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Vasconcelos AA, Estrada JC, Caruso IP, Kurtenbach E, Zingali RB, Almeida FCL. Toward the mechanism of jarastatin (rJast) inhibition of the integrin αVβ3. Int J Biol Macromol 2024; 255:128078. [PMID: 37972836 DOI: 10.1016/j.ijbiomac.2023.128078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/04/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Disintegrins are a family of cysteine-rich small proteins that were first identified in snake venom. The high divergence of disintegrins gave rise to a plethora of functions, all related to the interaction with integrins. Disintegrins evolved to interact selectively with different integrins, eliciting many physiological outcomes and being promising candidates for the therapy of many pathologies. We used NMR to determine the structure and dynamics of the recombinant disintegrin jarastatin (rJast) and its interaction with the cancer-related integrin αVβ3. rJast displayed the canonical fold of a medium-sized disintegrin and showed complex dynamic in multiple timescales. We used NMR experiments to map the interaction of rJast with αVβ3, and molecular docking followed by molecular dynamics (MD) simulation to describe the first structural model of a disintegrin/integrin complex. We showed that not only the RGD loop participates in the interaction, but also the N-terminal domain. rJast plasticity was essential for the interaction with αVβ3 and correlated with the main modes of motion depicted in the MD trajectories. In summary, our study provides novel structural insights that enhance our comprehension of the mechanisms underlying disintegrin functionality.
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Affiliation(s)
- Ariana A Vasconcelos
- Laboratório de RMN de Biomoléculas, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Centro Nacional de Ressonância Magnética Nuclear (CNRMN), Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jorge C Estrada
- Laboratório de Hemostase e Venenos, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Icaro P Caruso
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto, São Paulo, Brazil
| | - Eleonora Kurtenbach
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Russolina B Zingali
- Laboratório de Hemostase e Venenos, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Fabio C L Almeida
- Laboratório de RMN de Biomoléculas, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Centro Nacional de Ressonância Magnética Nuclear (CNRMN), Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Dias RVR, Pedro RP, Sanches MN, Moreira GC, Leite VBP, Caruso IP, de Melo FA, de Oliveira LC. Unveiling Metastable Ensembles of GRB2 and the Relevance of Interdomain Communication during Folding. J Chem Inf Model 2023; 63:6344-6353. [PMID: 37824286 DOI: 10.1021/acs.jcim.3c00955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
The folding process of multidomain proteins is a highly intricate phenomenon involving the assembly of distinct domains into a functional three-dimensional structure. During this process, each domain may fold independently while interacting with others. The folding of multidomain proteins can be influenced by various factors, including their composition, the structure of each domain, or the presence of disordered regions, as well as the surrounding environment. Misfolding of multidomain proteins can lead to the formation of nonfunctional structures associated with a range of diseases, including cancers or neurodegenerative disorders. Understanding this process is an important step for many biophysical analyses such as stability, interaction, malfunctioning, and rational drug design. One such multidomain protein is growth factor receptor-bound protein 2 (GRB2), an adaptor protein that is essential in regulating cell survival. GRB2 consists of one central Src homology 2 (SH2) domain flanked by two Src homology 3 (SH3) domains. The SH2 domain interacts with phosphotyrosine regions in other proteins, while the SH3 domains recognize proline-rich regions on protein partners during cell signaling. Here, we combined computational and experimental techniques to investigate the folding process of GRB2. Through computational simulations, we sampled the conformational space and mapped the mechanisms involved by the free energy profiles, which may indicate possible intermediate states. From the molecular dynamics trajectories, we used the energy landscape visualization method (ELViM), which allowed us to visualize a three-dimensional (3D) representation of the overall energy surface. We identified two possible parallel folding routes that cannot be seen in a one-dimensional analysis, with one occurring more frequently during folding. Supporting these results, we used differential scanning calorimetry (DSC) and fluorescence spectroscopy techniques to confirm these intermediate states in vitro. Finally, we analyzed the deletion of domains to compare our model outputs to previously published results, supporting the presence of interdomain modulation. Overall, our study highlights the significance of interdomain communication within the GRB2 protein and its impact on the formation, stability, and structural plasticity of the protein, which are crucial for its interaction with other proteins in key signaling pathways.
