1
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Zhang N, Li L, Mohri M, Siebert S, Lütteke T, Louton H, Bednarikova Z, Gazova Z, Nifantiev N, Jandowsky A, Frölich K, Eckert T, Loers G, Petridis AK, Bhunia A, Mohid SA, Scheidig AJ, Liu G, Zhang R, Lochnit G, Siebert HC. Protein - carbohydrate interaction studies using domestic animals as role models support the search of new glycomimetic molecules. Int J Biol Macromol 2024; 279:134951. [PMID: 39179069 DOI: 10.1016/j.ijbiomac.2024.134951] [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: 06/11/2024] [Revised: 08/14/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
The structural dynamics of the interactions between defensins or lysozymes and various saccharide chains that are covalently linked to lipids or proteins were analyzed in relation to the sub-molecular architecture of the carbohydrate binding sites of lectins. Using tissue materials from rare and endangered domestic animals as well as from dogs it was possible to compare these results with data obtained from a human glioblastoma tissue. The binding mechanisms were analyzed on a cellular and a sub-molecular size level using biophysical techniques (e.g. NMR, AFM, MS) which are supported by molecular modeling tools. This leads to characteristic structural patterns being helpful to understand glyco-biochemical pathways in which galectins, defensins or lysozymes are involved. Carbohydrate chains have a distinct impact on cell differentiation, cell migration and immunological processes. The absence or the presence of sialic acids and the conformational dynamics in glycans are often correlated with zoonoses such as influenza- and coronavirus-infections. Receptor-sensitive glycomimetics could be a solution. The new findings concerning the function of galectin-3 in the nucleus in relation to differentiation processes can be understood when the binding specificity of neuroleptic molecules as well as the interactions between proteins and nucleic acids are describable on a sub-molecular size level.
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Affiliation(s)
- Ning Zhang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China.
| | - Lan Li
- RI-B-NT - Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Marzieh Mohri
- RI-B-NT - Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Simone Siebert
- RI-B-NT - Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Thomas Lütteke
- Institut für Veterinärphysiologie und Biochemie, Fachbereich Veterinärmedizin, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392 Gießen, Germany
| | - Helen Louton
- Animal Health and Animal Welfare, Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6b, 18059 Rostock, Germany
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04001, Kosice, Slovakia
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04001, Kosice, Slovakia
| | - Nikolay Nifantiev
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia
| | - Anabell Jandowsky
- Tierpark Arche Warder, Zentrum für seltene Nutztierrassen e. V., Langwedeler Weg 11, 24646 Warder, Germany
| | - Kai Frölich
- Tierpark Arche Warder, Zentrum für seltene Nutztierrassen e. V., Langwedeler Weg 11, 24646 Warder, Germany
| | - Thomas Eckert
- Department of Chemistry and Biology, University of Applied Sciences Fresenius, Limburger Str. 2, 65510 Idstein, Germany; RISCC Research Institute for Scientific Computing and Consulting, Heuchelheim, Germany
| | - Gabriele Loers
- Center for Molecular Neurobiology Hamburg, University Medical Center, Hamburg-Eppendorf, University of Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Athanasios K Petridis
- Medical School, Heinrich-Heine-Universität Düsseldorf, Department of Neurosurgery, St. Lukes Hospital, Thessaloniki, Greece
| | - Anirban Bhunia
- Department of Chemical Sciences, Bose Institute, Unified Academic Campus, Sector V, EN 80, Kolkata 700091, India
| | - Sk Abdul Mohid
- Department of Chemical Sciences, Bose Institute, Unified Academic Campus, Sector V, EN 80, Kolkata 700091, India
| | - Axel J Scheidig
- Zoological Institute, Department of Structural Biology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Guiqin Liu
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China
| | - Ruiyan Zhang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China
| | - Günter Lochnit
- Institut für Biochemie, Fachbereich Humanmedizin, Justus-Liebig-Universität Gießen, Friedrichstrasse 24, 35390 Gießen, Germany
| | - Hans-Christian Siebert
- RI-B-NT - Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany.
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2
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Cazares-Álvarez JE, Báez-Astorga PA, Arroyo-Becerra A, Maldonado-Mendoza IE. Genome-Wide Identification of a Maize Chitinase Gene Family and the Induction of Its Expression by Fusarium verticillioides (Sacc.) Nirenberg (1976) Infection. Genes (Basel) 2024; 15:1087. [PMID: 39202446 PMCID: PMC11353892 DOI: 10.3390/genes15081087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Maize chitinases are involved in chitin hydrolysis. Chitinases are distributed across various organisms including animals, plants, and fungi and are grouped into different glycosyl hydrolase families and classes, depending on protein structure. However, many chitinase functions and their interactions with other plant proteins remain unknown. The economic importance of maize (Zea mays L.) makes it relevant for studying the function of plant chitinases and their biological roles. This work aims to identify chitinase genes in the maize genome to study their gene structure, family/class classification, cis-related elements, and gene expression under biotic stress, such as Fusarium verticillioides infection. Thirty-nine chitinase genes were identified and found to be distributed in three glycosyl hydrolase (GH) families (18, 19 and 20). Likewise, the conserved domains and motifs were identified in each GH family member. The identified cis-regulatory elements are involved in plant development, hormone response, defense, and abiotic stress response. Chitinase protein-interaction network analysis predicted that they interact mainly with cell wall proteins. qRT-PCR analysis confirmed in silico data showing that ten different maize chitinase genes are induced in the presence of F. verticillioides, and that they could have several roles in pathogen infection depending on chitinase structure and cell wall localization.
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Affiliation(s)
- Jesús Eduardo Cazares-Álvarez
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
| | - Paúl Alán Báez-Astorga
- CONAHCYT—Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
| | - Analilia Arroyo-Becerra
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico;
| | - Ignacio Eduardo Maldonado-Mendoza
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Sinaloa, Instituto Politécnico Nacional, Guasave 81049, Sinaloa, Mexico;
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3
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Bibekar P, Krapp L, Peraro MD. PeSTo-Carbs: Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces. J Chem Theory Comput 2024; 20:2985-2991. [PMID: 38602504 PMCID: PMC11044267 DOI: 10.1021/acs.jctc.3c01145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024]
Abstract
The Protein Structure Transformer (PeSTo), a geometric transformer, has exhibited exceptional performance in predicting protein-protein binding interfaces and distinguishing interfaces with nucleic acids, lipids, small molecules, and ions. In this study, we introduce PeSTo-Carbs, an extension of PeSTo specifically engineered to predict protein-carbohydrate binding interfaces. We evaluate the performance of this approach using independent test sets and compare them with those of previous methods. Furthermore, we highlight the model's capability to specialize in predicting interfaces involving cyclodextrins, a biologically and pharmaceutically significant class of carbohydrates. Our method consistently achieves remarkable accuracy despite the scarcity of available structural data for cyclodextrins.
