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Munusamy S, Conde R, Bertrand B, Munoz-Garay C. Biophysical approaches for exploring lipopeptide-lipid interactions. Biochimie 2020; 170:173-202. [PMID: 31978418 PMCID: PMC7116911 DOI: 10.1016/j.biochi.2020.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 01/19/2020] [Indexed: 02/07/2023]
Abstract
In recent years, lipopeptides (LPs) have attracted a lot of attention in the pharmaceutical industry due to their broad-spectrum of antimicrobial activity against a variety of pathogens and their unique mode of action. This class of compounds has enormous potential for application as an alternative to conventional antibiotics and for pest control. Understanding how LPs work from a structural and biophysical standpoint through investigating their interaction with cell membranes is crucial for the rational design of these biomolecules. Various analytical techniques have been developed for studying intramolecular interactions with high resolution. However, these tools have been barely exploited in lipopeptide-lipid interactions studies. These biophysical approaches would give precise insight on these interactions. Here, we reviewed these state-of-the-art analytical techniques. Knowledge at this level is indispensable for understanding LPs activity and particularly their potential specificity, which is relevant information for safe application. Additionally, the principle of each analytical technique is presented and the information acquired is discussed. The key challenges, such as the selection of the membrane model are also been briefly reviewed. A brief overview of topics to understand the generalities of lipopeptide (LP) science. Main analytical techniques used to reveal the interaction and the distorting effect of LP on artificial membranes. Guidelines for selecting of the most adequate membrane models for the given analytical technique.
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Affiliation(s)
- Sathishkumar Munusamy
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Renaud Conde
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico.
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Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study. Biophys J 2017; 111:2676-2688. [PMID: 28002744 DOI: 10.1016/j.bpj.2016.10.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/14/2016] [Accepted: 10/27/2016] [Indexed: 01/02/2023] Open
Abstract
A large number of antimicrobial peptides (AMPs) acts with high selectivity and specificity through interactions with membrane lipid components. These peptides undergo complex conformational changes in solution; upon binding to an interface, one major conformation is stabilized. Here we describe a study of the interaction between tritrpticin (TRP3), a cathelicidin AMP, and micelles of different chemical composition. The peptide's structure and dynamics were examined using one-dimensional and two-dimensional NMR. Our data showed that the interaction occurred by conformational selection and the peptide acquired similar structures in all systems studied, despite differences in detergent headgroup charge or dipole orientation. Fluorescence and paramagnetic relaxation enhancement experiments showed that the peptide is located in the interface region and is slightly more deeply inserted in 1-myristoyl-2-hydroxy-sn-glycero-3-phospho-1'-rac-glycerol (LMPG, anionic) than in 1-lauroyl-2-hydroxy-sn-glycero-3-phosphocholine (LLPC, zwitterionic) micelles. Moreover, the tilt angle of an assumed helical portion of the peptide is similar in both systems. In previous work we proposed that TRP3 acts by a toroidal pore mechanism. In view of the high hydrophobic core exposure, hydration, and curvature presented by micelles, the conformation of TRP3 in these systems could be related to the peptide's conformation in the toroidal pore.
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Silva AF, Torres MDT, Silva LDS, Alves FL, Pinheiro AADS, Miranda A, Capurro ML, Oliveira VX. New linear antiplasmodial peptides related to angiotensin II. Malar J 2015; 14:433. [PMID: 26537730 PMCID: PMC4634797 DOI: 10.1186/s12936-015-0974-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 10/28/2015] [Indexed: 01/18/2023] Open
Abstract
Background Antiplasmodial activities of angiotensin II and its analogues have been extensively investigated in Plasmodium gallinaceum and Plasmodium falciparum parasite species. Due to its vasoconstrictor property angiotensin II cannot be used as an anti-malarial drug. Methods This work presents the solid-phase syntheses and liquid chromatography and mass spectrometry characterization of ten linear peptides related to angiotensin II against mature P. gallinaceum sporozoites and erythrocyte invasion by P. falciparum. Conformational analyses were performed by circular dichroism. IC50 assays were performed to identify the ideal concentration used on the biological tests and haemolytical erythrocytic assays were made to verify the viability of the biological experiments. The contractile responses of the analogues were made to evaluate if they are promising candidates to be applied as antiplasmodial drugs. Results The results indicate two short-peptides constituted by hydrophobic residues (5 and 6) with antiplasmodial activity in these models, 89 and 94 % of biological activity against P. gallinaceum sporozoite, respectively, and around 50 % of activity against P. falciparum. Circular dichroism spectra suggested that all the peptides adopted β-turn conformation in different solutions, except peptide 3. Besides the biological assays IC50, the haemolysis assays and contractile response activities were applied for peptides 5 and 6, which did not present expressive results. Conclusions The hydrophobic portion and the arginine, tyrosine, proline, and phenylalanine, when present on peptide primary sequence, tend to increase the antiplasmodial activity. This class of peptides can be explored, as anti-malarial drugs, after in vivo model tests.The most active peptide presented 94 % activity on P. gallinaceum sporozoites and 53 % inhibited P. falciparum ring forms invasion ![]() Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0974-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adriana Farias Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Santa Adélia, 166, Santo André, SP, 09210-170, Brazil.
