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Osterne VJS, De Sloover G, Van Damme EJM. Revisiting legume lectins: Structural organization and carbohydrate-binding properties. Carbohydr Res 2024; 544:109241. [PMID: 39153325 DOI: 10.1016/j.carres.2024.109241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/18/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Legume lectins are a diverse family of carbohydrate-binding proteins that share significant similarities in their primary, secondary, and tertiary structures, yet exhibit remarkable variability in their quaternary structures and carbohydrate-binding specificities. The tertiary structure of legume lectins, characterized by a conserved β-sandwich fold, provides the scaffold for the formation of a carbohydrate-recognition domain (CRD) responsible for ligand binding. The structural basis for the binding is similar between members of the family, with key residues interacting with the sugar through hydrogen bonds, hydrophobic interactions, and van der Waals forces. Variability in substructures and residues within the CRD are responsible for the large array of specificities and enable legume lectins to recognize diverse sugar structures, while maintaining a consistent structural fold. Therefore, legume lectins can be classified into several specificity groups based on their preferred ligands, including mannose/glucose-specific, N-acetyl-d-galactosamine/galactose-specific, N-acetyl-d-glucosamine-specific, l-fucose-specific, and α-2,3 sialic acid-specific lectins. In this context, this review examined the structural aspects and carbohydrate-binding properties of representative legume lectins and their specific ligands in detail. Understanding the structure/binding relationships of lectins continues to provide valuable insights into their biological roles, while also assisting in the potential applications of these proteins in glycobiology, diagnostics, and therapeutics.
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Affiliation(s)
- Vinicius J S Osterne
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Proeftuinstraat 86, 9000, Ghent, Belgium
| | - Gilles De Sloover
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Proeftuinstraat 86, 9000, Ghent, Belgium
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Proeftuinstraat 86, 9000, Ghent, Belgium.
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2
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Seed Storage Protein, Functional Diversity and Association with Allergy. ALLERGIES 2023. [DOI: 10.3390/allergies3010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Plants are essential for humans as they serve as a source of food, fuel, medicine, oils, and more. The major elements that are utilized for our needs exist in storage organs, such as seeds. These seeds are rich in proteins, show a broad spectrum of physiological roles, and are classified based on their sequence, structure, and conserved motifs. With the improvements to our knowledge of the basic sequence and our structural understanding, we have acquired better insights into seed proteins and their role. However, we still lack a systematic analysis towards understanding the functional diversity associated within each family and their associations with allergy. This review puts together the information about seed proteins, their classification, and diverse functional roles along with their associations with allergy.
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Cloning, Characterization, Expression Analysis, and Agglutination Studies of Novel Gene Encoding β-D-Galactose, N-Acetyl-D-Glucosamine and Lactose-Binding Lectin from Rice Bean (Vigna umbellata). Mol Biotechnol 2021; 64:293-310. [PMID: 34611825 DOI: 10.1007/s12033-021-00410-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
Lectins are glycoproteins and known for their peculiar carbohydrate-binding activity and their insect-pest-resistant properties. Earlier we have published our research finding on novel gene encoding Bowman-Birk type protease inhibitor with insecticidal properties from rice bean. This paper presents first report on cloning, sequencing, and expression of RbL ORF of 843 bp encoding 280 amino acids long lectin precursor from rice bean (Vigna umbellata) seeds. Blast analysis revealed more than 90% similarity of RbL protein with Vigna aconitifolia and Vigna angularis lectins. Phylogenetic analysis also revealed a close relationship between RbL and other legume lectins. Sequence analysis of genomic DNA revealed intronless nature of RbL gene (GenBank accession No. MT043160). The isolated RbL ORF was expressed in E. coli BL-21(DE3) cells and maximum expression was recorded with 0.5 mM IPTG after 4 h incubation at 37 °C. Western blotting confirmed RbL protein expression in E. coli. Recombinant protein (His6-RbL) of ~ 35 kDa m.wt was purified using Ni-NTA affinity chromatography to the extent of 0.26 mg/ml. In silico analysis characterized RbL protein as acidic, stable, hydrophobic, and secretary protein with one signal peptide cleavage site (A26-A27) and four N-glycosylation sites. Template-based 3D model of RbL was structured using MODELLER tool and validated as good quality model. Structural analysis revealed dominance of β-pleated sheets and β-turns in RbL protein structure. β-D-galactose, N-acetyl-D-glucosamine, and lactose were predicted as putative ligands for RbL protein. Hydrogen bonding and hydrophobic forces were the major interactions between the predicted ligands and RbL protein. Agglutination and agglutination inhibition assays confirmed the binding specificity of RbL protein with the trypsinized rabbit erythrocytes and with the predicted ligands, respectively. Gene ontology analysis functionally annotated RbL protein as a plant defense protein. The novel information generated in the study is not mere pre-experimental findings but could also lay foundation for future research on exploring RbL gene and encoding protein for different biomedical and biotechnological applications.
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Nascimento KS, Silva MTL, Oliveira MV, Lossio CF, Pinto-Junior VR, Osterne VJS, Cavada BS. Dalbergieae lectins: A review of lectins from species of a primitive Papilionoideae (leguminous) tribe. Int J Biol Macromol 2019; 144:509-526. [PMID: 31857177 DOI: 10.1016/j.ijbiomac.2019.12.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/06/2019] [Accepted: 12/14/2019] [Indexed: 01/24/2023]
Abstract
Lectins are (glyco)proteins capable of reversibly binding to specific carbohydrates, thus having various functions and applications. Plant lectins are the best studied, and the Leguminoseae family is highlighted in a number of published works, especially species of the Papilionoideae subfamily. Dalbergieae is one of the tribes in this subfamily comprising 49 genera and over 1300 species. From this tribe, about 26 lectins were studied, among which we can highlight the Arachis hypogaea lectin, widely used in cancer studies. Dalbergieae lectins demonstrate various carbohydrate specificities and biological activities including anti-inflammatory, vasorelaxant, nociceptive, antibacterial, antiviral among others. Structurally, these lectins are quite similar in their three-dimensional folding but present significant differences in oligomerization patterns and in the conservation of carbohydrate-recognition domain. Despite the existence of structural data from some lectins, only sparse literature has reported on this tribe's diversity, not to mention the range of biological effects, determined through specific assays. Therefore, this work will review the most important studies on Dalbergieae lectins and their potential biomedical applications.
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Affiliation(s)
- Kyria Santiago Nascimento
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil.
| | - Mayara Torquato Lima Silva
- Departamento de Bioquímica, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil
| | - Messias Vital Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil
| | - Claudia Figueiredo Lossio
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil
| | | | - Vinicius Jose Silva Osterne
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil
| | - Benildo Sousa Cavada
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil.
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Cavada BS, Osterne VJS, Lossio CF, Pinto-Junior VR, Oliveira MV, Silva MTL, Leal RB, Nascimento KS. One century of ConA and 40 years of ConBr research: A structural review. Int J Biol Macromol 2019; 134:901-911. [DOI: 10.1016/j.ijbiomac.2019.05.100] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 01/30/2023]
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Cavada BS, Osterne VJS, Pinto-Junior VR, Nascimento KS. ConBr, the Lectin from Canavalia brasiliensis Mart. Seeds: Forty Years of Research. Curr Protein Pept Sci 2019; 20:600-613. [DOI: 10.2174/1389203720666190104123210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/30/2018] [Accepted: 12/29/2018] [Indexed: 12/16/2022]
Abstract
Lectins are defined as proteins or glycoproteins capable of specific and reversible binding to
carbohydrates. Inside this group of proteins, the most well-studied lectins belong to the Leguminosae
family, and inside this family, the Diocleinae subtribe includes the most characterized lectin Concanavalin
A (ConA), as well as ConBr, the lectin from Canavalia brasiliensis, the subject of this review.