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Affiliation(s)
- Parth Bibekar
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Lucien Krapp
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Swiss
Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
| | - Matteo Dal Peraro
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Swiss
Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
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4
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Williams HM, Moeller JB, Burns I, Schlosser A, Sorensen GL, Greenhough TJ, Holmskov U, Shrive AK. Crystal structures of human immune protein FIBCD1 suggest an extended binding site compatible with recognition of pathogen-associated carbohydrate motifs. J Biol Chem 2024; 300:105552. [PMID: 38072065 PMCID: PMC10825690 DOI: 10.1016/j.jbc.2023.105552] [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: 05/22/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/14/2024] Open
Abstract
Fibrinogen C domain-containing protein 1 (FIBCD1) is an immune protein proposed to be involved in host recognition of chitin on the surface of pathogens. As FIBCD1 readily binds acetylated molecules, we have determined the high-resolution crystal structures of a recombinant fragment of the FIBCD1 C-terminal domain complexed with small N-acetyl-containing ligands to determine the mode of recognition. All ligands bind at the conserved N-acetyl-binding site (S1) with galactose and glucose-derived ligands rotated 180° relative to each other. One subunit of a native structure derived from protein expressed in mammalian cells binds glycosylation from a neighboring subunit, in an extended binding site. Across the various structures, the primary S1 binding pocket is occupied by N-acetyl-containing ligands or acetate, with N-acetyl, acetate, or sulfate ion in an adjacent pocket S1(2). Inhibition binding studies of N-acetylglucosamine oligomers, (GlcNAc)n, n = 1, 2, 3, 5, 11, via ELISA along with microscale thermophoresis affinity assays indicate a strong preference of FIBCD1 for longer N-acetylchitooligosaccharides. Binding studies of mutant H396A, located beyond the S1(2) site, showed no significant difference from wildtype, but K381L, within the S1(2) pocket, blocked binding to the model ligand acetylated bovine serum albumin, suggesting that S1(2) may have functional importance in ligand binding. The binding studies, alongside structural definition of diverse N-acetyl monosaccharide binding in the primary S1 pocket and of additional, adjacent binding pockets, able to accommodate both carbohydrate and sulfate functional groups, suggest a versatility in FIBCD1 to recognize chitin oligomers and other pathogen-associated carbohydrate motifs across an extended surface.
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Affiliation(s)
- Harry M Williams
- School of Life Sciences, Keele University, Staffordshire, United Kingdom
| | - Jesper B Moeller
- Cancer and Inflammation Research Unit, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark; Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Ian Burns
- School of Life Sciences, Keele University, Staffordshire, United Kingdom
| | - Anders Schlosser
- Cancer and Inflammation Research Unit, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Grith L Sorensen
- Cancer and Inflammation Research Unit, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Uffe Holmskov
- Cancer and Inflammation Research Unit, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Annette K Shrive
- School of Life Sciences, Keele University, Staffordshire, United Kingdom.
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5
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Slezina MP, Odintsova TI. Plant Antimicrobial Peptides: Insights into Structure-Function Relationships for Practical Applications. Curr Issues Mol Biol 2023; 45:3674-3704. [PMID: 37185763 PMCID: PMC10136942 DOI: 10.3390/cimb45040239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023] Open
Abstract
Antimicrobial peptides (AMPs) are short polypeptide molecules produced by multicellular organisms that are involved in host defense and microbiome preservation. In recent years, AMPs have attracted attention as novel drug candidates. However, their successful use requires detailed knowledge of the mode of action and identification of the determinants of biological activity. In this review, we focused on structure-function relationships in the thionins, α-hairpinins, hevein-like peptides, and the unique Ib-AMP peptides isolated from Impatiens balsamina. We summarized the available data on the amino acid sequences and 3D structure of peptides, their biosynthesis, and their biological activity. Special attention was paid to the determination of residues that play a key role in the activity and the identification of the minimal active cores. We have shown that even subtle changes in amino acid sequences can affect the biological activity of AMPs, which opens up the possibility of creating molecules with improved properties, better therapeutic efficacy, and cheaper large-scale production.
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Affiliation(s)
- Marina P Slezina
- Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia
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6
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Madland E, Crasson O, Vandevenne M, Sørlie M, Aachmann FL. NMR and Fluorescence Spectroscopies Reveal the Preorganized Binding Site in Family 14 Carbohydrate-Binding Module from Human Chitotriosidase. ACS OMEGA 2019; 4:21975-21984. [PMID: 31891077 PMCID: PMC6933781 DOI: 10.1021/acsomega.9b03043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/26/2019] [Indexed: 05/02/2023]
Abstract
Carbohydrate-binding modules (CBM) play important roles in targeting and increasing the concentration of carbohydrate active enzymes on their substrates. Using NMR to get the solution structure of CBM14, we can gain insight into secondary structure elements and intramolecular interactions with our assigned nuclear overhauser effect peaks. This reveals that two conserved aromatic residues (Phe437 and Phe456) make up the hydrophobic core of the CBM. These residues are also responsible for connecting the two β-sheets together, by being part of β2 and β4, respectively, and together with disulfide bridges, they create CBM14's characteristic "hevein-like" fold. Most CBMs rely on aromatic residues for substrate binding; however, CBM14 contains just a single tryptophan (Trp465) that together with Asn466 enables substrate binding. Interestingly, an alanine mutation of a single residue (Leu454) located behind Trp465 renders the CBM incapable of binding. Fluorescence spectroscopy performed on this mutant reveals a significant blue shift, as well as a minor blue shift for its neighbor Val455. The reduction in steric hindrance causes the tryptophan to be buried into the hydrophobic core of the structure and therefore suggests a preorganized binding site for this CBM. Our results show that both Trp465 and Asn466 are affected when CBM14 interacts with both (GlcNAc)3 and β-chitin, that the binding interactions are weak, and that CBM14 displays a slightly higher affinity toward β-chitin.
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Affiliation(s)
- Eva Madland
- Department
of Biotechnology and Food Science, Norwegian Biopolymer Laboratory
(NOBIPOL), NTNU Norwegian University of
Science and Technology, Trondheim 7491, Norway
| | - Oscar Crasson
- InBioS—Center
for Protein Engineering, Institut de Chimie B6a, Université de Liège, Sart-Tilman, Liège 4000, Belgium
| | - Maryléne Vandevenne
- InBioS—Center
for Protein Engineering, Institut de Chimie B6a, Université de Liège, Sart-Tilman, Liège 4000, Belgium
| | - Morten Sørlie
- Department
of Chemistry, Biotechnology and Food Science, NMBU Norwegian University of Life Sciences, Ås 1430, Norway
| | - Finn L. Aachmann
- Department
of Biotechnology and Food Science, Norwegian Biopolymer Laboratory
(NOBIPOL), NTNU Norwegian University of
Science and Technology, Trondheim 7491, Norway
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7
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Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain. Sci Rep 2019; 9:18918. [PMID: 31831756 PMCID: PMC6908686 DOI: 10.1038/s41598-019-53815-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/05/2019] [Indexed: 12/17/2022] Open
Abstract
Interactions between proteins and their small molecule ligands are of great importance for the process of drug design. Here we report an unbiased molecular dynamics simulation of systems containing hevein domain (HEV32) with N-acetylglucosamine mono-, di- or trisaccharide. Carbohydrate molecules were placed outside the binding site. Three of six simulations (6 × 2 μs) led to binding of a carbohydrate ligand into the binding mode in agreement with the experimentally determined structure. Unbinding was observed in one simulation (monosaccharide). There were no remarkable intermediates of binding for mono and disaccharide. Trisaccharide binding was initiated by formation of carbohydrate-aromatic CH/π interactions. Our results indicate that binding of ligands followed the model of conformational selection because the conformation of the protein ready for ligand binding was observed before the binding. This study extends the concept of docking by dynamics on carbohydrate-protein interactions.