| | - Marcelo Der Torossian Torres
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Santa Adélia, 166, Santo André, SP, 09210-170, Brazil.
| | - Leandro de Souza Silva
- Instituto de Biofísica Carlos Chagas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Flávio Lopes Alves
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
| | - Ana Acácia de Sá Pinheiro
- Instituto de Biofísica Carlos Chagas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Antonio Miranda
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
| | - Margareth Lara Capurro
- Departamento de Parasitologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Vani Xavier Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Santa Adélia, 166, Santo André, SP, 09210-170, Brazil.
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Manzini MC, Perez KR, Riske KA, Bozelli JC, Santos TL, da Silva MA, Saraiva GK, Politi MJ, Valente AP, Almeida FC, Chaimovich H, Rodrigues MA, Bemquerer MP, Schreier S, Cuccovia IM. Peptide:lipid ratio and membrane surface charge determine the mechanism of action of the antimicrobial peptide BP100. Conformational and functional studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1985-99. [DOI: 10.1016/j.bbamem.2014.04.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 03/21/2014] [Accepted: 04/05/2014] [Indexed: 02/06/2023]
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Tinoco LW, Fraga JL, Anobom CD, Zolessi FR, Obal G, Toledo A, Pritsch O, Arruti C. Structural characterization of a neuroblast-specific phosphorylated region of MARCKS. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:837-49. [PMID: 24590112 DOI: 10.1016/j.bbapap.2014.02.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 02/07/2014] [Accepted: 02/20/2014] [Indexed: 11/19/2022]
Abstract
MARCKS (Myristoylated Alanine-Rich C Kinase substrate) is a natively unfolded protein that interacts with actin, Ca(2+)-Calmodulin, and some plasma membrane lipids. Such interactions occur at a highly conserved region that is specifically phosphorylated by PKC: the Effector Domain. There are two other conserved domains, MH1 (including a myristoylation site) and MH2, also located in the amino terminal region and whose structure and putative protein binding capabilities are currently unknown. MH2 sequence contains a serine that we described as being phosphorylated only in differentiating neurons (S25 in chick). Here, Circular Dichroism (CD) and Nuclear Magnetic Resonance (NMR) spectroscopy were used to characterize the phosphorylated and unphosphorylated forms of a peptide with the MARCKS sequence surrounding S25. The peptide phosphorylated at this residue is recognized by monoclonal antibody 3C3 (mAb 3C3). CD and NMR data indicated that S25 phosphorylation does not cause extensive modifications in the peptide structure. However, the sharper lines, the absence of multiple spin systems and relaxation dispersion data observed for the phosphorylated peptide suggested a more ordered structure. Surface Plasmon Resonance was employed to compare the binding properties of mAb 3C3 to MARCKS protein and peptide. SPR showed that mAb 3C3 binds to the whole protein and the peptide with a similar affinity, albeit different kinetics. The slightly ordered structure of the phosphorylated peptide might be at the origin of its ability to interact with mAb 3C3 antibody, but this binding did not noticeably modify the peptide structure.