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Affiliation(s)
- Raphael V R Dias
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Renan P Pedro
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Murilo N Sanches
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
| | - Giovana C Moreira
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Vitor B P Leite
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
| | - Icaro P Caruso
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Fernando A de Melo
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Leandro C de Oliveira
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
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3
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Almeida FCL, Sanches K, Caruso IP, Melo FA. NMR Relaxation Dispersion Experiments to Study Phosphopeptide Recognition by SH2 Domains: The Grb2-SH2-Phosphopeptide Encounter Complex. Methods Mol Biol 2023; 2705:135-151. [PMID: 37668973 DOI: 10.1007/978-1-0716-3393-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Protein interactions are at the essence of life. Proteins evolved not to have stable structures, but rather to be specialized in participating in a network of interactions. Every interaction involving proteins comprises the formation of an encounter complex, which may have two outcomes: (i) the dissociation or (ii) the formation of the final specific complex. Here, we present a methodology to characterize the encounter complex of the Grb2-SH2 domain with a phosphopeptide. This method can be generalized to other protein partners. It consists of the measurement of 15N CPMG relaxation dispersion (RD) profiles of the protein in the free state, which describes the residues that are in conformational exchange. We then acquire the dispersion profiles of the protein at a semisaturated concentration of the ligand. At this condition, the chemical exchange between the free and bound state leads to the observation of dispersion profiles in residues that are not in conformational exchange in the free state. This is due to fuzzy interactions that are typical of the encounter complexes. The transient "touching" of the ligand in the protein partner generates these new relaxation dispersion profiles. For the Grb2-SH2 domain, we observed a wider surface at SH2 for the encounter complex than the phosphopeptide (pY) binding site, which might explain the molecular recognition of remote phosphotyrosine. The Grb2-SH2-pY encounter complex is dominated by electrostatic interactions, which contribute to the fuzziness of the complex, but also have contribution of hydrophobic interactions.
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Affiliation(s)
- Fabio C L Almeida
- National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- Institute of Medical Biochemistry - IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Karoline Sanches
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- ARC Centre for Fragment-Based Design, Monash University, Parkville, VIC, Australia
| | - Icaro P Caruso
- National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), Sao Jose do Rio Preto, Sao Paulo, Brazil
| | - Fernando A Melo
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), Sao Jose do Rio Preto, Sao Paulo, Brazil
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Almeida VS, Miller LL, Delia JPG, Magalhães AV, Caruso IP, Iqbal A, Almeida FCL. Deciphering the Path of S-nitrosation of Human Thioredoxin: Evidence of an Internal NO Transfer and Implication for the Cellular Responses to NO. Antioxidants (Basel) 2022; 11:antiox11071236. [PMID: 35883729 PMCID: PMC9311519 DOI: 10.3390/antiox11071236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 01/27/2023] Open
Abstract
Nitric oxide (NO) is a free radical with a signaling capacity. Its cellular functions are achieved mainly through S-nitrosation where thioredoxin (hTrx) is pivotal in the S-transnitrosation to specific cellular targets. In this study, we use NMR spectroscopy and mass spectrometry to follow the mechanism of S-(trans)nitrosation of hTrx. We describe a site-specific path for S-nitrosation by measuring the reactivity of each of the 5 cysteines of hTrx using cysteine mutants. We showed the interdependence of the three cysteines in the nitrosative site. C73 is the most reactive and is responsible for all S-transnitrosation to other cellular targets. We observed NO internal transfers leading to C62 S-nitrosation, which serves as a storage site for NO. C69-SNO only forms under nitrosative stress, leading to hTrx nuclear translocation.