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8
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de Oliveira CFR, de Oliveira Flores TM, Henrique Cardoso M, Garcia Nogueira Oshiro K, Russi R, de França AFJ, dos Santos EA, Luiz Franco O, de Oliveira AS, Migliolo L. Dual Insecticidal Effects of Adenanthera pavonina Kunitz-Type Inhibitor on Plodia interpunctella is Mediated by Digestive Enzymes Inhibition and Chitin-Binding Properties. Molecules 2019; 24:E4344. [PMID: 31795088 PMCID: PMC6930628 DOI: 10.3390/molecules24234344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 11/16/2022] Open
Abstract
The Indianmeal moth, Plodia interpunctella, is one of the most damaging pests of stored products. We investigated the insecticidal properties of ApKTI, a Kunitz trypsin inhibitor from Adenanthera pavonina seeds, against P. interpunctella larvae through bioassays with artificial diet. ApKTI-fed larvae showed reduction of up to 88% on larval weight and 75% in survival. Trypsin enzymes extracted from P. interpunctella larvae were inhibited by ApKTI, which also demonstrated capacity to bind to chitin. Kinetic studies revealed a non-competitive inhibition mechanism of ApKTI for trypsin, which were further corroborated by molecular docking studies. Furthermore, we have demonstrated that ApKTI exhibits a hydrophobic pocket near the reactive site loop probably involved in chitin interactions. Taken together, these data suggested that the insecticidal activity of ApKTI for P. interpunctella larvae involves a dual and promiscuous mechanisms biding to two completely different targets. Both processes might impair the P. interpunctella larval digestive process, leading to larvae death before reaching the pupal stage. Further studies are encouraged using ApKTI as a biotechnological tool to control insect pests in field conditions.
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Affiliation(s)
| | - Taylla Michelle de Oliveira Flores
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, 79117-900, Brazil; (T.M.d.O.F.); (M.H.C.); (K.G.N.O.); (O.L.F.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal da Paraíba, João Pessoa, PB, 58059-900, Brazil
| | - Marlon Henrique Cardoso
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, 79117-900, Brazil; (T.M.d.O.F.); (M.H.C.); (K.G.N.O.); (O.L.F.)
- Centro de Análises Bioquímica e Proteômicas, Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, 70790-160, Brazil
| | - Karen Garcia Nogueira Oshiro
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, 79117-900, Brazil; (T.M.d.O.F.); (M.H.C.); (K.G.N.O.); (O.L.F.)
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Raphael Russi
- Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-900, Brazil; (R.R.); (A.F.J.d.F.); (E.A.d.S.); (A.S.d.O.)
| | - Anderson Felipe Jácome de França
- Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-900, Brazil; (R.R.); (A.F.J.d.F.); (E.A.d.S.); (A.S.d.O.)
| | - Elizeu Antunes dos Santos
- Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-900, Brazil; (R.R.); (A.F.J.d.F.); (E.A.d.S.); (A.S.d.O.)
| | - Octávio Luiz Franco
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, 79117-900, Brazil; (T.M.d.O.F.); (M.H.C.); (K.G.N.O.); (O.L.F.)
- Centro de Análises Bioquímica e Proteômicas, Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, 70790-160, Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Adeliana Silva de Oliveira
- Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-900, Brazil; (R.R.); (A.F.J.d.F.); (E.A.d.S.); (A.S.d.O.)
| | - Ludovico Migliolo
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, 79117-900, Brazil; (T.M.d.O.F.); (M.H.C.); (K.G.N.O.); (O.L.F.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal da Paraíba, João Pessoa, PB, 58059-900, Brazil
- Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-900, Brazil; (R.R.); (A.F.J.d.F.); (E.A.d.S.); (A.S.d.O.)
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9
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Biari KE, Gaudioso Á, Fernández-Alonso MC, Jiménez-Barbero J, Cañada FJ. Peptidoglycan Recognition by Wheat Germ Agglutinin. A View by NMR. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19849240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Wheat germ agglutinin (WGA) is a lectin composed of 4 homologous hevein domains. It has been shown that WGA binds N-acetyl glucosamine (GlcNAc)-related oligosaccharides and has applications as commercial reagent to detect glycans containing such modified residues. Peptidoglycan (PGN), the main component of the bacterial cell wall, is a polymeric material made of repeating disaccharide units of GlcNAc- N-acetylmuramic acid cross-linked with short polypeptide fragments. Wheat germ agglutinin is able to bind bacterial cells, a phenomenon that could correlate with its plant-defense capacities, but there is no information at the molecular level about how WGA binds to the PGN. Herein, we present structural data on the binding of a short PGN fragment to WGA by means of saturation transfer difference nuclear magnetic resonance studies. The results show that the GlcNAc residue establishes the major contacts with WGA, followed by the N-acetylmuramic acid residue. In contrast, the peptide moiety displays minor contacts at the binding site.
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Affiliation(s)
- Khouzaima el Biari
- Centro de Investigaciones Biológicas, CIB CSIC, c/Ramiro de Maeztu 9, Madrid, Spain
- Département de Biologie, Faculté des Sciences, Université Ibn Zohr, Agadir, Morocco
| | - Ángel Gaudioso
- Centro de Investigaciones Biológicas, CIB CSIC, c/Ramiro de Maeztu 9, Madrid, Spain
| | | | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
- Departament of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, Bilbao, Spain
| | - F. Javier Cañada
- Centro de Investigaciones Biológicas, CIB CSIC, c/Ramiro de Maeztu 9, Madrid, Spain
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10
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Van Holle S, Van Damme EJM. Messages From the Past: New Insights in Plant Lectin Evolution. FRONTIERS IN PLANT SCIENCE 2019; 10:36. [PMID: 30761173 PMCID: PMC6362431 DOI: 10.3389/fpls.2019.00036] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 01/10/2019] [Indexed: 05/25/2023]
Abstract
Lectins are a large and diverse class of proteins, found in all kingdoms of life. Plants are known to express different types of carbohydrate-binding proteins, each containing at least one particular lectin domain which enables them to specifically recognize and bind carbohydrate structures. The group of plant lectins is heterogeneous in terms of structure, biological activity and function. Lectins control various aspects of plant development and defense. Some lectins facilitate recognition of exogenous danger signals or play a role in endogenous signaling pathways, while others are considered as storage proteins or involved in symbiotic relationships. In this study, we revisit the origin of the different plant lectin families in view of the recently reshaped tree of life. Due to new genomic sampling of previously unknown microbial lineages, the tree of life has expanded and was reshaped multiple times. In addition, more plant genomes especially from basal Phragmoplastophyta, bryophytes, and Salviniales (e.g., Chara braunii, Marchantia polymorpha, Physcomitrella patens, Azolla filiculoides, and Salvinia cucullata) have been analyzed, and annotated genome sequences have become accessible. We searched 38 plant genome sequences including core eudicots, monocots, gymnosperms, fern, lycophytes, bryophytes, charophytes, chlorophytes, glaucophytes, and rhodophytes for lectin motifs, performed an extensive comparative analysis of lectin domain architectures, and determined the phylogenetic and evolutionary history of lectins in the plant lineage. In conclusion, we describe the conservation of particular domains in plant lectin sequences obtained from algae to higher plants. The strong conservation of several lectin motifs highlights their significance for plants.