Since 1979, several studies have been published in the literature regarding this lectin, from its isolation
and characterization to its several biological activities. This year, 2019, will mark 40 years since researchers
have begun to study ConBr and 100 years since the discovery of ConA, making 2019 a momentous
year for lectinology. Owing to the abundance of studies involving ConBr, this review will
focus on ConBr’s purification, physicochemical properties, functional and structural analyses, biological
activities and biotechnological applications. This will give researchers a broad glimpse into the
potential of this lectin, as well as it characteristics, as we look ahead to its expanding applications in
glycomics and biotechnology.
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Affiliation(s)
- Benildo Sousa Cavada
- BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Ceara, Brazil
| | | | - Vanir Reis Pinto-Junior
- BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Ceara, Brazil
| | - Kyria Santiago Nascimento
- BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Ceara, Brazil
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Gadiyaram V, Vishveshwara S, Vishveshwara S. From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses. J Chem Inf Model 2019; 59:1715-1727. [DOI: 10.1021/acs.jcim.9b00002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vasundhara Gadiyaram
- IISc Mathematics Initiative (IMI), Indian Institute of Science, C V Raman Road, Bengaluru, Karnataka 560012, India
| | - Smitha Vishveshwara
- Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801-3080, United States
| | - Saraswathi Vishveshwara
- Molecular Biophysics Unit, Indian Institute of Science, C V Raman Road, Bengaluru, Karnataka 560012, India
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8
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Cavada BS, Pinto-Junior VR, Osterne VJS, Nascimento KS. ConA-Like Lectins: High Similarity Proteins as Models to Study Structure/Biological Activities Relationships. Int J Mol Sci 2018; 20:ijms20010030. [PMID: 30577614 PMCID: PMC6337138 DOI: 10.3390/ijms20010030] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 01/03/2023] Open
Abstract
Lectins are a widely studied group of proteins capable of specific and reversible binding to carbohydrates. Undoubtedly, the best characterized are those extracted from plants of the Leguminosae family. Inside this group of proteins, those from the Diocleinae subtribe have attracted attention, in particular Concanavalin A (ConA), the best-studied lectin of the group. Diocleinae lectins, also called ConA-like lectins, present a high similarity of sequence and three-dimensional structure and are known to present inflammatory, vasoactive, antibiotic, immunomodulatory and antitumor activities, among others. This high similarity of lectins inside the ConA-like group makes it possible to use them to study structure/biological activity relationships by the variability of both carbohydrate specificity and biological activities results. It is in this context the following review aims to summarize the most recent data on the biochemical and structural properties, as well as biological activities, of ConA-like lectins and the use of these lectins as models to study structure/biological activity relationships.
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Affiliation(s)
- Benildo S Cavada
- BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza-CE 60440-970, Brazil.
| | - Vanir R Pinto-Junior
- BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza-CE 60440-970, Brazil.
| | - Vinicius J S Osterne
- BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza-CE 60440-970, Brazil.
| | - Kyria S Nascimento
- BioMol-Lab, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza-CE 60440-970, Brazil.
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9
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Bauhinia lectins: Biochemical properties and biotechnological applications. Int J Biol Macromol 2018; 119:811-820. [DOI: 10.1016/j.ijbiomac.2018.07.156] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/06/2018] [Accepted: 07/25/2018] [Indexed: 01/13/2023]
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10
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Neco AHB, Pinto-Junior VR, Araripe DA, Santiago MQ, Osterne VJS, Lossio CF, Nobre CAS, Oliveira MV, Silva MTL, Martins MGQ, Cajazeiras JB, Marques GFO, Costa DR, Nascimento KS, Assreuy AMS, Cavada BS. Structural analysis, molecular docking and molecular dynamics of an edematogenic lectin from Centrolobium microchaete seeds. Int J Biol Macromol 2018; 117:124-133. [DOI: 10.1016/j.ijbiomac.2018.05.166] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/11/2018] [Accepted: 05/23/2018] [Indexed: 12/30/2022]
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11
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Crystal structure of DlyL, a mannose-specific lectin from Dioclea lasiophylla Mart. Ex Benth seeds that display cytotoxic effects against C6 glioma cells. Int J Biol Macromol 2018; 114:64-76. [DOI: 10.1016/j.ijbiomac.2018.03.080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 12/27/2022]
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12
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Osman MEM, Konozy EHE. Insight into Erythrina Lectins: Properties, Structure and Proposed Physiological Significance. ACTA ACUST UNITED AC 2017. [DOI: 10.2174/1874847301705010057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genus Erythrina, collectively known as “coral tree”, are pantropical plants, comprising of more than 112 species. Since the early 1980s, seven of these have been found to possess hemagglutinating activity, although not yet characterized. However, around two dozen galactose-binding lectins have been isolated and fully characterized with respect to their sugar specificity, glycoconjugates agglutination, dependence of activity on metal ions, primary and secondary structures and stability. Three lectins have been fully sequenced and the crystal structures of the two proteins have been solved with and without the haptenic sugar. Lectins isolation and characterization from most of these species usually originated from the seeds, although the proteins from other vegetative tissues have also been reported. The main objective of this review is to summarize the physicochemical and biological properties of the reported purified Erythrina lectins to date. Structural comparisons, based on available lectins sequences, are also made to relate the intrinsic physical and chemical properties of these proteins. Particular attention is also given to the proposed biological significance of the lectins from the genus Erythrina.
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Nascimento KS, Santiago MQ, Pinto-Junior VR, Osterne VJS, Martins FWV, Nascimento APM, Wolin IAV, Heinrich IA, Martins MGQ, Silva MTL, Lossio CF, Rocha CRC, Leal RB, Cavada BS. Structural analysis of Dioclea lasiocarpa lectin: A C6 cells apoptosis-inducing protein. Int J Biochem Cell Biol 2017; 92:79-89. [DOI: 10.1016/j.biocel.2017.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 12/16/2022]
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14
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Chaotropes trigger conformational rearrangements differently in Concanavalin A. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1333-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Legume Lectins: Proteins with Diverse Applications. Int J Mol Sci 2017; 18:ijms18061242. [PMID: 28604616 PMCID: PMC5486065 DOI: 10.3390/ijms18061242] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 12/26/2022] Open
Abstract
Lectins are a diverse class of proteins distributed extensively in nature. Among these proteins; legume lectins display a variety of interesting features including antimicrobial; insecticidal and antitumor activities. Because lectins recognize and bind to specific glycoconjugates present on the surface of cells and intracellular structures; they can serve as potential target molecules for developing practical applications in the fields of food; agriculture; health and pharmaceutical research. This review presents the current knowledge of the main structural characteristics of legume lectins and the relationship of structure to the exhibited specificities; provides an overview of their particular antimicrobial; insecticidal and antitumor biological activities and describes possible applications based on the pattern of recognized glyco-targets.