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Affiliation(s)
- Vitor S. Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
- National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil
- Institute of Chemistry, Rural Federal University of Rio de Janeiro (UFRRJ), Seropédica 23897-000, Brazil
| | - Lara L. Miller
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
| | - João P. G. Delia
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
| | - Augusto V. Magalhães
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
| | - Icaro P. Caruso
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
- Institute of Chemistry, Rural Federal University of Rio de Janeiro (UFRRJ), Seropédica 23897-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto 15054-000, Brazil
| | - Anwar Iqbal
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
- Department of Chemical Sciences, University of Lakki Marwat, Lakki Marwat 28420, Pakistan
| | - Fabio C. L. Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil; (V.S.A.); (L.L.M.); (J.P.G.D.); (A.V.M.); (I.P.C.); (A.I.)
- Correspondence:
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5
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Nunes DBSM, Vieira C, Sá JM, Araújo GC, Caruso IP, Souza FP. M2-2 gene as a new alternative molecular marker for phylogenetic, phylodynamic, and evolutionary studies of hRSV. Virus Res 2022; 318:198850. [PMID: 35750131 DOI: 10.1016/j.virusres.2022.198850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 10/18/2022]
Abstract
The human Respiratory Syncytial Virus (hRSV) is the main causative agent of acute respiratory infections (ARI), such as pneumonia and bronchiolitis. One of the factors that lead to success in viral replication is the interaction of the M2-2 protein with the ribosomal complex. This interaction is responsible for the phase change of viral activity, acting as an inhibitor or inducer of viral replication, according to the concentration of mRNA. Based on the importance of M2-2 gene and protein have to viral physiology, we performed here evaluations of genetic diversity, phylogenetic reconstructions, phylodynamics, and selection test. Our results suggested an alternative way of classifying this virus in clades A and B, based on a new phylogenetic marker, the M2-2 gene. Therefore, our study is the first one to investigate the dynamics of the evolutionary diversification process of hRSV from the perspective of the M2-2 viral gene. In our study was also identified that the M2-2 gene is under the effect of purifying selection originated by population genetic bottlenecks. Therefore, the M2-2 gene demonstrated an interesting potential to be applied in evolutionary studies involving hRSV, recovering phylogenetic signals and traits of natural selection under the evolution of this virus.
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Affiliation(s)
- Denis Bruno S M Nunes
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), Campus A.C. Simões, AL, Brazil
| | - Camila Vieira
- Department of Basic Sciences, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, SP, Brazil
| | - Jéssica M Sá
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil
| | - Gabriela C Araújo
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil
| | - Icaro P Caruso
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil; Institute of Medical Biochemistry Leopoldo de Meis and National Center for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
| | - Fátima P Souza
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil.
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Almeida FCL, Sanches K, Pinheiro-Aguiar R, Almeida VS, Caruso IP. Protein Surface Interactions-Theoretical and Experimental Studies. Front Mol Biosci 2021; 8:706002. [PMID: 34307462 PMCID: PMC8298896 DOI: 10.3389/fmolb.2021.706002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
In this review, we briefly describe a theoretical discussion of protein folding, presenting the relative contribution of the hydrophobic effect versus the stabilization of proteins via direct surface forces that sometimes may be overlooked. We present NMR-based studies showing the stability of proteins lacking a hydrophobic core which in turn present hydrophobic surface clusters, such as plant defensins. Protein dynamics measurements by NMR are the key feature to understand these dynamic surface clusters. We contextualize the measurement of protein dynamics by nuclear relaxation and the information available at protein surfaces and water cavities. We also discuss the presence of hydrophobic surface clusters in multidomain proteins and their participation in transient interactions which may regulate the function of these proteins. In the end, we discuss how surface interaction regulates the reactivity of certain protein post-translational modifications, such as S-nitrosation.