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Slavokhotova AA, Shelenkov AA, Andreev YA, Odintsova TI. Hevein-Like Antimicrobial Peptides of Plants. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523064 DOI: 10.1134/s0006297917130065] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Plant antimicrobial peptides represent one of the evolutionarily oldest innate immunity components providing the first line of host defense to pathogen attacks. This review is dedicated to a small, currently actively studied family of hevein-like peptides that can be found in various monocot and dicot plants. The review thoroughly describes all known peptides belonging to this family including data on their structures, functions, and antimicrobial activity. The main features allowing to assign these peptides to a separate family are given, and the specific characteristics of each peptide are described. Further, the mode of action for hevein-like peptides, their role in plant immune system, and the applications of these molecules in biotechnology and medicine are considered.
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Affiliation(s)
- A A Slavokhotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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12
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Takashima T, Ohnuma T, Fukamizo T. NMR analysis of substrate binding to a two-domain chitinase: Comparison between soluble and insoluble chitins. Carbohydr Res 2018; 458-459:52-59. [DOI: 10.1016/j.carres.2018.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 01/24/2018] [Accepted: 02/07/2018] [Indexed: 12/23/2022]
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13
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Human Chitotriosidase: Catalytic Domain or Carbohydrate Binding Module, Who's Leading HCHT's Biological Function. Sci Rep 2017; 7:2768. [PMID: 28584264 PMCID: PMC5459812 DOI: 10.1038/s41598-017-02382-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 04/10/2017] [Indexed: 01/07/2023] Open
Abstract
Chitin is an important structural component of numerous fungal pathogens and parasitic nematodes. The human macrophage chitotriosidase (HCHT) is a chitinase that hydrolyses glycosidic bonds between the N-acetyl-D-glucosamine units of this biopolymer. HCHT belongs to the Glycoside Hydrolase (GH) superfamily and contains a well-characterized catalytic domain appended to a chitin-binding domain (ChBDCHIT1). Although its precise biological function remains unclear, HCHT has been described to be involved in innate immunity. In this study, the molecular basis for interaction with insoluble chitin as well as with soluble chito-oligosaccharides has been determined. The results suggest a new mechanism as a common binding mode for many Carbohydrate Binding Modules (CBMs). Furthermore, using a phylogenetic approach, we have analysed the modularity of HCHT and investigated the evolutionary paths of its catalytic and chitin binding domains. The phylogenetic analyses indicate that the ChBDCHIT1 domain dictates the biological function of HCHT and not its appended catalytic domain. This observation may also be a general feature of GHs. Altogether, our data have led us to postulate and discuss that HCHT acts as an immune catalyser.
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Schubert M. Insights into Carbohydrate Recognition by 3D Structure Determination of Protein–Carbohydrate Complexes Using NMR. NMR IN GLYCOSCIENCE AND GLYCOTECHNOLOGY 2017:101-122. [DOI: 10.1039/9781782623946-00101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
This chapter provides an overview of protein–carbohydrate complex structures determined with NMR spectroscopy and deposited in the Protein Data Bank (PDB). These 14 structures include protein–carbohydrate interactions ranging from nanomolar to millimolar affinities. Two complexes are discussed in detail, one representing a tightly bound complex and one a weak but specific interaction. This review illustrates that NMR spectroscopy is a competitive method for three-dimensional structure determination of protein–carbohydrate complexes, especially in the case of weak interactions. The number of biological functions in which protein–carbohydrate interactions are involved is steadily growing. Essential functions of the immune system such as the distinction between self and non-self, or the resolution of inflammation, involve critical protein–carbohydrate recognition events. It is therefore expected that by providing atomic details, NMR spectroscopy can make a significant contribution in the near future to unexplored pathways of the immune system and of many other biological processes.
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Affiliation(s)
- Mario Schubert
- Department of Molecular Biology, University of Salzburg 5020 Salzburg Austria
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Takashima T, Ohnuma T, Fukamizo T. NMR assignments and ligand-binding studies on a two-domain family GH19 chitinase allergen from Japanese cedar (Cryptomeria japonica) pollen. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:85-90. [PMID: 28032262 DOI: 10.1007/s12104-016-9725-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/15/2016] [Indexed: 06/06/2023]
Abstract
A two-domain family GH19 chitinase from Japanese cedar (Cryptomeria japonica) pollen, CJP-4, which consists of an N-terminal CBM18 domain and a GH19 catalytic domain, is known to be an important allergen, that causes pollinosis. We report here the resonance assignments of the NMR spectrum of CJP-4. The backbone resonances were almost completely assigned, and the secondary structure was estimated based on the chemical shift values. The addition of a chitin dimer to the enzyme solution perturbed the chemical shifts of the resonances of amino acid residues forming a long extended binding site spanning from the CBM18 domain to the GH19 catalytic domain.
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Affiliation(s)
- Tomoya Takashima
- Department of Advanced Bioscience, Kindai University, 3327-204, Nakamachi, Nara, 631-8505, Japan
| | - Takayuki Ohnuma
- Department of Advanced Bioscience, Kindai University, 3327-204, Nakamachi, Nara, 631-8505, Japan
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kindai University, 3327-204, Nakamachi, Nara, 631-8505, Japan.
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16
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Dang L, Van Damme EJM. Genome-wide identification and domain organization of lectin domains in cucumber. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 108:165-176. [PMID: 27434144 DOI: 10.1016/j.plaphy.2016.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 07/04/2016] [Accepted: 07/09/2016] [Indexed: 05/21/2023]
Abstract
Lectins are ubiquitous proteins in plants and play important roles in a diverse set of biological processes, such as plant defense and cell signaling. Despite the availability of the Cucumis sativus L. genome sequence since 2009, little is known with respect to the occurrence of lectins in cucumber. In this study, a total of 146 putative lectin genes belonging to 10 different lectin families were identified and localized in the cucumber genome. Domain architecture analysis revealed that most of these lectin gene sequences contain multiple domains, where lectin domains are linked with other domains, as such creating chimeric lectin sequences encoding proteins with dual activities. This study provides an overview of lectin motifs in cucumber and will help to understand their potential biological role(s).
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Affiliation(s)
- Liuyi Dang
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
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Mueller GA, Randall TA, Glesner J, Pedersen LC, Perera L, Edwards LL, DeRose EF, Chapman MD, London RE, Pomés A. Serological, genomic and structural analyses of the major mite allergen Der p 23. Clin Exp Allergy 2016; 46:365-76. [PMID: 26602749 DOI: 10.1111/cea.12680] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/28/2015] [Accepted: 11/12/2015] [Indexed: 01/11/2023]
Abstract
BACKGROUND Der p 23 was recently identified in a European population as a major allergen and potentially a chitin binding protein. OBJECTIVE This study sought to assess the importance of Der p 23 among other Dermatophagoides allergens in a North American population and to determine the structure for functional characterization. METHODS IgE binding to Der p 23, Der p 1, Der p 2, Der p 5, Der p 7 and Der p 8 was measured by ELISA. RNA-seq data from D. pteronyssinus were compared as estimates of allergen expression levels. The structure was analysed by X-ray crystallography and NMR. RESULTS Despite a high prevalence of Der p 23, (75% vs. 87% and 79% for Der p 1 and Der p 2, respectively), the anti-Der p 23 IgE levels were relatively low. The patient response to the 6 allergens tested was variable (n = 47), but on average anti-Der p 1 and anti-Der p 2 together accounted for 85% of the specific IgE. In terms of abundance, the RNA expression level of Der p 23 is the lowest of the major allergens, thirty fold less than Der p 1 and sevenfold less than Der p 2. The structure of Der p 23 is a small, globular protein stabilized by two disulphide bonds, which is structurally related to allergens such as Blo t 12 that contain carbohydrate binding domains that bind chitin. Functional assays failed to confirm chitin binding by Der p 23. CONCLUSIONS AND CLINICAL RELEVANCE Der p 23 accounts for a small percentage of the IgE response to mite allergens, which is dominated by Der p 1 and Der p 2. The prevalence and amount of specific IgE to Der p 23 and Der p 2 are disproportionately high compared to the expression of other Dermatophagoides allergens.