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Affiliation(s)
- Luzineide W Tinoco
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Cidade Universitária, CCS, Bloco H, Rio de Janeiro 21941-902, RJ, Brazil.
| | - Jully L Fraga
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Cidade Universitária, CCS, Bloco H, Rio de Janeiro 21941-902, RJ, Brazil.
| | - Cristiane D Anobom
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, CT, Bloco A, Rio de Janeiro 21941-909, RJ, Brazil.
| | - Flavio R Zolessi
- Laboratorio de Cultivo de Tejidos, Sección Biología Celular, DBCM, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| | - Gonzalo Obal
- Unidad de Biofísica de Proteínas, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay.
| | - Andrea Toledo
- Laboratorio de Cultivo de Tejidos, Sección Biología Celular, DBCM, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| | - Otto Pritsch
- Unidad de Biofísica de Proteínas, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay.
| | - Cristina Arruti
- Laboratorio de Cultivo de Tejidos, Sección Biología Celular, DBCM, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
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Gomes-Neto F, Valente AP, Almeida FCL. Modeling the interaction of dodecylphosphocholine micelles with the anticoccidial peptide PW2 guided by NMR data. Molecules 2013; 18:10056-80. [PMID: 23966088 PMCID: PMC6270265 DOI: 10.3390/molecules180810056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial peptides are highly dynamic entities that acquire structure upon binding to a membrane interface. To better understand the structure and the mechanism for the molecular recognition of dodecylphosphocholine (DPC) micelles by the anticoccidial peptide PW2, we performed molecular dynamics (MD) simulations guided by NMR experimental data, focusing on strategies to explore the transient nature of micelles, which rearrange on a millisecond to second timescale. We simulated the association of PW2 with a pre-built DPC micelle and with free-DPC molecules that spontaneously forms micelles in the presence of the peptide along the simulation. The simulation with spontaneous micelle formation provided the adequate environment which replicated the experimental data. The unrestrained MD simulations reproduced the NMR structure for the entire 100 ns MD simulation time. Hidden discrete conformational states could be described. Coulomb interactions are important for initial approximation and hydrogen bonds for floating the aromatic region at the interface, being essential for the stabilization of the interaction. Arg9 is strongly attached with phosphate. We observed a helix elongation process stabilized by the intermolecular peptide-micelle association. Full association that mimics the experimental data only happens after complete micelle re-association. Fast micelle dynamics without dissociation of surfactants leads to only superficial binding.
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Affiliation(s)
- Francisco Gomes-Neto
- Laboratory of Toxinology, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21045-900, Brazil; E-Mail:
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro - Institute of Structural Biology and Bioimaging, Rio de Janeiro 21941-920, Brazil; E-Mail:
| | - Ana Paula Valente
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro - Institute of Structural Biology and Bioimaging, Rio de Janeiro 21941-920, Brazil; E-Mail:
| | - Fabio C. L. Almeida
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro - Institute of Structural Biology and Bioimaging, Rio de Janeiro 21941-920, Brazil; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +55-21-3104-2326; Fax: +55-21-3104-2326
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de Medeiros LN, Angeli R, Sarzedas CG, Barreto-Bergter E, Valente AP, Kurtenbach E, Almeida FCL. Backbone dynamics of the antifungal Psd1 pea defensin and its correlation with membrane interaction by NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1798:105-13. [PMID: 19632194 DOI: 10.1016/j.bbamem.2009.07.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 06/25/2009] [Accepted: 07/08/2009] [Indexed: 11/26/2022]
Abstract
Plant defensins are cysteine-rich cationic peptides, components of the innate immune system. The antifungal sensitivity of certain exemplars was correlated to the level of complex glycosphingolipids in the membrane of fungi strains. Psd1 is a 46 amino acid residue defensin isolated from pea seeds which exhibit antifungal activity. Its structure is characterized by the so-called cysteine-stabilized alpha/beta motif linked by three loops as determined by two-dimensional NMR. In the present work we explored the measurement of heteronuclear Nuclear Overhauser Effects, R1 and R2 (15)N relaxation ratios, and chemical shift to probe the backbone dynamics of Psd1 and its interaction with membrane mimetic systems with phosphatidylcholine (PC) or dodecylphosphocholine (DPC) with glucosylceramide (CMH) isolated from Fusarium solani. The calculated R2 values predicted a slow motion around the highly conserved among Gly12 residue and also in the region of the Turn3 His36-Trp38. The results showed that Psd1 interacts with vesicles of PC or PC:CMH in slightly different forms. The interaction was monitored by chemical shift perturbation and relaxation properties. Using this approach we could map the loops as the binding site of Psd1 with the membrane. The major binding epitope showed conformation exchange properties in the mus-ms timescale supporting the conformation selection as the binding mechanism. Moreover, the peptide corresponding to part of Loop1 (pepLoop1: Gly12 to Ser19) is also able to interact with DPC micelles acquiring a stable structure and in the presence of DPC:CMH the peptide changes to an extended conformation, exhibiting NOE mainly with the carbohydrate and ceramide parts of CMH.