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Affiliation(s)
- Fabio C L Almeida
- Institute of Medical Biochemistry-IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Karoline Sanches
- Institute of Medical Biochemistry-IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Multiuser Center for Biomolecular Innovation (CMIB), Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São Paulo, Brazil
| | - Ramon Pinheiro-Aguiar
- Institute of Medical Biochemistry-IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vitor S Almeida
- Institute of Medical Biochemistry-IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Icaro P Caruso
- Institute of Medical Biochemistry-IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Multiuser Center for Biomolecular Innovation (CMIB), Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São Paulo, Brazil
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7
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Neves-Martins TC, Mebus-Antunes NC, Caruso IP, Almeida FCL, Da Poian AT. Unique structural features of flaviviruses' capsid proteins: new insights on structure-function relationship. Curr Opin Virol 2021; 47:106-112. [PMID: 33721656 DOI: 10.1016/j.coviro.2021.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 10/21/2022]
Abstract
The Flaviviridae family comprises important human pathogens, including Dengue, Zika, West Nile, Yellow Fever and Japanese Encephalitis viruses. The viral genome, a positive-sense single-stranded RNA, is packaged by a single protein, the capsid protein, which is a small and highly basic protein that form intertwined homodimers in solution. Atomic-resolution structures of four flaviviruses capsid proteins were solved either in solution by nuclear magnetic resonance spectroscopy, or after protein crystallization by X-ray diffraction. Analyses of these structures revealed very particular properties, namely (i) the predominance of quaternary contacts maintaining the structure; (ii) a highly electropositive surface throughout the protein; and (iii) a flexible helix (α1). The goal of this review is to discuss the role of these features in protein structure-function relationship.
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Affiliation(s)
- Thais C Neves-Martins
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil
| | - Nathane C Mebus-Antunes
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil
| | - Icaro P Caruso
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil; Multiuser Center for Biomolecular Innovation (CMIB) and Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), 15054-000, São José do Rio Preto, SP, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil; National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil.
| | - Andrea T Da Poian
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil.
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8
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Sanches K, Caruso IP, Almeida FCL, Melo FA. The dynamics of free and phosphopeptide-bound Grb2-SH2 reveals two dynamically independent subdomains and an encounter complex with fuzzy interactions. Sci Rep 2020; 10:13040. [PMID: 32747626 PMCID: PMC7398917 DOI: 10.1038/s41598-020-70034-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/20/2020] [Indexed: 01/18/2023] Open
Abstract
The growth factor receptor-bound protein 2 (Grb2) is a key factor in the regulation of cell survival, proliferation, differentiation, and metabolism. In its structure, the central Src homology 2 (SH2) domain is flanked by two Src homology 3 (SH3). SH2 is the most important domain in the recognition of phosphotyrosines. Here, we present the first dynamical characterization of Grb2-SH2 domain in the free state and in the presence of phosphopeptide EpYINSQV at multiple timescales, which revealed valuable information to the understanding of phophotyrosine sensing mechanism. Grb2-SH2 presented two dynamically independent subdomains, subdomain I involved in pY recognition and subdomain II is the pY + 2 specificity pocket. Under semi-saturated concentrations of pY-pep we observed fuzzy interactions, which led to chemical exchange observed by NMR. This information was used to describe the encounter complex. The association with pY-pep is dynamic, involving fuzzy interactions and multiple conformations of pY-pep with negative and hydrophobic residues, creating an electrostatic-potential that drives the binding of pY-pep. The recognition face is wider than the binding site, with many residues beyond the central SH2 binding site participating in the association complex, which contribute to explain previously reported capability of Grb2 to recognize remote pY.
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Affiliation(s)
- Karoline Sanches
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto, São Paulo, Brazil
| | - Icaro P Caruso
- Institute of Medical Biochemistry - IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto, São Paulo, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry - IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil. .,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Fernando A Melo
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto, São Paulo, Brazil.