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Pinto-Junior VR, Osterne VJS, Santiago MQ, Correia JLA, Pereira-Junior FN, Leal RB, Pereira MG, Chicas LS, Nagano CS, Rocha BAM, Silva-Filho JC, Ferreira WP, Rocha CRC, Nascimento KS, Assreuy AMS, Cavada BS. Structural studies of a vasorelaxant lectin from Dioclea reflexa Hook seeds: Crystal structure, molecular docking and dynamics. Int J Biol Macromol 2017; 98:12-23. [DOI: 10.1016/j.ijbiomac.2017.01.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/16/2017] [Accepted: 01/20/2017] [Indexed: 01/15/2023]
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17
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Molecular modeling, docking and dynamics simulations of the Dioclea lasiophylla Mart. Ex Benth seed lectin: An edematogenic and hypernociceptive protein. Biochimie 2017; 135:126-136. [DOI: 10.1016/j.biochi.2017.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/09/2017] [Indexed: 12/18/2022]
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18
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Osterne VJS, Silva-Filho JC, Santiago MQ, Pinto-Junior VR, Almeida AC, Barreto AAGC, Wolin IAV, Nascimento APM, Amorim RMF, Rocha BAM, Delatorre P, Nagano CS, Leal RB, Assreuy AMS, Nascimento KS, Cavada BS. Structural characterization of a lectin from Canavalia virosa seeds with inflammatory and cytotoxic activities. Int J Biol Macromol 2017; 94:271-282. [DOI: 10.1016/j.ijbiomac.2016.10.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/08/2016] [Accepted: 10/09/2016] [Indexed: 01/25/2023]
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Structure prediction and functional analysis of a non-permutated lectin from Dioclea grandiflora. Biochimie 2016; 131:54-67. [DOI: 10.1016/j.biochi.2016.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 09/19/2016] [Indexed: 01/22/2023]
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Structural characterization of a Vatairea macrocarpa lectin in complex with a tumor-associated antigen: A new tool for cancer research. Int J Biochem Cell Biol 2016; 72:27-39. [DOI: 10.1016/j.biocel.2015.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 12/05/2015] [Accepted: 12/31/2015] [Indexed: 11/22/2022]
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Hu G, Xiao F, Li Y, Li Y, Vongsangnak W. Protein-Protein Interface and Disease: Perspective from Biomolecular Networks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 160:57-74. [PMID: 27928579 DOI: 10.1007/10_2016_40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions are involved in many important biological processes and molecular mechanisms of disease association. Structural studies of interfacial residues in protein complexes provide information on protein-protein interactions. Characterizing protein-protein interfaces, including binding sites and allosteric changes, thus pose an imminent challenge. With special focus on protein complexes, approaches based on network theory are proposed to meet this challenge. In this review we pay attention to protein-protein interfaces from the perspective of biomolecular networks and their roles in disease. We first describe the different roles of protein complexes in disease through several structural aspects of interfaces. We then discuss some recent advances in predicting hot spots and communication pathway analysis in terms of amino acid networks. Finally, we highlight possible future aspects of this area with respect to both methodology development and applications for disease treatment.
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Affiliation(s)
- Guang Hu
- Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou, 215006, China.
| | - Fei Xiao
- School of Basic Medicine and Biological Sciences, Medical College of Soochow University, Suzhou, 215123, China
| | - Yuqian Li
- School of Electronic Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yuan Li
- Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou, 215006, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
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Structural analysis of a Dioclea sclerocarpa lectin: Study on the vasorelaxant properties of Dioclea lectins. Int J Biol Macromol 2016; 82:464-70. [DOI: 10.1016/j.ijbiomac.2015.10.052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 10/18/2015] [Accepted: 10/19/2015] [Indexed: 12/11/2022]
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23
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Alves AC, Vasconcelos MA, Santiago MQ, Pinto-Junior VR, Silva Osterne VJ, Lossio CF, Bringel PHSF, Castro RR, Nagano CS, Delatorre P, Souza LAG, Nascimento KS, Assreuy AMS, Cavada BS. A novel vasorelaxant lectin purified from seeds of Clathrotropis nitida: partial characterization and immobilization in chitosan beads. Arch Biochem Biophys 2015; 588:33-40. [PMID: 26545483 DOI: 10.1016/j.abb.2015.10.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/27/2015] [Accepted: 10/29/2015] [Indexed: 02/02/2023]
Abstract
A novel lectin from seeds of Clathrotropis nitida (CNA) was purified and characterized. CNA is a glycoprotein containing approximately 3.3% carbohydrates in its structure. CNA promoted intense agglutination of rabbit erythrocytes, which was inhibited by galactosides and porcine stomach mucin (PSM). The lectin maintained its hemagglutinating activity after incubation in a wide range of temperatures (30-60 °C) and pH (6.0-7.0), and its binding activity was dependent on divalent cations (Ca(+2) and Mg(+2)). SDS-PAGE showed an electrophoretic profile consisting of a single band of 28 kDa, as confirmed by electrospray ionization mass spectrometry, which indicated an average molecular mass of 27,406 ± 2 Da and the possible presence of isoforms and glycoforms. In addition, CNA exhibited no toxicity to Artemia sp. nauplii and elicited reversible and dose-dependent vasorelaxation in precontracted aortic rings. CNA was successfully immobilized on chitosan beads and was able to capture PSM in solution. This study demonstrated that CNA is a lectin that has potential as a biotechnological tool in glycomics and glycoproteomics applications.
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Affiliation(s)
- Ana Cecilia Alves
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Mayron Alves Vasconcelos
- Laboratório Integrado de Biomoléculas - LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Mayara Queiroz Santiago
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Vanir Reis Pinto-Junior
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Vinicius Jose Silva Osterne
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Claudia Figueiredo Lossio
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Pedro Henrique Souza Ferreira Bringel
- Instituto Superior de Ciências Biomédicas-ISCB and Faculdade de Filosofia Dom Aureliano Matos-FAFIDAM, Universidade Estadual do Ceará, Fortaleza, Ceará, Brazil
| | - Rondinelle Ribeiro Castro
- Instituto Superior de Ciências Biomédicas-ISCB and Faculdade de Filosofia Dom Aureliano Matos-FAFIDAM, Universidade Estadual do Ceará, Fortaleza, Ceará, Brazil
| | - Celso Shiniti Nagano
- Laboratório de Espectrometria de Massas Aplicada a Proteínas - LEMAP, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Plinio Delatorre
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza - Campus I, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | | | - Kyria Santiago Nascimento
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Ana Maria Sampaio Assreuy
- Instituto Superior de Ciências Biomédicas-ISCB and Faculdade de Filosofia Dom Aureliano Matos-FAFIDAM, Universidade Estadual do Ceará, Fortaleza, Ceará, Brazil
| | - Benildo Sousa Cavada
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil.
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Ng TB, Chan YS, Ng CCW, Wong JH. Purification and Characterization of a Lectin from Green Split Peas (Pisum sativum). Appl Biochem Biotechnol 2015; 177:1374-85. [PMID: 26304129 DOI: 10.1007/s12010-015-1821-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/17/2015] [Indexed: 10/23/2022]
Abstract
Lectins have captured the attention of a large number of researchers on account of their various exploitable activities, including antitumor, immunomodulatory, antifungal, as well as HIV reverse transcriptase inhibitory activities. A mannose/glucose-specific lectin was isolated from green split peas (a variety of Pisum sativum) and characterized. The purification step involved anion-exchange chromatography on a DEAE-cellulose column, cation-exchange chromatography on an SP-Sepharose column, and gel filtration by fast protein liquid chromatography (FPLC) on Superdex 200. The purified lectin had a native molecular mass of around 50 kDa as determined by size exclusion chromatography. It appeared as a heterotetramer, composed of two distinct polypeptide bands with a molecular mass of 6 and 19 kDa, respectively, in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The N-terminal sequence of green split pea lectin shows some degree of homology compared to lectins from other legume species. Its hemagglutinating activity was inhibited by glucose, mannose, and sucrose, and attenuated at pH values higher than 12 or lower than 3. Hemagglutinating activity was preserved at temperatures lower than 80 °C. The lectin did not show antifungal activity toward fungi including Fusarium oxysporum, Botrytis cinerea, and Mycosphaerella arachidicola. Green split pea lectin showed a mitogenic effect toward murine splenocytes and could inhibit the activity of HIV-1 reverse transcriptase.
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Affiliation(s)
- Tzi Bun Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
| | - Yau Sang Chan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Charlene Cheuk Wing Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Jack Ho Wong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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25
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Pinto-Junior VR, Correia JLA, Pereira RI, Pereira-Junior FN, Santiago MQ, Osterne VJS, Madeira JC, Cajazeiras JB, Nagano CS, Delatorre P, Assreuy AMS, Nascimento KS, Cavada BS. Purification and molecular characterization of a novel mannose-specific lectin from Dioclea reflexa hook seeds with inflammatory activity. J Mol Recognit 2015; 29:134-41. [PMID: 26464029 DOI: 10.1002/jmr.2512] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/01/2015] [Accepted: 09/05/2015] [Indexed: 12/16/2022]
Abstract
A novel lectin present in Dioclea reflexa seeds (DrfL) was discovered and described in this study. DrfL was purified in a single step by affinity chromatography in a Sephadex G-50 column. The lectin strongly agglutinated rabbit erythrocytes and was inhibited by α-methyl-D-mannoside, D-mannose, and D-glucose. The hemagglutinating activity of DrfL is optimum at pH 5.0-7.0, stable up to 50 °C, and dependent on divalent cations. Similar to other lectins of the subtribe Diocleinae, the analysis by mass spectrometry indicated that DrfL has three chains (α, β, and γ) with masses of 25,562, 12,874, and 12,706 Da, respectively, with no disulfide bonds or glycosylation. DrfL showed inflammatory activity in the paw edema model and exhibited low cytotoxicity against Artemia sp.
