protein forms dimers in solution as confirmed by SAXS data analysis. The SAXS data also indicated that rPTPetaCD dimers are elongated and have an average radius of gyration of 2.65 nm and a D(max) of 8.5 nm. To further study the rPTPetaCD conformation in solution, we built rPTPetaCD homology models using as scaffolds the crystallographic structures of RPTPalpha-D1 and RPTPmicro-D1 dimers. These models were, then, superimposed onto ab initio low-resolution SAXS structures. The structural comparisons and sequence alignment analysis of the putative dimerization interfaces provide support to the notion that the rPTPetaCD dimer architecture is more closely related to the crystal structure of autoinhibitory RPTPalpha-D1 dimer than to the dimeric arrangement exemplified by RPTPmicro-D1. Finally, the characterization of rPTPetaCD by fluorescence anisotropy measurements demonstrates that the dimer dissociation is concentration dependent with a dissociation constant of 21.6 +/- 2.0 microM.
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Affiliation(s)
- Huita C Matozo
- Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, São Carlos, Brazil
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20
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Sidorova NY, Muradymov S, Rau DC. Differences in hydration coupled to specific and nonspecific competitive binding and to specific DNA Binding of the restriction endonuclease BamHI. J Biol Chem 2006; 281:35656-66. [PMID: 17008319 DOI: 10.1074/jbc.m608018200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Using the osmotic stress technique together with a self-cleavage assay we measure directly differences in sequestered water between specific and nonspecific DNA-BamHI complexes as well as the numbers of water molecules released coupled to specific complex formation. The difference between specific and nonspecific binding free energy of the BamHI scales linearly with solute osmolal concentration for seven neutral solutes used to set water activity. The observed osmotic dependence indicates that the nonspecific DNA-BamHI complex sequesters some 120-150 more water molecules than the specific complex. The weak sensitivity of the difference in number of waters to the solute identity suggests that these waters are sterically inaccessible to solutes. This result is in close agreement with differences in the structures determined by x-ray crystallography. We demonstrate additionally that when the same solutes that were used in competition experiments are used to probe changes accompanying the binding of free BamHI to its specific DNA sequence, the measured number of water molecules released in the binding process is strikingly solute-dependent (with up to 10-fold difference between solutes). This result is expected for reactions resulting in a large change in a surface exposed area.
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Affiliation(s)
- Nina Y Sidorova
- Laboratory of Physical and Structural Biology, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA.
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21
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Rau DC. Sequestered water and binding energy are coupled in complexes of lambda Cro repressor with non-consensus binding sequences. J Mol Biol 2006; 361:352-61. [PMID: 16828799 DOI: 10.1016/j.jmb.2006.06.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 06/07/2006] [Accepted: 06/14/2006] [Indexed: 11/28/2022]
Abstract
We use the osmotic pressure dependence of dissociation rates and relative binding constants to infer differences in sequestered water among complexes of lambda Cro repressor with varied DNA recognition sequences. For over a 1000-fold change in association constant, the number of water molecules sequestered by non-cognate complexes varies linearly with binding free energy. One extra bound water molecule is coupled with the loss of approximately 150 cal/mol complex in binding free energy. Equivalently, every tenfold decrease in binding constant at constant salt and temperature is associated with eight to nine additional water molecules sequestered in the non-cognate complex. The relative insensitivity of the difference in water molecules to the nature of the osmolyte used to probe the reaction suggests that the water is sterically sequestered. If the previously measured changes in heat capacity for lambda Cro binding to different non-cognate sequences are attributed solely to this change in water, then the heat capacity change per incorporated water is almost the same as the difference between ice and water. The associated changes in enthalpies and entropies, however, indicate that the change in complex structure involves more than a simple incorporation of fixed water molecules that act as adaptors between non-complementary surfaces.