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Rudge MVC, Souza FP, Abbade JF, Hallur RLS, Marcondes JPC, Piculo F, Marini G, Vesentini G, Thabane L, Witkin SS, Calderon IMP, Barbosa AMP, Rudge MV, Barbosa AMP, Calderon IMP, Souza FP, Abbade JF, Hallur LSR, Piculo F, Marini G, Vesentini G, Thabane L, Palma MS, Graeff CFO, Arni RK, Herculano RD, Salvadori DF, Mateus S, Dal Pai Silva M, Magalhães CG, Costa RA, Lima SAM, Felisbino SL, Barbosa W, Atallah A, Girão MJB, Di Bella Z, Uchoa SM, Payão S, Hijas A, Berghman B, De Bie R, Sobrevia L, Junginger B, Alves FCB, Rossignoli PS, Prudencio CB, Orlandi MIG, Gonçalves MI, Nunes SK, Catinelli BB, Quiroz S, Sarmento BV, Pinheiro FA, Sartorão CI, Lucas RR, Reyes DRA, Quiroz SBCV, Enriquez EMA, Oliveira RG, Floriano JF, Marcondes JPC, Barneze S, Dangió TD, Pascon T, Rossignoli P, Freitas JV, Takano L, Reis F, Caldeirão TD, Fernandes JN, Carr AM, Gaitero MVC, Corrente JE, Nunes HRC, Candido AF, Costa SMB, Dangió TD, Pascon T, Melo JVF, Takano L, Reis FVDS, Caldeirão TD, Carr AM, Garcia GA, Rabadan GB, Bassin HCM, Suyama KS, Damasceno LN, Takemoto MLS, Menezes MD, Bussaneli DG, Nogueira VKC, Lima PR, Lourenço IO, Marostica de Sá J, Megid RA, Caruso IP, Rasmussen LT, Prata GM, Piculo F, Vesentini G, Arantes MA, Ferraz GAR, Camargo LP, Kron MR, Corrente JE, Nunes HRC. Study protocol to investigate biomolecular muscle profile as predictors of long-term urinary incontinence in women with gestational diabetes mellitus. BMC Pregnancy Childbirth 2020; 20:117. [PMID: 32075598 PMCID: PMC7031907 DOI: 10.1186/s12884-020-2749-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 01/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pelvic floor muscles (PFM) and rectus abdominis muscles (RAM) of pregnant diabetic rats exhibit atrophy, co-localization of fast and slow fibers and an increased collagen type I/III ratio. However, the role of similar PFM or RAM hyperglycemic-related myopathy in women with gestational diabetes mellitus (GDM) remains poorly investigated. This study aims to assess the frequency of pelvic floor muscle disorders and pregnancy-specific urinary incontinence (PS-UI) 12 months after the Cesarean (C) section in women with GDM. Specifically, differences in PFM/RAM hyperglycemic myopathy will be evaluated. METHODS The Diamater is an ongoing cohort study of four groups of 59 pregnant women each from the Perinatal Diabetes Research Centre (PDRC), Botucatu Medical School (FMB)-UNESP (São Paulo State University), Brazil. Diagnosis of GDM and PS-UI will be made at 24-26 weeks, with a follow-up at 34-38 weeks of gestation. Inclusion in the study will occur at the time of C-section, and patients will be followed at 24-48 h, 6 weeks and 6 and 12 months postpartum. Study groups will be classified as (1) GDM plus PS-UI; (2) GDM without PS-UI; (3) Non-GDM plus PS-UI; and (4) Non-GDM without PS-UI. We will analyze relationships between GDM, PS-UI and hyperglycemic myopathy at 12 months after C-section. The mediator variables to be evaluated include digital palpation, vaginal squeeze pressure, 3D pelvic floor ultrasound, and 3D RAM ultrasound. RAM samples obtained during C-section will be analyzed for ex-vivo contractility, morphological, molecular and OMICS profiles to further characterize the hyperglycemic myopathy. Additional variables to be evaluated include maternal age, socioeconomic status, educational level, ethnicity, body mass index, weight gain during pregnancy, quality of glycemic control and insulin therapy. DISCUSSION To our knowledge, this will be the first study to provide data on the prevalence of PS-UI and RAM and PFM physical and biomolecular muscle profiles after C-section in mothers with GDM. The longitudinal design allows for the assessment of cause-effect relationships between GDM, PS-UI, and PFMs and RAMs myopathy. The findings may reveal previously undetermined consequences of GDM.