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Affiliation(s)
- Vanir R Pinto-Junior
- Laboratório de Moléculas Biologicamente Ativas (Biomol-Lab), Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Jorge L A Correia
- Laboratório de Moléculas Biologicamente Ativas (Biomol-Lab), Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Ronniery I Pereira
- Laboratório de Moléculas Biologicamente Ativas (Biomol-Lab), Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Francisco N Pereira-Junior
- Laboratório de Moléculas Biologicamente Ativas (Biomol-Lab), Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Mayara Q Santiago
- Laboratório de Moléculas Biologicamente Ativas (Biomol-Lab), Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Vinicius J S Osterne
- Laboratório de Moléculas Biologicamente Ativas (Biomol-Lab), Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Juliana C Madeira
- Laboratório de Fisio-Farmacologia da Inflamação (LAFFIN), Institute of Biomedical Sciences, State University of Ceará, Fortaleza, CE, Brazil
| | - João B Cajazeiras
- Laboratório de Moléculas Biologicamente Ativas (Biomol-Lab), Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Celso S Nagano
- Laboratório de Espectrometria de Massas aplicado a Proteínas (LEMAP), Federal University of Ceará, Fortaleza, CE, Brazil
| | - Plinio Delatorre
- Laboratório de Biologia Molecular Estrutural e Oncogenética (LBMEO), Department of Molecular Biology, Federal University of Paraíba, João Pessoa, PB, Brazil
| | - Ana M S Assreuy
- Laboratório de Fisio-Farmacologia da Inflamação (LAFFIN), Institute of Biomedical Sciences, State University of Ceará, Fortaleza, CE, Brazil
| | - Kyria S Nascimento
- Laboratório de Moléculas Biologicamente Ativas (Biomol-Lab), Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Benildo S Cavada
- Laboratório de Moléculas Biologicamente Ativas (Biomol-Lab), Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
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26
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Vasconcelos MAD, Alves AC, Carneiro RF, Dias AHS, Martins FWV, Cajazeiras JB, Nagano CS, Teixeira EH, Nascimento KSD, Cavada BS. Purification and primary structure of a novel mannose-specific lectin from Centrolobium microchaete Mart seeds. Int J Biol Macromol 2015; 81:600-7. [PMID: 26321423 DOI: 10.1016/j.ijbiomac.2015.08.059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
Abstract
This study aimed to purify and characterize a novel mannose-binding lectin from the seeds of Centrolobium microchaete. Centrolobium microchaete lectin (CML) was purified by affinity chromatography in mannose-Sepharose-4B column. CML agglutinated rabbit erythrocytes and was inhibited by D-mannose, α-methyl-D-mannoside, D-glucose, N-Acetyl-D-glucosamine and sucrose. The lectin was stable at pH 7.0 and 8.0 and temperatures up to 60°C. The monomeric form of CML showed approximately 28kDa, and its native form is probably a homodimer, as determined by gel filtration chromatography. The primary structure of CML was determined by tandem mass spectrometry that showed CML as a protein with two distinct forms (isolectins CML-1 and CML-2) with 246 and 247 residues, respectively. CML-2 possesses one residue of Asn more than CML-1 in C-terminal. The primary structure of CML agrees with the molecular weights found by electrospray ionization mass spectrometry: 27,224 and 27,338Da for CML-1 and CML-2, respectively. CML is a metal-dependent glycoprotein. Moreover, the glycan composition of CML and its structure were predicted.
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Affiliation(s)
- Mayron Alves de Vasconcelos
- Laboratório Integrado de Biomoléculas-LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, 60430-160, Fortaleza, Ceará, Brazil.
| | - Ana Cecília Alves
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil
| | - Rômulo Farias Carneiro
- Laboratório de Biotecnologia Marinha-BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Artur Hermano Sampaio Dias
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil
| | - Francisco William Viana Martins
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil
| | - João Batista Cajazeiras
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil
| | - Celso Shiniti Nagano
- Laboratório de Biotecnologia Marinha-BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Edson Holanda Teixeira
- Laboratório Integrado de Biomoléculas-LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, 60430-160, Fortaleza, Ceará, Brazil
| | - Kyria Santiago do Nascimento
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil
| | - Benildo Sousa Cavada
- Laboratório de Moléculas Biologicamente Ativas - BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n bloco 907, 60440-970, Fortaleza, Ceará, Brazil.
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27
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Zamora-Caballero S, Pérez A, Sanz L, Bravo J, Calvete JJ. Quaternary structure of Dioclea grandiflora lectin assessed by equilibrium sedimentation and crystallographic analysis of recombinant mutants. FEBS Lett 2015; 589:2290-6. [PMID: 26226421 DOI: 10.1016/j.febslet.2015.07.020] [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: 06/29/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 10/23/2022]
Abstract
The structural basis of the pH dependency of the dimer-tetramer transition exhibited by Brinda's type II Diocleinae lectins was investigated by equilibrium sedimentation and X-ray crystal structure determination of recombinant wild-type and site-directed single and double mutants of the pH-stable tetrameric Dioclea grandiflora lectin (r-αDGL). Releasing the peripheral site interdimeric contact between R60 and D78 rendered a mutant displaying dimer-tetramer equilibrium in the pH range equivalent to pKa±1 of the γ-COOH. Mutation of both histidines 51 and 131, but not the mutation of each His separately, abolished the formation of the Diocleinae canonical tetramer in the pH range 2.5-8.5. The X-ray structure of the double mutant r-αDGL H51G/H131N suggests that H131 plays a crucial role in networking loop 114-125 residues from all four subunits at the central cavity of the tetrameric lectin, and that H51 maintains the central cavity loops in a proper spatial orientation to make H131-mediated interdimer contacts.
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Affiliation(s)
- Sara Zamora-Caballero
- Unidad de Transducción de Señales, Instituto de Biomedicina de Valencia, CSIC, Spain
| | - Alicia Pérez
- Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Spain
| | - Libia Sanz
- Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Spain
| | - Jerónimo Bravo
- Unidad de Transducción de Señales, Instituto de Biomedicina de Valencia, CSIC, Spain.
| | - Juan J Calvete
- Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Spain.
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28
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Sousa BL, Silva Filho JC, Kumar P, Pereira RI, Łyskowski A, Rocha BAM, Delatorre P, Bezerra GA, Nagano CS, Gruber K, Cavada BS. High-resolution structure of a new Tn antigen-binding lectin from Vatairea macrocarpa and a comparative analysis of Tn-binding legume lectins. Int J Biochem Cell Biol 2014; 59:103-10. [PMID: 25499445 DOI: 10.1016/j.biocel.2014.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/10/2014] [Accepted: 12/03/2014] [Indexed: 11/28/2022]
Abstract
Plant lectins have been studied as histological markers and promising antineoplastic molecules for a long time, and structural characterization of different lectins bound to specific cancer epitopes has been carried out successfully. The crystal structures of Vatairea macrocarpa (VML) seed lectin in complex with GalNAc-α-O-Ser (Tn antigen) and GalNAc have been determined at the resolution of 1.4Å and 1.7Å, respectively. Molecular docking analysis of this new structure and other Tn-binding legume lectins to O-mucin fragments differently decorated with this antigen provides a comparative binding profile among these proteins, stressing that subtle alterations that may not influence monosaccharide binding can, nonetheless, directly impact the ability of these lectins to recognize naturally occurring antigens. In addition to the specific biological effects of VML, the structural and binding similarities between it and other lectins commonly used as histological markers (e.g., VVLB4 and SBA) strongly suggest VML as a candidate tool for cancer research.