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Affiliation(s)
- Luciano Neves de Medeiros
- Instituto de Biofísica Carlos Chagas Filho, Programa de Biologia Molecular e Estrutural, Universidade Federal do Rio de Janeiro, Brazil
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Melo MN, Sousa FJR, Carneiro FA, Castanho MARB, Valente AP, Almeida FCL, Da Poian AT, Mohana-Borges R. Interaction of the Dengue virus fusion peptide with membranes assessed by NMR: The essential role of the envelope protein Trp101 for membrane fusion. J Mol Biol 2009; 392:736-46. [PMID: 19619560 PMCID: PMC7094664 DOI: 10.1016/j.jmb.2009.07.035] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 07/06/2009] [Accepted: 07/13/2009] [Indexed: 11/30/2022]
Abstract
Dengue virus (DV) infection depends on a step of membrane fusion, which occurs in the acidic environment of the endosome. This process is mediated by virus surface envelope glycoprotein, in which the loop between residues D98-G112 is considered to be crucial, acting as a fusion peptide. Here, we have characterized functionally and structurally the interaction between the DV fusion peptide and different model membranes by fluorescence and NMR. Its interaction was strongest in dodecylphosphocholine (DPC) micelles and anionic phosphatidylcholine/phosphatidylglycerol vesicles, the only vesicle that was fused by DV fusion peptide. The three-dimensional structure of DV fusion peptide bound to DPC micelles was solved by solution homonuclear NMR with an r.m.s.d. of 0.98 A. The most striking result obtained from the solution structure was the hydrophobic triad formed by residues W101, L107, and F108, pointing toward the same direction, keeping the segment between G102 and G106 in a loop conformation. The interaction of DV fusion peptide with phosphatidylcholine/phosphatidylglycerol vesicles was also mapped by transfer-nuclear Overhauser enhancement (NOE) experiments, in which the majority of the NOE cross-peaks were from the hydrophobic triad, corroborating the DPC-bound structure. Substitution of the residue W101 by an alanine residue completely abolished membrane binding and, thus, fusion by the peptide and its NOE cross-peaks. In conclusion, the 15-residue DV fusion peptide has intrinsic ability to promote membrane fusion, most likely due to the hydrophobic interaction among the residues W101, L107, and F108, which maintains its loop in the correct spatial conformation.
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Affiliation(s)
- Manuel Nuno Melo
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ, Brazil
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Cardó-Vila M, Zurita AJ, Giordano RJ, Sun J, Rangel R, Guzman-Rojas L, Anobom CD, Valente AP, Almeida FCL, Lahdenranta J, Kolonin MG, Arap W, Pasqualini R. A ligand peptide motif selected from a cancer patient is a receptor-interacting site within human interleukin-11. PLoS One 2008; 3:e3452. [PMID: 18941632 PMCID: PMC2565473 DOI: 10.1371/journal.pone.0003452] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 09/24/2008] [Indexed: 01/30/2023] Open
Abstract
Interleukin-11 (IL-11) is a pleiotropic cytokine approved by the FDA against chemotherapy-induced thrombocytopenia. From a combinatorial selection in a cancer patient, we isolated an IL-11-like peptide mapping to domain I of the IL-11 (sequence CGRRAGGSC). Although this motif has ligand attributes, it is not within the previously characterized interacting sites. Here we design and validate in-tandem binding assays, site-directed mutagenesis and NMR spectroscopy to show (i) the peptide mimics a receptor-binding site within IL-11, (ii) the binding of CGRRAGGSC to the IL-11R alpha is functionally relevant, (iii) Arg4 and Ser8 are the key residues mediating the interaction, and (iv) the IL-11-like motif induces cell proliferation through STAT3 activation. These structural and functional results uncover an as yet unrecognized receptor-binding site in human IL-11. Given that IL-11R alpha has been proposed as a target in human cancer, our results provide clues for the rational design of targeted drugs.
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Affiliation(s)
- Marina Cardó-Vila
- The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Amado J. Zurita
- The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Ricardo J. Giordano
- The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Jessica Sun
- The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Roberto Rangel
- The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Liliana Guzman-Rojas
- The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | | | - Ana P. Valente
- National NMR Center, Federal University, Rio de Janeiro, Brazil
| | | | - Johanna Lahdenranta
- The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Mikhail G. Kolonin
- The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Wadih Arap
- The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (WA); (RP)
| | - Renata Pasqualini
- The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (WA); (RP)
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