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Affiliation(s)
- G A Mueller
- Genome Integrity and Structural Biology Laboratory, Research Triangle Park, NC, USA
| | - T A Randall
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - J Glesner
- INDOOR Biotechnologies, Inc., Charlottesville, VA, USA
| | - L C Pedersen
- Genome Integrity and Structural Biology Laboratory, Research Triangle Park, NC, USA
| | - L Perera
- Genome Integrity and Structural Biology Laboratory, Research Triangle Park, NC, USA
| | - L L Edwards
- Genome Integrity and Structural Biology Laboratory, Research Triangle Park, NC, USA
| | - E F DeRose
- Genome Integrity and Structural Biology Laboratory, Research Triangle Park, NC, USA
| | - M D Chapman
- INDOOR Biotechnologies, Inc., Charlottesville, VA, USA
| | - R E London
- Genome Integrity and Structural Biology Laboratory, Research Triangle Park, NC, USA
| | - A Pomés
- INDOOR Biotechnologies, Inc., Charlottesville, VA, USA
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18
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Highlights on Hevea brasiliensis (pro)hevein proteins. Biochimie 2016; 127:258-70. [DOI: 10.1016/j.biochi.2016.06.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/07/2016] [Indexed: 12/11/2022]
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Marchetti R, Perez S, Arda A, Imberty A, Jimenez‐Barbero J, Silipo A, Molinaro A. "Rules of Engagement" of Protein-Glycoconjugate Interactions: A Molecular View Achievable by using NMR Spectroscopy and Molecular Modeling. ChemistryOpen 2016; 5:274-96. [PMID: 27547635 PMCID: PMC4981046 DOI: 10.1002/open.201600024] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectroscopic methods permitted us to deeply dissect the fine structural details of biologically relevant molecular recognition processes with high resolution. This Review focuses on the development and use of modern nuclear magnetic resonance (NMR) techniques to dissect binding events. These spectroscopic methods, complementing X-ray crystallography and molecular modeling methodologies, will be taken into account as indispensable tools to provide a complete picture of protein-glycoconjugate binding mechanisms related to biomedicine applications against infectious diseases.
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Affiliation(s)
- Roberta Marchetti
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Serge Perez
- Department Molecular Pharmacochemistry UMR 5063CNRS and University of GrenobleAlpes, BP 5338041 Grenoble cedex 9France
| | - Ana Arda
- Bizkaia Technological ParkCIC bioGUNEBuilding 801A-148160Derio-BizkaiaSpain
| | - Anne Imberty
- Centre de Recherche sur les CNRSand University of Grenoble Macromolécules Végétales, UPR 5301Alpes, BP 5338041Grenoble cedex 9France
| | | | - Alba Silipo
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Antonio Molinaro
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
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Tam JP, Wang S, Wong KH, Tan WL. Antimicrobial Peptides from Plants. Pharmaceuticals (Basel) 2015; 8:711-57. [PMID: 26580629 PMCID: PMC4695807 DOI: 10.3390/ph8040711] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/06/2015] [Accepted: 09/01/2015] [Indexed: 12/25/2022] Open
Abstract
Plant antimicrobial peptides (AMPs) have evolved differently from AMPs from other life forms. They are generally rich in cysteine residues which form multiple disulfides. In turn, the disulfides cross-braced plant AMPs as cystine-rich peptides to confer them with extraordinary high chemical, thermal and proteolytic stability. The cystine-rich or commonly known as cysteine-rich peptides (CRPs) of plant AMPs are classified into families based on their sequence similarity, cysteine motifs that determine their distinctive disulfide bond patterns and tertiary structure fold. Cystine-rich plant AMP families include thionins, defensins, hevein-like peptides, knottin-type peptides (linear and cyclic), lipid transfer proteins, α-hairpinin and snakins family. In addition, there are AMPs which are rich in other amino acids. The ability of plant AMPs to organize into specific families with conserved structural folds that enable sequence variation of non-Cys residues encased in the same scaffold within a particular family to play multiple functions. Furthermore, the ability of plant AMPs to tolerate hypervariable sequences using a conserved scaffold provides diversity to recognize different targets by varying the sequence of the non-cysteine residues. These properties bode well for developing plant AMPs as potential therapeutics and for protection of crops through transgenic methods. This review provides an overview of the major families of plant AMPs, including their structures, functions, and putative mechanisms.
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Affiliation(s)
- James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Shujing Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Ka H Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Wei Liang Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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21
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Marchetti R, Molinaro A, Silipo A. NMR as a Tool to Unveil the Molecular Basis of Glycan-mediated Host–Pathogen Interactions. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nature of the relationship between microbes and hosts spans the broad spectrum from beneficial (symbiosis) to pathogenic (disease); one of the key factors determining the establishment of any type of host–microbe interaction is the pattern of glycoconjugates exposed on cell surfaces, many known as virulence factors since they are pivotal for adhesion to host tissue, immunoevasion and immunosuppression, causing disease in the host. The recognition of these pathogen glycostructures by specific host receptors is an important means of immune defense. In this context, NMR represents a valuable tool to investigate the conformational properties of both host/pathogen signaling molecules and to disclose their interaction at a molecular level. This chapter provides an overview of several protein–carbohydrate interaction systems studied by NMR, and their implications in human and plant diseases.
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Affiliation(s)
- Roberta Marchetti
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
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Kinetic characterization of Aspergillus niger chitinase CfcI using a HPAEC-PAD method for native chitin oligosaccharides. Carbohydr Res 2015; 407:73-8. [DOI: 10.1016/j.carres.2015.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/23/2015] [Indexed: 01/14/2023]
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Molecular simulations of hevein/(GlcNAc)3 complex with weakened OH/O and CH/π hydrogen bonds: implications for their role in complex stabilization. Carbohydr Res 2015; 408:1-7. [PMID: 25816996 DOI: 10.1016/j.carres.2015.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 11/23/2022]
Abstract
Carbohydrate-protein complexes are often characterized by interactions via aromatic amino acid residues. Several mechanisms have been proposed to explain these stacking-like interactions between pyranose sugars and aromatic moieties. The physical basis of these interactions is being explained as either dispersion CH/π or hydrophobic. In order to elucidate the nature of these interactions, we performed a series of molecular dynamics simulation of hevein domain (HEV32) in complex with (β-D-GlcNAc)3. Selected OH/O and CH/π hydrogen bonds involved in carbohydrate recognition were artificially weakened in 100 ns molecular dynamics simulations. Separate weakening of either OH/O or CH/π hydrogen bonds was not sufficient to destabilize the complex. This indicates that other effects, not solely CH/π dispersion interactions, contribute significantly to the stability of the complex. Significant destabilization of complexes was reached only by simultaneous weakening of OH/O and CH/π hydrogen bonds. This also shows that classical hydrogen bonds and CH/π interactions are working in concert to stabilize this carbohydrate-protein test case.