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Affiliation(s)
- Marilza V C Rudge
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil.
| | - Fátima P Souza
- Physics Department, Institute of Biosciences, Letters and Exact Sciences, Multiuser Center for Biomolecular Innovation, UNESP-São Paulo State University, Sao Paulo, Brazil
| | - Joelcio F Abbade
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil
| | - Raghavendra L S Hallur
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil
| | - João Paulo C Marcondes
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil
| | - Fernanda Piculo
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil.,Physiotherapy Department, Faculdades Integradas de Bauru, FIB, Sao Paulo, Brazil
| | - Gabriela Marini
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil.,Universidade do Sagrado Coração (USC), Jardim Brasil, Bauru, Sao Paulo, Brazil
| | - Giovana Vesentini
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil
| | - Lehana Thabane
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare-Hamilton, Hamilton, ON, Canada
| | - Steven S Witkin
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA.,Institute of Tropical Medicine, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Iracema M P Calderon
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil
| | - Angélica M P Barbosa
- Department of Gynecology and Obstetrics, Botucatu Medical School (FMB), São Paulo State University (UNESP), CEP18618-687, Sao Paulo, Brazil.,School of Philosophy and Sciences, Department of Physiotherapy and Occupational Therapy, UNESP-São Paulo State University, Marília, Sao Paulo, Brazil
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Floriano JF, Caruso IP, Barbosa AM, Graeff CF, de Souza FP, Rudge MV. The Application of NMR Metabolomics in the Study of the Wound Healing Process. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Caruso IP, Panwalkar V, Coronado MA, Dingley AJ, Cornélio ML, Willbold D, Arni RK, Eberle RJ. Structure and interaction of Corynebacterium pseudotuberculosis cold shock protein A with Y-box single-stranded DNA fragment. FEBS J 2017; 285:372-390. [PMID: 29197185 DOI: 10.1111/febs.14350] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/07/2017] [Accepted: 11/29/2017] [Indexed: 11/28/2022]
Abstract
Cold shock proteins (Csps) function to preserve cell viability at low temperatures by binding to nucleic acids and consequently control gene expression. The mesophilic bacterium Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis in animals, and infection in livestock is a considerable economic burden worldwide. In this report, the structure of cold shock protein A from Cp (Cp-CspA) and biochemical analysis of its temperature-dependent interaction with a Y-box ssDNA motif is presented. The Cp-CspA structure contains five β-strands making up a β-barrel fold with 11 hydrophobic core residues and two salt bridges that confers it with a melting temperature of ~ 54 °C that is similar to mesophilic Bs-CspB. Chemical shift perturbations analysis revealed that residues in the nucleic acid-binding motifs (RNP 1 and 2) and loop 3 are involved in binding to the Y-box fragment either by direct interaction or by conformational rearrangements remote from the binding region. Fluorescence quenching experiments of Cp-CspA showed that the dissociation constants for Y-box ssDNA binding is nanomolar and the binding affinity decreased as the temperature increased, indicating that the interaction is enthalpically driven and the hydrogen bonds and van der Waals forces are important contributions for complex stabilization. The Y31 of Cp-CspA is a particular occurrence among Csps from mesophilic bacteria that provide a possible explanation for the higher binding affinity to ssDNA than that observed for Bs-CspB. Anisotropy measurements indicated that the reduction in molecular mobility of Cp-CspA upon Y-box binding is characterized by a cooperative process. DATABASE Resonance assignment and structural data are available in the Biological Magnetic Resonance Data Bank and Protein Data Bank under accession number 26802 and 5O6F, respectively.
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Affiliation(s)
- Icaro P Caruso
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Vineet Panwalkar
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Monika A Coronado
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Andrew J Dingley
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Marinônio L Cornélio
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Dieter Willbold
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Raghuvir K Arni
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Raphael J Eberle
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
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Coronado MA, Caruso IP, Oliveira VMD, Contessoto VG, Leite VBP, Kawai LA, Arni RK, Eberle RJ. Cold Shock Protein A from Corynebacterium pseudotuberculosis: Role of Electrostatic Forces in the Stability of the Secondary Structure. Protein Pept Lett 2017; 24:358-367. [PMID: 28176661 DOI: 10.2174/0929866524666170207153808] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/25/2017] [Accepted: 01/25/2017] [Indexed: 11/22/2022]
Abstract
The conformational stability of the Cold shock protein A (CspA) from C. pseudotuberculosis (Cp), a nucleic acid binding protein in function of pH and salt concentration was examined by using differential scanning calorimetry and CD spectroscopy in combination with computational analysis to identify the specify amino acids undergoing change. Our approach identified a sodiumbinding site in CpCspA and at pH 8.0 a significant reduction in the β-sheet content was observed which resulted in a decrease of the protein thermal stability. The computational analyses identified His30 and His65 as the amino acids with the largest charge shifts at different pHs. His30/His65 are part of the extensive hydrogen bonding network and along with the ion-binding site are essential for the conformational stability of CspA.