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Affiliation(s)
- Donald C Rau
- Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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22
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Faber-Barata J, Mohana-Borges R, Lima LMTR. Specificity in DNA recognition by a peptide from papillomavirus E2 protein. FEBS Lett 2006; 580:1919-24. [PMID: 16542651 DOI: 10.1016/j.febslet.2006.02.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 02/13/2006] [Accepted: 02/17/2006] [Indexed: 12/24/2022]
Abstract
The E2 proteins of papillomavirus specifically bind to double-stranded DNA containing the consensus sequence ACCG-N4-CGGT, where N is any nucleotide. Here, we show the binding and recognition of dissimilar DNA sequences by an 18 amino-acid peptide (alpha1E2), which corresponds to the DNA-recognition helix, alpha-helix-1. Isothermal DNA binding assays performed with the DNA consensus sequence show saturable curves with alpha1E2 peptide, and the alpha1E2 peptide is converted to an ordered conformation upon complexation. Measurements performed with non-specific DNA sequence fail to saturate, a behavior characteristic of non-specific binding. Binding of the alpha1E2 peptide to these DNA sequences display a different counter-ion dependence, indicating a dissimilar, sequence-dependent mechanism of interaction. Quantitative stoichiometric measurements revealed the specificity in alpha1E2 peptide recognition of the ACCG half-site, demonstrating capacity for discrimination of nucleic acid bases sequences without the need of a whole protein architecture.
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Affiliation(s)
- Joana Faber-Barata
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, sala Bs-34, Ilha do Fundão, 21941-590, Rio de Janeiro, RJ, Brazil
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23
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Blakaj DM, Kattamuri C, Khrapunov S, Hegde RS, Brenowitz M. Indirect readout of DNA sequence by papillomavirus E2 proteins depends upon net cation uptake. J Mol Biol 2006; 358:224-40. [PMID: 16513133 DOI: 10.1016/j.jmb.2006.01.093] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2005] [Revised: 01/08/2006] [Accepted: 01/27/2006] [Indexed: 10/25/2022]
Abstract
The papillomavirus E2 proteins bind with high affinity to palindromic DNA sequences consisting of two highly conserved four base-pair sequences flanking a variable "spacer" of identical length (ACCG NNNN CGGT). While intimate contacts are observed between the bound proteins and conserved DNA in the available co-crystal structures, no contact is seen between the proteins and the spacer DNA. The ability of human papillomavirus strain 16 (HPV-16) E2 and bovine papillomavirus strain 1 (BPV-1) E2 to discriminate among binding sites with different spacer sequences is dependent on their sensitivity to the unique conformational and/or dynamic properties of the spacer DNA in a process termed "indirect readout". Differential sequence-specific K(+) uptake in low ionic strength solutions lacking Mg(2+) is observed upon E2 protein binding to sites containing the AATT, TTAA or ACGT spacer sequences. In contrast, the cation displacement typical of protein-DNA complex formation is observed at high K(+) concentrations or in the presence of Mg(2+). These results are interpreted to reflect the sequence-specific stabilization of bent DNA conformations by cations localized within the narrowed minor grooves of the protein-bound DNA and the intrinsic structure and flexibility of the DNA target. Mg(2+) differentially affects the binding of the HPV-16 E2 DNA binding domain (HPV16-E2/D) and the BPV-1 E2 DNA binding domain (BPV1-E2/D) to sites bearing different spacer sequences. This study suggests that monovalent and divalent cations contribute to the discrimination of DNA structure and flexibility that could in turn contribute to the specificity with which HPV16-E2/D and BPV1-E2/D mediate DNA replication and gene transcription.
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Affiliation(s)
- Dukagjin M Blakaj
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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24
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Ferreiro DU, Dellarole M, Nadra AD, de Prat-Gay G. Free energy contributions to direct readout of a DNA sequence. J Biol Chem 2005; 280:32480-4. [PMID: 16000299 DOI: 10.1074/jbc.m505706200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The energetic contributions of individual DNA-contacting side chains to specific DNA recognition in the human papillomavirus 16 E2C-DNA complex is small (less than 1.0 kcal mol(-1)), independent of the physical and chemical nature of the interaction, and is strictly additive. The sum of the individual contributions differs 1.0 kcal mol(-1) from the binding energy of the wild-type protein. This difference corresponds to the contribution from the deformability of the DNA, known as "indirect readout." Thus, we can dissect the energetic contribution to DNA binding into 90% direct and 10% indirect readout components. The lack of high energy interactions indicates the absence of "hot spots," such as those found in protein-protein interfaces. These results are compatible with a highly dynamic and "wet" protein-DNA interface, yet highly specific and tight, where individual interactions are constantly being formed and broken.
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Affiliation(s)
- Diego U Ferreiro
- Instituto Leloir, Consejo Nacional de Investigaciones Científicas y Técnicas, and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
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