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Sánchez-Vallet A, Mesters JR, Thomma BP. The battle for chitin recognition in plant-microbe interactions. FEMS Microbiol Rev 2015; 39:171-83. [DOI: 10.1093/femsre/fuu003] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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25
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Martínez-Caballero S, Cano-Sánchez P, Mares-Mejía I, Díaz-Sánchez AG, Macías-Rubalcava ML, Hermoso JA, Rodríguez-Romero A. Comparative study of two GH19 chitinase-like proteins fromHevea brasiliensis, one exhibiting a novel carbohydrate-binding domain. FEBS J 2014; 281:4535-54. [DOI: 10.1111/febs.12962] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/12/2014] [Accepted: 08/06/2014] [Indexed: 10/24/2022]
Affiliation(s)
| | - Patricia Cano-Sánchez
- Instituto de Química; Universidad Nacional Autónoma de México; Ciudad Universitaria México
| | - Israel Mares-Mejía
- Instituto de Química; Universidad Nacional Autónoma de México; Ciudad Universitaria México
| | - Angel G. Díaz-Sánchez
- Instituto de Química; Universidad Nacional Autónoma de México; Ciudad Universitaria México
| | | | - Juan A. Hermoso
- Departamento de Cristalografía y Biología Estructural; Instituto de Química-Física ‘Rocasolano’; CSIC Madrid Spain
| | - Adela Rodríguez-Romero
- Instituto de Química; Universidad Nacional Autónoma de México; Ciudad Universitaria México
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Solís D, Bovin NV, Davis AP, Jiménez-Barbero J, Romero A, Roy R, Smetana K, Gabius HJ. A guide into glycosciences: How chemistry, biochemistry and biology cooperate to crack the sugar code. Biochim Biophys Acta Gen Subj 2014; 1850:186-235. [PMID: 24685397 DOI: 10.1016/j.bbagen.2014.03.016] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 01/17/2023]
Abstract
BACKGROUND The most demanding challenge in research on molecular aspects within the flow of biological information is posed by the complex carbohydrates (glycan part of cellular glycoconjugates). How the 'message' encoded in carbohydrate 'letters' is 'read' and 'translated' can only be unraveled by interdisciplinary efforts. SCOPE OF REVIEW This review provides a didactic step-by-step survey of the concept of the sugar code and the way strategic combination of experimental approaches characterizes structure-function relationships, with resources for teaching. MAJOR CONCLUSIONS The unsurpassed coding capacity of glycans is an ideal platform for generating a broad range of molecular 'messages'. Structural and functional analyses of complex carbohydrates have been made possible by advances in chemical synthesis, rendering production of oligosaccharides, glycoclusters and neoglycoconjugates possible. This availability facilitates to test the glycans as ligands for natural sugar receptors (lectins). Their interaction is a means to turn sugar-encoded information into cellular effects. Glycan/lectin structures and their spatial modes of presentation underlie the exquisite specificity of the endogenous lectins in counterreceptor selection, that is, to home in on certain cellular glycoproteins or glycolipids. GENERAL SIGNIFICANCE Understanding how sugar-encoded 'messages' are 'read' and 'translated' by lectins provides insights into fundamental mechanisms of life, with potential for medical applications.
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Affiliation(s)
- Dolores Solís
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 07110 Bunyola, Mallorca, Illes Baleares, Spain.
| | - Nicolai V Bovin
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho-Maklaya 16/10, 117871 GSP-7, V-437, Moscow, Russian Federation.
| | - Anthony P Davis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - Antonio Romero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - René Roy
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada.
| | - Karel Smetana
- Charles University, 1st Faculty of Medicine, Institute of Anatomy, U nemocnice 3, 128 00 Prague 2, Czech Republic.
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 München, Germany.
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Mandal SM, Porto WF, Dey P, Maiti MK, Ghosh AK, Franco OL. The attack of the phytopathogens and the trumpet solo: Identification of a novel plant antifungal peptide with distinct fold and disulfide bond pattern. Biochimie 2013; 95:1939-48. [PMID: 23835303 DOI: 10.1016/j.biochi.2013.06.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/28/2013] [Indexed: 02/08/2023]
Abstract
Phytopathogens cause economic losses in agribusiness. Plant-derived compounds have been proposed to overcome this problem, including the antimicrobial peptides (AMPs). This paper reports the identification of Ps-AFP1, a novel AMP isolated from the Pisum sativum radicle. Ps-AFP1 was purified and evaluated against phytopathogenic fungi, showing clear effectiveness. In silico analyses were performed, suggesting an unusual fold and disulfide bond pattern. A novel fold and a novel AMP class were here proposed, the αβ-trumpet fold and αβ-trumpet peptides, respectively. The name αβ-trumpet was created due to the peptide's fold, which resembles the musical instrument. The Ps-AFP1 mechanism of action was also proposed. Microscopic analyses revealed that Ps-AFP1 could affect the fungus during the hyphal elongation from spore germination. Furthermore, confocal microscopy performed with Ps-AFP1 labeled with FITC shows that the peptide was localized at high concentration along the fungal cell surface. Due to low cellular disruption rates, it seems that the main target is the fungal cell wall. The binding thermogram and isothermal titration, molecular dynamics and docking analyses were also performed, showing that Ps-AFP1 could bind to chitin producing a stable complex. Data here reported provided novel structural-functional insights into the αβ-trumpet peptide fold.
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Affiliation(s)
- Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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del Carmen Fernández-Alonso M, Díaz D, Berbis MÁ, Marcelo F, Cañada J, Jiménez-Barbero J. Protein-carbohydrate interactions studied by NMR: from molecular recognition to drug design. Curr Protein Pept Sci 2013; 13:816-30. [PMID: 23305367 PMCID: PMC3706953 DOI: 10.2174/138920312804871175] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/12/2012] [Accepted: 07/25/2012] [Indexed: 02/04/2023]
Abstract
Diseases that result from infection are, in general, a consequence of specific interactions between a pathogenic organism and the cells. The study of host-pathogen interactions has provided insights for the design of drugs with therapeutic properties. One area that has proved to be promising for such studies is the constituted by carbohydrates which participate in biological processes of paramount importance. On the one hand, carbohydrates have shown to be information carriers with similar, if not higher, importance than traditionally considered carriers as amino acids and nucleic acids. On the other hand, the knowledge on molecular recognition of sugars by lectins and other carbohydrate-binding proteins has been employed for the development of new biomedical strategies. Biophysical techniques such as X-Ray crystallography and NMR spectroscopy lead currently the investigation on this field. In this review, a description of traditional and novel NMR methodologies employed in the study of sugar-protein interactions is briefly presented in combination with a palette of NMR-based studies related to biologically and/or pharmaceutically relevant applications.