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Affiliation(s)
- Monika A Coronado
- Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Icaro P Caruso
- Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Vinicius M de Oliveira
- Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Vinícius G Contessoto
- Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Vitor B P Leite
- Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Liege A Kawai
- Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Raghuvir K Arni
- Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Raphael J Eberle
- Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Rua Cristovao Colombo 2265, Sao Jose do Rio Preto-SP, 15054-000. Brazil
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Kumar R, Caruso IP, Ullah A, Lopes Cornelio M, Andres Fossey M, Pereira de Souza F, Krishnaswamy Arni R. Exploring the Binding Mechanism of Flavonoid Quercetin to Phospholipase A2: Fluorescence Spectroscopy and Computational Approach. ACTA ACUST UNITED AC 2017. [DOI: 10.21767/2248-9215.100033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Mariutti RB, Souza TACB, Ullah A, Caruso IP, de Moraes FR, Zanphorlin LM, Tartaglia NR, Seyffert N, Azevedo VA, Le Loir Y, Murakami MT, Arni RK. Crystal structure of Staphylococcus aureus exfoliative toxin D-like protein: Structural basis for the high specificity of exfoliative toxins. Biochem Biophys Res Commun 2015; 467:171-7. [PMID: 26299923 DOI: 10.1016/j.bbrc.2015.08.083] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 08/19/2015] [Indexed: 11/29/2022]
Abstract
Exfoliative toxins are serine proteases secreted by Staphylococcus aureus that are associated with toxin-mediated staphylococcal syndromes. To date, four different serotypes of exfoliative toxins have been identified and 3 of them (ETA, ETB, and ETD) are linked to human infection. Among these toxins, only the ETD structure remained unknown, limiting our understanding of the structural determinants for the functional differentiation between these toxins. We recently identified an ETD-like protein associated to S. aureus strains involved in mild mastitis in sheep. The crystal structure of this ETD-like protein was determined at 1.95 Å resolution and the structural analysis provide insights into the oligomerization, stability and specificity and enabled a comprehensive structural comparison with ETA and ETB. Despite the highly conserved molecular architecture, significant differences in the composition of the loops and in both the N- and C-terminal α-helices seem to define ETD-like specificity. Molecular dynamics simulations indicate that these regions defining ET specificity present different degrees of flexibility and may undergo conformational changes upon substrate recognition and binding. DLS and AUC experiments indicated that the ETD-like is monomeric in solution whereas it is present as a dimer in the asymmetric unit indicating that oligomerization is not related to functional differentiation among these toxins. Differential scanning calorimetry and circular dichroism assays demonstrated an endothermic transition centered at 52 °C, and an exothermic aggregation in temperatures up to 64 °C. All these together provide insights about the mode of action of a toxin often secreted in syndromes that are not associated with either ETA or ETB.
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Affiliation(s)
- Ricardo B Mariutti
- Multi User Center for Biomolecular Innovation, Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
| | | | - Anwar Ullah
- Multi User Center for Biomolecular Innovation, Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
| | - Icaro P Caruso
- Multi User Center for Biomolecular Innovation, Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
| | - Fábio R de Moraes
- Multi User Center for Biomolecular Innovation, Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
| | - Leticia M Zanphorlin
- Bioethanol Science and Technology Laboratory (CTBE), National Center for Research in Energy and Materials, Campinas, SP, 13083-970, Brazil
| | - Natayme R Tartaglia
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil; INRA, UMR1253 STLO, Science et Technologie du Lait et de l'œuf, F-35042 Rennes, France; Agrocampus Ouest, UMR1253 STLO, F-35042 Rennes, France
| | - Nubia Seyffert
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil
| | - Vasco A Azevedo
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil
| | - Yves Le Loir
- INRA, UMR1253 STLO, Science et Technologie du Lait et de l'œuf, F-35042 Rennes, France; Agrocampus Ouest, UMR1253 STLO, F-35042 Rennes, France
| | - Mário T Murakami
- Brazilian Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials, Campinas, SP, 13083-970, Brazil
| | - Raghuvir K Arni
- Multi User Center for Biomolecular Innovation, Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP, Brazil.