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Affiliation(s)
- Bruno Lopes Sousa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Av. Mister Hull s/n, Bloco 907, Box 6043, 60440-970 Fortaleza, Ceará, Brazil
| | - José Caetano Silva Filho
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Av. Mister Hull s/n, Bloco 907, Box 6043, 60440-970 Fortaleza, Ceará, Brazil
| | - Prashant Kumar
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, A-8010 Graz, Austria
| | - Ronniery Ilário Pereira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Av. Mister Hull s/n, Bloco 907, Box 6043, 60440-970 Fortaleza, Ceará, Brazil
| | - Andrzej Łyskowski
- Department of Biochemistry and Biotechnology, Rzeszów University of Technology, 35-959 Rzeszów, Poland
| | - Bruno Anderson Matias Rocha
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Av. Mister Hull s/n, Bloco 907, Box 6043, 60440-970 Fortaleza, Ceará, Brazil
| | - Plínio Delatorre
- Departamento de Biologia Molecular, Universidade Federal da Paraíba, Cidade Universitária, 58059-900 João Pessoa, Brazil
| | - Gustavo Arruda Bezerra
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Celso Shiniti Nagano
- Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Av. Mister Hull s/n, Bloco 827, Fortaleza, Brazil
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, A-8010 Graz, Austria
| | - Benildo Sousa Cavada
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Av. Mister Hull s/n, Bloco 907, Box 6043, 60440-970 Fortaleza, Ceará, Brazil.
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29
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Structural basis of ConM binding with resveratrol, an anti-inflammatory and antioxidant polyphenol. Int J Biol Macromol 2014; 72:1136-42. [PMID: 25192853 DOI: 10.1016/j.ijbiomac.2014.08.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 08/12/2014] [Accepted: 08/13/2014] [Indexed: 12/31/2022]
Abstract
Resveratrol can also inhibit the activation of proinflammatory mediators and cytokines at the early gene expression stage. It is well known that lectins are sugar-binding proteins that act as both pro- and anti-inflammatory molecules. Thus, the objective of this work was to verify the binding of a polyphenol compound with a lectin of Canavalia maritima (ConM) based on their ability to inhibit pro-inflammatory processes. To accomplish this, ConM was purified and crystallized, and resveratrol was soaked at 5mM for 2h of incubation. The crystal belongs to the monoclinic space group C2, the final refinement resulted in an Rfactor of 16.0% and an Rfree of 25.5%. Resveratrol binds in the rigid β-sheet through H-bonds and hydrophobic interaction with amino acids that compose the fifth and sixth β-strands of the rigid β-sheet of ConM. The ConM and resveratrol inhibited DPPH oxidation, showing synergic activity with the most effective ratio of 2:3 and carbohydrate binding site is not directly related to antioxidant activity. It is the interaction between ConM and resveratrol that indicates the synergism of these two molecules in acting as free radicals scavengers and in reducing the inflammatory process through the inhibition of many pro-inflammatory events.
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Santiago MQ, Leitão CCF, Pereira FN, Pinto VR, Osterne VJS, Lossio CF, Cajazeiras JB, Silva HC, Arruda FVS, Pereira LP, Assreuy AMS, Nascimento KS, Nagano CS, Cavada BS. Purification, characterization and partial sequence of a pro-inflammatory lectin from seeds of Canavalia oxyphylla Standl. & L. O. Williams. J Mol Recognit 2014; 27:117-23. [PMID: 24446375 DOI: 10.1002/jmr.2340] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/05/2013] [Accepted: 11/08/2013] [Indexed: 11/12/2022]
Abstract
Recent studies have shown that lectins are promising tools for use in various biotechnological processes, as well as studies of various pathological mechanisms, isolation, and characterization of glycoconjugates and understanding the mechanisms underlying pathological mechanisms conditions, including the inflammatory response. This study aimed to purify, characterize physicochemically, and predict the biological activity of Canavalia oxyphylla lectin (CoxyL) in vitro and in vivo. CoxyL was purified by a single-step affinity chromatography in Sephadex® G-50 column. Sodium dodecyl sulfate polyacrylamide gel electrophoresis showed that the pure lectin consists of a major band of 30 kDa (α-chain) and two minor components (β-chain and γ-chain) of 16 and 13 kDa, respectively. These data were further confirmed by electrospray ionization mass spectrometry, suggesting that CoxyL is a typical ConA-like lectin. In comparison with the average molecular mass of α-chain, the partial amino acid sequence obtained corresponds to approximately 45% of the total CoxyL sequence. CoxyL presented hemagglutinating activity that was specifically inhibited by monosaccharides (D-glucose, D-mannose, and α-methyl-D-mannoside) and glycoproteins (ovalbumin and fetuin). Moreover, CoxyL was shown to be thermostable, exhibiting full hemagglutinating activity up to 60°C, and it was pH-sensitive for 1 h, exhibiting maximal activity at pH 7.0. CoxyL caused toxicity to Artemia nauplii and induced paw edema in rats. This biological activity highlights the importance of lectins as important tools to better understand the mechanisms underlying inflammatory responses.
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Affiliation(s)
- Mayara Q Santiago
- Laboratório de Moléculas Biologicamente Ativas (Biomol-Lab), Department of Biochemistry and Molecular Biology, Federal University of Ceará, Av. Humberto Monte s/n, Bloco 907, Lab. 1075, Campus do Pici, Fortaleza, CE, 60440-970, Brazil
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Bhattacharyya M, Bhat CR, Vishveshwara S. An automated approach to network features of protein structure ensembles. Protein Sci 2014; 22:1399-416. [PMID: 23934896 DOI: 10.1002/pro.2333] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/12/2013] [Indexed: 12/14/2022]
Abstract
Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of β2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.
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32
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Purification, Partial Characterization, and CNBr-Sepharose Immobilization of a Vasorelaxant Glucose/Mannose Lectin from Canavalia virosa Seeds. Appl Biochem Biotechnol 2014; 172:3342-53. [DOI: 10.1007/s12010-014-0751-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/20/2014] [Indexed: 10/25/2022]
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Molecular modeling of lectin-like protein from Acacia farnesiana reveals a possible anti-inflammatory mechanism in Carrageenan-induced inflammation. BIOMED RESEARCH INTERNATIONAL 2013; 2013:253483. [PMID: 24490151 PMCID: PMC3893743 DOI: 10.1155/2013/253483] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/05/2013] [Accepted: 11/05/2013] [Indexed: 11/17/2022]
Abstract
Acacia farnesiana lectin-like protein (AFAL) is a chitin-binding protein and has been classified as phytohaemagglutinin from Phaseolus vulgaris (PHA). Legume lectins are examples for structural studies, and this family of proteins shows a remarkable conservation in primary, secondary, and tertiary structures. Lectins have ability to reduce the effects of inflammation caused by phlogistic agents, such as carrageenan (CGN). This paper explains the anti-inflammatory activity of AFAL through structural comparison with anti-inflammatory legume lectins. The AFAL model was obtained by molecular modeling and molecular docking with glycan and carrageenan were performed to explain the AFAL structural behavior and biological activity. Pisum sativum lectin was the best template for molecular modeling. The AFAL structure model is folded as a β sandwich. The model differs from template in loop regions, number of β strands and carbohydrate-binding site. Carrageenan and glycan bind to different sites on AFAL. The ability of AFAL binding to carrageenan can be explained by absence of the sixth β -strand (posterior β sheets) and two β strands in frontal region. AFAL can inhibit pathway inflammatory process by carrageenan injection by connecting to it and preventing its entry into the cell and triggers the reaction.