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Asensio JL, Ardá A, Cañada FJ, Jiménez-Barbero J. Carbohydrate-aromatic interactions. Acc Chem Res 2013; 46:946-54. [PMID: 22704792 DOI: 10.1021/ar300024d] [Citation(s) in RCA: 359] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recognition of saccharides by proteins has far reaching implications in biology, technology, and drug design. Within the past two decades, researchers have directed considerable effort toward a detailed understanding of these processes. Early crystallographic studies revealed, not surprisingly, that hydrogen-bonding interactions are usually involved in carbohydrate recognition. But less expectedly, researchers observed that despite the highly hydrophilic character of most sugars, aromatic rings of the receptor often play an important role in carbohydrate recognition. With further research, scientists now accept that noncovalent interactions mediated by aromatic rings are pivotal to sugar binding. For example, aromatic residues often stack against the faces of sugar pyranose rings in complexes between proteins and carbohydrates. Such contacts typically involve two or three CH groups of the pyranoses and the π electron density of the aromatic ring (called CH/π bonds), and these interactions can exhibit a variety of geometries, with either parallel or nonparallel arrangements of the aromatic and sugar units. In this Account, we provide an overview of the structural and thermodynamic features of protein-carbohydrate interactions, theoretical and experimental efforts to understand stacking in these complexes, and the implications of this understanding for chemical biology. The interaction energy between different aromatic rings and simple monosaccharides based on quantum mechanical calculations in the gas phase ranges from 3 to 6 kcal/mol range. Experimental values measured in water are somewhat smaller, approximately 1.5 kcal/mol for each interaction between a monosaccharide and an aromatic ring. This difference illustrates the dependence of these intermolecular interactions on their context and shows that this stacking can be modulated by entropic and solvent effects. Despite their relatively modest influence on the stability of carbohydrate/protein complexes, the aromatic platforms play a major role in determining the specificity of the molecular recognition process. The recognition of carbohydrate/aromatic interactions has prompted further analysis of the properties that influence them. Using a variety of experimental and theoretical methods, researchers have worked to quantify carbohydrate/aromatic stacking and identify the features that stabilize these complexes. Researchers have used site-directed mutagenesis, organic synthesis, or both to incorporate modifications in the receptor or ligand and then quantitatively analyzed the structural and thermodynamic features of these interactions. Researchers have also synthesized and characterized artificial receptors and simple model systems, employing a reductionistic chemistry-based strategy. Finally, using quantum mechanics calculations, researchers have examined the magnitude of each property's contribution to the interaction energy.
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Affiliation(s)
- Juan Luis Asensio
- Chemical & Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid
| | - Ana Ardá
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Jesús Jiménez-Barbero
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
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Arnaud J, Audfray A, Imberty A. Binding sugars: from natural lectins to synthetic receptors and engineered neolectins. Chem Soc Rev 2013; 42:4798-813. [PMID: 23353569 DOI: 10.1039/c2cs35435g] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The large diversity and complexity of glycan structures together with their crucial role in many biological or pathological processes require the development of new high-throughput techniques for analyses. Lectins are classically used for characterising, imaging or targeting glycoconjugates and, when printed on microarrays, they are very useful tools for profiling glycomes. Development of recombinant lectins gives access to reliable and reproducible material, while engineering of new binding sites on existing scaffolds allows tuning of specificity. From the accumulated knowledge on protein-carbohydrate interactions, it is now possible to use nucleotide and peptide (bio)synthesis for producing new carbohydrate-binding molecules. Such a biomimetic approach can also be addressed by boron chemistry and supra-molecular chemistry for the design of fully artificial glycosensors.
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Affiliation(s)
- Julie Arnaud
- Centre de Recherche sur les Macromolécules Végétales (CERMAV-CNRS), affiliated to Grenoble-Université and ICMG, Grenoble, France
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Naumann TA, Price NPJ. Truncation of class IV chitinases from Arabidopsis by secreted fungal proteases. MOLECULAR PLANT PATHOLOGY 2012; 13:1135-1139. [PMID: 22512872 PMCID: PMC6638631 DOI: 10.1111/j.1364-3703.2012.00805.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Plant class IV chitinases have a small amino-terminal chitin-binding domain and a larger chitinase domain, and are involved in plant defence against fungal infection. Our previous work on the chitinases ChitA and ChitB from the model monocotyledon Zea mays showed that the chitin-binding domain is removed by secreted fungal proteases called fungalysins. In this article, we extend this work to dicotyledons. The effects of fungalysin-like proteases on four class IV chitinases from the model dicotyledon Arabidopsis thaliana were analysed. Four Arabidopsis chitinases were heterologously expressed in Pichia pastoris, purified and shown to have chitinase activity against a chitohexaose (dp6) substrate. The incubation of these four chitinases with Fv-cmp, a fungalysin protease secreted by Fusarium verticillioides, resulted in the truncation of AtchitIV3 and AtchitIV5. Moreover, incubation with secreted proteins from Alternaria brassicae, a pathogen of A. thaliana and brassica crops, also led to a similar truncation of AtchitIV3 and AtchitIV4. Our finding that class IV chitinases from both dicotyledons (A. thaliana) and monocotyledons (Z. mays) are truncated by proteases secreted by specialized pathogens of each plant suggests that this may be a general mechanism of plant-fungal pathogenicity.
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Affiliation(s)
- Todd A Naumann
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL 61604, USA.
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Porto WF, Souza VA, Nolasco DO, Franco OL. In silico identification of novel hevein-like peptide precursors. Peptides 2012; 38:127-36. [PMID: 22981805 DOI: 10.1016/j.peptides.2012.07.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 07/27/2012] [Accepted: 07/27/2012] [Indexed: 01/10/2023]
Abstract
Lectins are proteins with ability to bind reversibly and non-enzymatically to a specific carbohydrate. They are involved in numerous biological processes and show enormous biotechnological potential. Among plant lectins, the hevein domain is extremely common, being observed in several kinds of lectins. Moreover, this domain is also observed in an important class of antimicrobial peptides named hevein-like peptides. Due to higher cysteine residues conservation, hevein-like peptides could be mined among the sequence databases. By using the pattern CX(4,5)CC[GS]X(2)GXCGX[GST]X(2,3)[FWY]C[GS]X[AGS] novel hevein-like peptide precursors were found from three different plants: Oryza sativa, Vitis vinifera and Selaginella moellendorffii. In addition, an hevein-like peptide precursor from the phytopathogenic fungus Phaeosphaeria nodorum was also identified. The molecular models indicate that they have the same scaffold as others, composed of an antiparallel β-sheet and short helices. Nonetheless, the fungal hevein-like peptide probably has a different disulfide bond pattern. Despite this difference, the complexes between peptide and N,N,N-triacetylglucosamine are stable, according to molecular dynamics simulations. This is the first report of an hevein-like peptide from an organism outside the plant kingdom. The exact role of an hevein-like peptide in the fungal biology must be clarified, while in plants they are clearly involved in plant defense. In summary, data here reported clear shows that an in silico strategy could lead to the identification of novel hevein-like peptides that could be used as biotechnological tools in the fields of health and agribusiness.
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Affiliation(s)
- William F Porto
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
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Ellis CR, Maiti B, Noid WG. Specific and nonspecific effects of glycosylation. J Am Chem Soc 2012; 134:8184-93. [PMID: 22524526 DOI: 10.1021/ja301005f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Glycosylation regulates vital cellular processes and dramatically influences protein folding and stability. In particular, experiments have demonstrated that asparagine (N)-linked disaccharides drive a "conformational switch" in a model peptide. The present work investigates this conformational switch via extensive atomically detailed replica exchange molecular dynamics simulations in explicit solvent. To distinguish the effects of specific and nonspecific interactions upon the peptide conformational ensemble, these simulations considered model peptides that were N-linked to a disaccharide and to a steric crowder of the same shape. The simulations are remarkably consistent with experiment and provide detailed insight into the peptide structure ensemble. They suggest that steric crowding by N-linked disaccharides excludes extended conformations, but does not significantly impact the tetrahedral structure of the surrounding solvent or otherwise alter the peptide free energy surface. However, the combination of steric crowding with specific hydrogen bonds and hydrophobic stacking interactions more dramatically impacts the peptide ensemble and stabilizes new structures.