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Lindae A, Eberle RJ, Caruso IP, Coronado MA, de Moraes FR, Azevedo V, Arni RK. Expression, purification and characterization of cold shock protein A of Corynebacterium pseudotuberculosis. Protein Expr Purif 2015; 112:15-20. [DOI: 10.1016/j.pep.2015.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 03/27/2015] [Accepted: 04/14/2015] [Indexed: 10/23/2022]
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Santana VS, Mariutti RB, Eberle RJ, Ullah A, Caruso IP, Arni RK. Preparation and Characterization of Monomodal Grapevine Virus A Capsid Protein. Protein Pept Lett 2015; 22:712-8. [PMID: 26112976 DOI: 10.2174/0929866522666150625111607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/18/2015] [Accepted: 06/25/2015] [Indexed: 11/22/2022]
Abstract
Grapevine virus A (GVA), a flexible filament of approximately 800 nm in length is composed of capsid subunits that spontaneously assembles around a positive sense genomic RNA. In addition to encapsidation, plant viruses capsid proteins (CPs) participate in other processes throughout infection and GVA CP is involved in cell-to-cell translocation of the virus. A protocol was developed to obtain low-molecular weight GVA-CP that is not prone to aggregation and spontaneous assembly and this was characterized by circular dichroism and dynamic light scattering. These results indicate the suitably of GVA-CP for X-ray crystallographic and NMR studies that should lead to the elucidation of the first three-dimensional structure of a flexible filamentous virus from the Betaflexiviridae family.
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Affiliation(s)
| | | | | | | | | | - Raghuvir K Arni
- Centro Multiusuário de Inovação Biomolecular, Departamento de Física, Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo 2265, São Jose do Rio Preto-SP, 15054-000, Brazil.
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Caruso IP, Vilegas W, Fossey MA, Cornélio ML. Exploring the binding mechanism of Guaijaverin to human serum albumin: fluorescence spectroscopy and computational approach. Spectrochim Acta A Mol Biomol Spectrosc 2012; 97:449-455. [PMID: 22820048 DOI: 10.1016/j.saa.2012.06.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/22/2012] [Accepted: 06/25/2012] [Indexed: 06/01/2023]
Abstract
The Guaijaverin (Gua) is a polyphenolic substance which exhibits some pharmacological activities such as antibacterial and antioxidant activities. Here we have investigated the binding of Gua with human serum albumin (HSA) at physiological pH 7.0. In this study, the fluorescence spectroscopy, ab initio and molecular modeling calculations were applied. The Stern-Volmer quenching constant (K(SV)) and its modified form (K(a)) were calculated at 298, 303 and 308 K, with the corresponding thermodynamic parameters ΔH, ΔG and ΔS as well. The fluorescence quenching method was used to determine the number of binding sites (n) and binding constants (K(b)) values at 298, 303 and 308 K. The distance between donor (HSA) and acceptor (Gua) was estimated according to fluorescence resonance energy transfer. The geometry optimization of Gua was performed in its ground state by using ab initio DFT/B3LYP functional with a 6-31G(d,p) basis set used in calculations. Molecular modeling calculation indicated that the Gua is located within the hydrophobic pocket of the subdomain IIA of HSA. The theoretical results obtained by molecular modeling were corroborated by fluorescence spectroscopy data.
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Affiliation(s)
- Icaro P Caruso
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo, 2265, CEP 15054-000, São José do Rio Preto, SP, Brazil.
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