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34
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Moreira GMSG, Conceição FR, McBride AJA, Pinto LDS. Structure predictions of two Bauhinia variegata lectins reveal patterns of C-terminal properties in single chain legume lectins. PLoS One 2013; 8:e81338. [PMID: 24260572 PMCID: PMC3834338 DOI: 10.1371/journal.pone.0081338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/15/2013] [Indexed: 11/18/2022] Open
Abstract
Bauhinia variegata lectins (BVL-I and BVL-II) are single chain lectins isolated from the plant Bauhinia variegata. Single chain lectins undergo post-translational processing on its N-terminal and C-terminal regions, which determines their physiological targeting, carbohydrate binding activity and pattern of quaternary association. These two lectins are isoforms, BVL-I being highly glycosylated, and thus far, it has not been possible to determine their structures. The present study used prediction and validation algorithms to elucidate the likely structures of BVL-I and -II. The program Bhageerath-H was chosen from among three different structure prediction programs due to its better overall reliability. In order to predict the C-terminal region cleavage sites, other lectins known to have this modification were analysed and three rules were created: (1) the first amino acid of the excised peptide is small or hydrophobic; (2) the cleavage occurs after an acid, polar, or hydrophobic residue, but not after a basic one; and (3) the cleavage spot is located 5-8 residues after a conserved Leu amino acid. These rules predicted that BVL-I and -II would have fifteen C-terminal residues cleaved, and this was confirmed experimentally by Edman degradation sequencing of BVL-I. Furthermore, the C-terminal analyses predicted that only BVL-II underwent α-helical folding in this region, similar to that seen in SBA and DBL. Conversely, BVL-I and -II contained four conserved regions of a GS-I association, providing evidence of a previously undescribed X4+unusual oligomerisation between the truncated BVL-I and the intact BVL-II. This is the first report on the structural analysis of lectins from Bauhinia spp. and therefore is important for the characterisation C-terminal cleavage and patterns of quaternary association of single chain lectins.
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Affiliation(s)
- Gustavo M. S. G. Moreira
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fabricio R. Conceição
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Alan J. A. McBride
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Luciano da S. Pinto
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
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Purification, partial characterization and immobilization of a mannose-specific lectin from seeds of Dioclea lasiophylla mart. Molecules 2013; 18:10857-69. [PMID: 24008245 PMCID: PMC6270569 DOI: 10.3390/molecules180910857] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 11/16/2022] Open
Abstract
Lectin from the seeds of Dioclea lasiophylla (DlyL) was purified in a single step by affinity chromatography on a Sephadex® G-50 column. DlyL strongly agglutinated rabbit erythrocytes and was inhibited by monosaccharides (D-mannose and α-methyl-d-mannoside) and glycoproteins (ovalbumin and fetuin). Similar to other Diocleinae lectins, DlyL has three chains, α, β and γ, with mass of 25,569 ± 2, 12,998 ± 1 and 12,588 ± 1 Da, respectively, and has no disulfide bonds. The hemagglutinating activity of DlyL was optimal in pH 8.0, stable at a temperature of 70 °C and decreased in EDTA solution, indicating that lectin activity is dependent on divalent metals. DlyL exhibited low toxicity on Artemia sp. nauplii, but this effect was dependent on the concentration of lectin in solution. DlyL immobilized on cyanogen bromide-activated Sepharose® 4B bound 0.917 mg of ovalbumin per cycle, showing the ability to become a tool for glycoproteomics studies.
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Bezerra MJB, Rodrigues NVFC, Pires ADF, Bezerra GA, Nobre CB, Alencar KLDL, Soares PMG, Nascimento KSD, Nagano CS, Martins JL, Gruber K, Sampaio AH, Delatorre P, Rocha BAM, Assreuy AMS, Cavada BS. Crystal structure of Dioclea violacea lectin and a comparative study of vasorelaxant properties with Dioclea rostrata lectin. Int J Biochem Cell Biol 2013; 45:807-15. [DOI: 10.1016/j.biocel.2013.01.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/23/2012] [Accepted: 01/14/2013] [Indexed: 12/16/2022]
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Freymann DM, Nakamura Y, Focia PJ, Sakai R, Swanson GT. Structure of a tetrameric galectin from Cinachyrella sp. (ball sponge). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1163-74. [PMID: 22948917 PMCID: PMC3489101 DOI: 10.1107/s0907444912022834] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 05/18/2012] [Indexed: 11/10/2022]
Abstract
The galectins are a family of proteins that bind with highest affinity to N-acetyllactosamine disaccharides, which are common constituents of asparagine-linked complex glycans. They play important and diverse physiological roles, particularly in the immune system, and are thought to be critical metastatic agents for many types of cancer cells, including gliomas. A recent bioactivity-based screen of marine sponge (Cinachyrella sp.) extract identified an ancestral member of the galectin family based on its unexpected ability to positively modulate mammalian ionotropic glutamate receptor function. To gain insight into the mechanistic basis of this activity, the 2.1 Å resolution X-ray structure of one member of the family, galectin CchG-1, is reported. While the protomer exhibited structural similarity to mammalian prototype galectin, CchG-1 adopts a novel tetrameric arrangement in which a rigid toroidal-shaped 'donut' is stabilized in part by the packing of pairs of vicinal disulfide bonds. Twofold symmetry between binding-site pairs provides a basis for a model for interaction with ionotropic glutamate receptors.
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Affiliation(s)
- Douglas M Freymann
- Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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Li T, Yin X, Liu D, Ma X, Lv H, Sun S. Isolation and characterization of a novel lectin with antifungal and antiproliferative activities from Sophora alopecuroides seeds. Acta Biochim Biophys Sin (Shanghai) 2012; 44:606-13. [PMID: 22634632 DOI: 10.1093/abbs/gms037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sophora alopecuroides lectin (SAL), a novel lectin from the seeds of Sophora alopecuroides, was purified by ion-exchange chromatography on diethylaminoethyl (DEAE)- and carboxymethyl (CM)-Sepharose columns, followed by gel filtration on a Sephadex 75 10/300 GL column. SAL was found to be a monomer of 39916.3 Da, as determined by tricine-sodium dodecyl sulphate-polyacrylamide gel electrophoresis and high-performance liquid chromatography (HPLC). The N-terminal 10-amino acid sequence of SAL, KPWALSFSFG, resembles those of other legume lectins. SAL exhibits hemagglutinating activity against rabbit erythrocytes at 11.9 μg/ml. Its hemagglutinating activity is stable in the pH range 7-11 and in the temperature range 30-90°C, and is stimulated by Mn(2+). The hemagglutinating activity of SAL is most potently inhibited by 50-mM d-galactose. SAL suppresses mycelial growth in Penicillium digitatum and Alternaria alternata; the IC(50) of the antifungal activity toward P. digitatum and A. alternata were found to be 3.125 and 3.338 μM, respectively. SAL suppresses the proliferation of human cervical cancer cells (HeLa) at an IC(50) of 6.25 μM (P< 0.05). But it has no inhibiting effect on bacteria. This is the first report of a lectin from seeds of S. alopecuroides.
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Affiliation(s)
- Tingting Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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de Vasconcelos MA, Cunha CO, Arruda FVS, Carneiro VA, Mercante FM, Neto LGDN, de Sousa GS, Rocha BAM, Teixeira EH, Cavada BS, dos Santos RP. Lectin from Canavalia brasiliensis seeds (ConBr) is a valuable biotechnological tool to stimulate the growth of Rhizobium tropici in vitro. Molecules 2012; 17:5244-54. [PMID: 22565477 PMCID: PMC6268693 DOI: 10.3390/molecules17055244] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 04/22/2012] [Accepted: 04/25/2012] [Indexed: 12/14/2022] Open
Abstract
To study the interactions between a Rhizobium tropici strain and lectins isolated from the seeds of Canavalia ensiformis (ConA) and Canavalia brasiliensis (ConBr), a lectin fluorescence assay was performed. In addition, an experiment was designed to evaluate the effect of the two lectins on bacterial growth. Both lectins were found to bind to R. tropici cells, but the interactions were inhibited by D-mannose. Interestingly, only ConBr stimulated bacterial growth in proportion to the concentrations used (15.6–500 µg/mL), and the bacterial growth stimulation was inhibited by D-mannose as well. Structure/Function analyses by bioinformatics were carried out to evaluate the volume and carbohydrate recognition domain (CRD) configuration of ConA and ConBr. The difference of spatial arrangement and volume of CRD may indicate the variation between biological activities of both lectins. The results suggest that ConBr could be a promising tool for studies focusing on the interactions between rhizobia and host plants.
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Affiliation(s)
- Mayron Alves de Vasconcelos
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE 60440-970, Brazil; (M.A.V.); (C.O.C.); (B.A.M.R.)
| | - Claudio Oliveira Cunha
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE 60440-970, Brazil; (M.A.V.); (C.O.C.); (B.A.M.R.)
| | - Francisco Vassiliepe Sousa Arruda
- Integrated Laboratory of Biomolecules (LIBS), School of Medicine, Federal University of Ceara, Sobral, CE 62042-280, Brazil; (F.V.S.A.); (V.A.C.); (L.G.N.N.); (E.H.T.)
| | - Victor Alves Carneiro
- Integrated Laboratory of Biomolecules (LIBS), School of Medicine, Federal University of Ceara, Sobral, CE 62042-280, Brazil; (F.V.S.A.); (V.A.C.); (L.G.N.N.); (E.H.T.)
| | | | - Luiz Gonzaga do Nascimento Neto
- Integrated Laboratory of Biomolecules (LIBS), School of Medicine, Federal University of Ceara, Sobral, CE 62042-280, Brazil; (F.V.S.A.); (V.A.C.); (L.G.N.N.); (E.H.T.)
| | - Giselly Soares de Sousa
- Computer Engineering/Biotechnology Center of Sobral, Federal University of Ceara, CE 62011-000, Brazil;
| | - Bruno Anderson Matias Rocha
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE 60440-970, Brazil; (M.A.V.); (C.O.C.); (B.A.M.R.)
| | - Edson Holanda Teixeira
- Integrated Laboratory of Biomolecules (LIBS), School of Medicine, Federal University of Ceara, Sobral, CE 62042-280, Brazil; (F.V.S.A.); (V.A.C.); (L.G.N.N.); (E.H.T.)
| | - Benildo Sousa Cavada
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, CE 60440-970, Brazil; (M.A.V.); (C.O.C.); (B.A.M.R.)
- Authors to whom correspondence should be addressed; (B.S.C.); (R.P.S.); Tel./Fax: +55-85-3366-9818 (B.S.C.); Tel.: +55-88-3613-2829 (R.P.S.)
| | - Ricardo Pires dos Santos
- Computer Engineering/Biotechnology Center of Sobral, Federal University of Ceara, CE 62011-000, Brazil;
- Authors to whom correspondence should be addressed; (B.S.C.); (R.P.S.); Tel./Fax: +55-85-3366-9818 (B.S.C.); Tel.: +55-88-3613-2829 (R.P.S.)
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Souza Teixeira C, da Silva HC, de Moura TR, Pereira-Júnior FN, do Nascimento KS, Nagano CS, Sampaio AH, Delatorre P, Rocha BAM, Cavada BS. Crystal structure of the lectin of Camptosema pedicellatum: implications of a conservative substitution at the hydrophobic subsite. J Biochem 2012; 152:87-98. [PMID: 22554687 DOI: 10.1093/jb/mvs047] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Lectins have been used as models for studies of the molecular basis of protein-carbohydrate interaction and specificity by deciphering codes present in the glycan structures. The purpose of the present study was to purify and solve the complete primary and crystal structure of the lectin of Camptosema pedicellatum (CPL) complexed with 5-bromo-4-chloro-3-indolyl-α-d-mannose (X-Man) using tandem mass spectrometry. CPL was purified by single-step affinity chromatography. Mass spectrometry findings revealed that purified CPL features a combination of chains weighing 25,298 ± 2 (α-chain), 12,835 ± 2 (β-chain) and 12,481 ± 2 Da (γ-chain). The solved crystal structure of CPL features a conservative mutation in the hydrophobic subsite, a constituent of the carbohydrate recognition domain (CRD), indicating the relevance of hydrophobic interactions in the establishment of interactions with carbohydrates. The substitution and the analysis of the interactions with X-Man also revealed that the hydrophobic effect caused by a minor change in the hydrophobic subsite interferes in the formation of H-bonds due to the reorientation of the indolyl group in the CRD.
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Affiliation(s)
- Claudener Souza Teixeira
- BioMol-Lab, Laboratório de Moléculas Biologicamente Ativas, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará 60440-970, Brazil
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Batista da Nóbrega R, Rocha BA, Gadelha CAA, Santi-Gadelha T, Pires AF, Assreuy AMS, Nascimento KS, Nagano CS, Sampaio AH, Cavada BS, Delatorre P. Structure of Dioclea virgata lectin: Relations between carbohydrate binding site and nitric oxide production. Biochimie 2012; 94:900-6. [DOI: 10.1016/j.biochi.2011.12.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 12/09/2011] [Indexed: 01/28/2023]
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Kumar R, Panwar B, Chauhan JS, Raghava GPS. Analysis and prediction of cancerlectins using evolutionary and domain information. BMC Res Notes 2011; 4:237. [PMID: 21774797 PMCID: PMC3161874 DOI: 10.1186/1756-0500-4-237] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 07/20/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Predicting the function of a protein is one of the major challenges in the post-genomic era where a large number of protein sequences of unknown function are accumulating rapidly. Lectins are the proteins that specifically recognize and bind to carbohydrate moieties present on either proteins or lipids. Cancerlectins are those lectins that play various important roles in tumor cell differentiation and metastasis. Although the two types of proteins are linked, still there is no computational method available that can distinguish cancerlectins from the large pool of non-cancerlectins. Hence, it is imperative to develop a method that can distinguish between cancer and non-cancerlectins. RESULTS All the models developed in this study are based on a non-redundant dataset containing 178 cancerlectins and 226 non-cancerlectins in which no two sequences have more than 50% sequence similarity. We have applied the similarity search based technique, i.e. BLAST, and achieved a maximum accuracy of 43.25%. The amino acids compositional analysis have shown that certain residues (e.g. Leucine, Proline) were preferred in cancerlectins whereas some other (e.g. Asparatic acid, Asparagine) were preferred in non-cancerlectins. It has been found that the PROSITE domain "Crystalline beta gamma" was abundant in cancerlectins whereas domains like "SUEL-type lectin domain" were found mainly in non-cancerlectins. An SVM-based model has been developed to differentiate between the cancer and non-cancerlectins which achieved a maximum Matthew's correlation coefficient (MCC) value of 0.32 with an accuracy of 64.84%, using amino acid compositions. We have developed a model based on dipeptide compositions which achieved an MCC value of 0.30 with an accuracy of 64.84%. Thereafter, we have developed models based on split compositions (2 and 4 parts) and achieved an MCC value of 0.31, 0.32 with accuracies of 65.10% and 66.09%, respectively. An SVM model based on Position Specific Scoring Matrix (PSSM), generated by PSI-BLAST, was developed and achieved an MCC value of 0.36 with an accuracy of 68.34%. Finally, we have integrated the PROSITE domain information with PSSM and developed an SVM model that has achieved an MCC value of 0.38 with 69.09% accuracy. CONCLUSION BLAST has been found inefficient to distinguish between cancer and non-cancerlectins. We analyzed the protein sequences of cancer and non-cancerlectins and identified interesting patterns. We have been able to identify PROSITE domains that are preferred in cancer and non-cancerlectins and thus provided interesting insights into the two types of proteins. The method developed in this study will be useful for researchers studying cancerlectins, lectins and cancer biology. The web-server based on the above study, is available at http://www.imtech.res.in/raghava/cancer_pred/
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Affiliation(s)
- Ravi Kumar
- Bioinformatics Centre Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Bharat Panwar
- Bioinformatics Centre Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Jagat S Chauhan
- Bioinformatics Centre Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Gajendra PS Raghava
- Bioinformatics Centre Institute of Microbial Technology, Sector-39A, Chandigarh, India
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Rocha BA, Delatorre P, Oliveira TM, Benevides RG, Pires AF, Sousa AA, Souza LA, Assreuy AMS, Debray H, de Azevedo WF, Sampaio AH, Cavada BS. Structural basis for both pro- and anti-inflammatory response induced by mannose-specific legume lectin from Cymbosema roseum. Biochimie 2011; 93:806-16. [DOI: 10.1016/j.biochi.2011.01.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 01/14/2011] [Indexed: 10/18/2022]
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Bhattacharyya M, Vishveshwara S. Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis. BMC STRUCTURAL BIOLOGY 2010; 10:27. [PMID: 20704697 PMCID: PMC2929236 DOI: 10.1186/1472-6807-10-27] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 08/12/2010] [Indexed: 11/11/2022]
Abstract
Background One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results In this study, we have explored the ligand induced conformational changes in H.pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione) for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H.pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co-operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in any protein of known structure.
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Wong JH, Wan CT, Ng TB. Characterisation of a haemagglutinin from Hokkaido red bean (Phaseolus vulgaris cv. Hokkaido red bean). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2010; 90:70-77. [PMID: 20355014 DOI: 10.1002/jsfa.3782] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
BACKGROUND A haemagglutinin was purified from Japanese Hokkaido red beans (Phaseolus vulgaris cv. Hokkaido red bean) with a procedure that included three chromatographic media. RESULTS Haemagglutinating activity was adsorbed on DEAE cellulose, Affi-gel blue gel and Mono S. The pure haemagglutinin was a homodimer and each subunit was around 30 kDa in molecular mass. The haemagglutinating activity of this agglutinin could not be inhibited by a variety of simple sugars at 200 mmol L(-1) concentration including alpha-L-fucose, D(+)-galactose, D(+)-glucose, D(+)-glucosamine, D(-)galactosamine, galacturonic acid, (+)-lactose, D(+)-melibose, L(-)-mannose, D(+)-mannose, D-mannosamine, D(+)-raffinose, L-rhamnose, (+)-xylose and galacturonic acid. The haemagglutinating activity was fully retained at pH 4-11 and at 0-80 degrees C, but was completely lost at extreme pH values (0-2 and 13-14) and at very high temperatures (90 degrees C and 100 degrees C). The haemagglutinin exhibited a weak mitogenic activity toward mouse splenocytes, a stronger anti-proliferative activity than Con A toward HepG2 (human hepatoma) cells and inhibited >80% of HIV-1 reverse transcriptase inhibitory activity at 3.3 micromol L(-1). It was devoid of anti-fungal activity. CONCLUSION Hokkaido red bean haemagglutinin possesses a potent anti-proliferative effect on HepG2 cells.
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Affiliation(s)
- Jack H Wong
- Department of Biochemistry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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Batista FAH, Goto LS, Garcia W, de Moraes DI, de Oliveira Neto M, Polikarpov I, Cominetti MR, Selistre-de-Araújo HS, Beltramini LM, Araújo APU. Camptosemin, a tetrameric lectin of Camptosema ellipticum: structural and functional analysis. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 39:1193-205. [DOI: 10.1007/s00249-009-0571-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 12/03/2009] [Accepted: 12/14/2009] [Indexed: 11/25/2022]
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Bhattacharyya M, Vishveshwara S. Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks. BMC STRUCTURAL BIOLOGY 2009; 9:8. [PMID: 19243584 PMCID: PMC2656534 DOI: 10.1186/1472-6807-9-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 02/25/2009] [Indexed: 11/17/2022]
Abstract
Background The genome of a wide variety of prokaryotes contains the luxS gene homologue, which encodes for the protein S-ribosylhomocysteinelyase (LuxS). This protein is responsible for the production of the quorum sensing molecule, AI-2 and has been implicated in a variety of functions such as flagellar motility, metabolic regulation, toxin production and even in pathogenicity. A high structural similarity is present in the LuxS structures determined from a few species. In this study, we have modelled the structures from several other species and have investigated their dimer interfaces. We have attempted to correlate the interface features of LuxS with the phenotypic nature of the organisms. Results The protein structure networks (PSN) are constructed and graph theoretical analysis is performed on the structures obtained from X-ray crystallography and on the modelled ones. The interfaces, which are known to contain the active site, are characterized from the PSNs of these homodimeric proteins. The key features presented by the protein interfaces are investigated for the classification of the proteins in relation to their function. From our analysis, structural interface motifs are identified for each class in our dataset, which showed distinctly different pattern at the interface of LuxS for the probiotics and some extremophiles. Our analysis also reveals potential sites of mutation and geometric patterns at the interface that was not evident from conventional sequence alignment studies. Conclusion The structure network approach employed in this study for the analysis of dimeric interfaces in LuxS has brought out certain structural details at the side-chain interaction level, which were elusive from the conventional structure comparison methods. The results from this study provide a better understanding of the relation between the luxS gene and its functional role in the prokaryotes. This study also makes it possible to explore the potential direction towards the design of inhibitors of LuxS and thus towards a wide range of antimicrobials.
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Insights into the structural basis of the pH-dependent dimer-tetramer equilibrium through crystallographic analysis of recombinant Diocleinae lectins. Biochem J 2008; 409:417-28. [PMID: 17937659 DOI: 10.1042/bj20070942] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The structural ground underlying the pH-dependency of the dimer-tetramer transition of Diocleinae lectins was investigated by equilibrium sedimentation and X-ray crystal structure determination of wild-type and site-directed mutants of recombinant lectins. Synthetic genes coding for the full-length alpha-chains of the seed lectins of Dioclea guianensis (termed r-alphaDguia) and Dioclea grandiflora (termed r-alphaDGL) were designed and expressed in Escherichia coli. This pioneering approach, which will be described in detail in the present paper, yielded recombinant lectins displaying carbohydrate-binding activity, dimer-tetramer equilibria and crystal structures indistinguishable from their natural homologues. Conversion of the pH-stable tetrameric r-alphaDGL into a structure exhibiting pH-dependent dimer-tetramer transition was accomplished through mutations that abolished the interdimeric interactions at the central cavity of the tetrameric lectins. Both the central and the peripheral interacting regions bear structural information for formation of the canonical legume lectin tetramer. We hypothesize that the strength of the ionic contacts at these sites may be modulated by the pH, leading to dissociation of those lectin structures that are not locked into a pH-stable tetramer through interdimeric contacts networking the central cavity loops.
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Moreno FBMB, de Oliveira TM, Martil DE, Viçoti MM, Bezerra GA, Abrego JRB, Cavada BS, Filgueira de Azevedo W. Identification of a new quaternary association for legume lectins. J Struct Biol 2008; 161:133-43. [DOI: 10.1016/j.jsb.2007.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 09/27/2007] [Accepted: 10/04/2007] [Indexed: 10/22/2022]
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Bezerra GA, Oliveira TM, Moreno FBMB, de Souza EP, da Rocha BAM, Benevides RG, Delatorre P, de Azevedo WF, Cavada BS. Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: New insights into the understanding of the structure–biological activity relationship in legume lectins. J Struct Biol 2007; 160:168-76. [PMID: 17881248 DOI: 10.1016/j.jsb.2007.07.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Revised: 06/21/2007] [Accepted: 07/30/2007] [Indexed: 11/15/2022]
Abstract
Plant lectins, especially those purified from species of the Leguminosae family, represent the best studied group of carbohydrate-binding proteins. The legume lectins from Diocleinae subtribe are highly similar proteins that present significant differences in the potency/efficacy of their biological activities. The structural studies of the interactions between lectins and sugars may clarify the origin of the distinct biological activities observed in this high similar class of proteins. In this way, this work presents a crystallographic study of the ConM and CGL (agglutinins from Canavalia maritima and Canavalia gladiata, respectively) in the following complexes: ConM/CGL:Man(alpha1-2)Man(alpha1-O)Me, ConM/CGL:Man(alpha1-3)Man(alpha1-O)Me and ConM/CGL:Man(alpha1-4)Man(alpha1-O)Me, which crystallized in different conditions and space group from the native proteins. The structures were solved by molecular replacement, presenting satisfactory values for R(factor) and R(free). Comparisons between ConM, CGL and ConA (Canavalia ensiformis lectin) binding mode with the dimannosides in subject, presented different interactions patterns, which may account for a structural explanation of the distincts biological properties observed in the lectins of Diocleinae subtribe.
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Affiliation(s)
- Gustavo Arruda Bezerra
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Biomol-LAB, Campus do Pici S/N, Fortaleza, Ceará, Brazil
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