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Affiliation(s)
- Christopher R Ellis
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Naumann TA, Wicklow DT, Price NPJ. Identification of a chitinase-modifying protein from Fusarium verticillioides: truncation of a host resistance protein by a fungalysin metalloprotease. J Biol Chem 2011; 286:35358-35366. [PMID: 21878653 PMCID: PMC3195611 DOI: 10.1074/jbc.m111.279646] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/23/2011] [Indexed: 11/06/2022] Open
Abstract
Chitinase-modifying proteins (cmps) are proteases secreted by fungal pathogens that truncate the plant class IV chitinases ChitA and ChitB during maize ear rot. cmp activity has been characterized for Bipolaris zeicola and Stenocarpella maydis, but the identities of the proteases are not known. Here, we report that cmps are secreted by multiple species from the genus Fusarium, that cmp from Fusarium verticillioides (Fv-cmp) is a fungalysin metalloprotease, and that it cleaves within a sequence that is conserved in class IV chitinases. Protein extracts from Fusarium cultures were found to truncate ChitA and ChitB in vitro. Based on this activity, Fv-cmp was purified from F. verticillioides. N-terminal sequencing of truncated ChitA and MALDI-TOF-MS analysis of reaction products showed that Fv-cmp is an endoprotease that cleaves a peptide bond on the C-terminal side of the lectin domain. The N-terminal sequence of purified Fv-cmp was determined and compared with a set of predicted proteins, resulting in its identification as a zinc metalloprotease of the fungalysin family. Recombinant Fv-cmp also truncated ChitA, confirming its identity, but had reduced activity, suggesting that the recombinant protease did not mature efficiently from its propeptide-containing precursor. This is the first report of a fungalysin that targets a nonstructural host protein and the first to implicate this class of virulence-related proteases in plant disease.
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Affiliation(s)
- Todd A Naumann
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois 61604.
| | - Donald T Wicklow
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois 61604
| | - Neil P J Price
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois 61604
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Solution structure of a defense peptide from wheat with a 10-cysteine motif. Biochem Biophys Res Commun 2011; 411:14-8. [DOI: 10.1016/j.bbrc.2011.06.058] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 06/06/2011] [Indexed: 11/22/2022]
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Naumann TA. Modification of recombinant maize ChitA chitinase by fungal chitinase-modifying proteins. MOLECULAR PLANT PATHOLOGY 2011; 12:365-72. [PMID: 21453431 PMCID: PMC6640348 DOI: 10.1111/j.1364-3703.2010.00677.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In commercial maize, there are at least two different alleles of the chiA gene that encode alloforms of ChitA chitinase, a protein that is abundant in developing seed. Both known alloforms are modified by Bz-cmp, a chitinase-modifying protein (cmp) secreted by the fungal pathogen Bipolaris zeicola. One alloform (ChitA-B73) is also modified by Stm-cmp, a protein secreted by the fungal pathogen Stenocarpella maydis, whereas the other (ChitA-LH82) is resistant. The two ChitA alloforms possess six differences or polymorphisms (P1-P6). To determine whether the P2 polymorphism in the chitin-binding domain is responsible for resistance or susceptibility to modification by Stm-cmp, and to determine whether Stm-cmp and Bz-cmp are proteases, heterologous expression strains of the yeast Pichia pastoris that produce recombinant maize ChitA (rChitA) alloforms and mutant rChitAs were created. rChitA alloforms and mutant rChitAs were purified from yeast cultures and used as substrates in assays with Stm-cmp and Bz-cmp. As with native protein, Bz-cmp modified both rChitA-LH82 and rChitA-B73, whereas Stm-cmp modified rChitA-B73 only. Mutant rChitAs, in which the P2 amino acids were changed to those of the other alloform, resulted in a significant exchange in Stm-cmp susceptibility. Amino-terminal sequencing of unmodified and modified rChitA-B73 demonstrated that Stm-cmp cleaves the peptide bond on the amino-terminal side of the P2 alanine, whereas Bz-cmp cleaves in the poly-glycine hinge region, the site of P3. The results demonstrate that Stm-cmp and Bz-cmp are proteases that truncate ChitA chitinase at the amino terminus, but at different sites. Both sites correspond to polymorphisms in the two alloforms, suggesting that the sequence diversity at P2 and P3 is the result of selective pressure to prevent truncation by fungal proteases.
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Affiliation(s)
- Todd A Naumann
- Bacterial Food-borne Pathogens and Mycology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL 61604, USA.
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37
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Roldós V, Cañada FJ, Jiménez-Barbero J. Carbohydrate-Protein Interactions: A 3D View by NMR. Chembiochem 2011; 12:990-1005. [DOI: 10.1002/cbic.201000705] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Indexed: 12/29/2022]
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38
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Chávez MI, Vila-Perelló M, Cañada FJ, Andreu D, Jiménez-Barbero J. Effect of a serine-to-aspartate replacement on the recognition of chitin oligosaccharides by truncated hevein. A 3D view by using NMR. Carbohydr Res 2010; 345:1461-8. [DOI: 10.1016/j.carres.2010.02.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 02/11/2010] [Accepted: 02/20/2010] [Indexed: 11/24/2022]
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Kezuka Y, Kojima M, Mizuno R, Suzuki K, Watanabe T, Nonaka T. Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering. Proteins 2010; 78:2295-305. [DOI: 10.1002/prot.22742] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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40
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Barneto JL, Avalos M, Babiano R, Cintas P, Jiménez JL, Palacios JC. A new model for mapping the peptide backbone: predicting proton chemical shifts in proteins. Org Biomol Chem 2010; 8:857-63. [PMID: 20135044 DOI: 10.1039/b921121g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper describes a methodology that correlates experimental chemical shifts (at the alpha proton) of proteins with their geometrical data (both dihedral angles and distances) obtained from 13 representative proteins, which are taken from the Protein Data Bank (PDB) and the BioMagRes Data Bank (BMRB). To this end, the experimentally measured proton chemical shifts of simple amides have been correlated with DFT-based calculated structures, at the B3PW91/6-31G* level. This results in a series of mathematical relationships, which are extrapolated to the above-mentioned proteins giving rise to a modified equation for such skeleta. It is relevant to note that the equation is also supported by a clear comparison with NMR data of a protein beyond the chosen set, such as insulin, even with lower errors. The model also relates the dependence of chemical shifts on hydrophobic and anisotropic effects at the amino acid residues.
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Affiliation(s)
- José Luis Barneto
- Departamento de Química Orgánica e Inorgánica, QUOREX Research Group, Facultad de Ciencias, Universidad de Extremadura, E-06071, Badajoz, Spain.
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41
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Kövér KE, Szilágyi L, Batta G, Uhrín D, Jiménez-Barbero J. Biomolecular Recognition by Oligosaccharides and Glycopeptides: The NMR Point of View. COMPREHENSIVE NATURAL PRODUCTS II 2010:197-246. [DOI: 10.1016/b978-008045382-8.00193-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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Yokoyama S, Iida Y, Kawasaki Y, Minami Y, Watanabe K, Yagi F. The chitin-binding capability of Cy-AMP1 from cycad is essential to antifungal activity. J Pept Sci 2009; 15:492-7. [PMID: 19466694 DOI: 10.1002/psc.1147] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antimicrobial peptides are important components of the host innate immune responses by exerting broad-spectrum microbicidal activity against pathogenic microbes. Cy-AMP1 found in the cycad (Cycas revoluta) seeds has chitin-binding ability, and the chitin-binding domain was conserved in knottin-type and hevein-type antimicrobial peptides. The recombinant Cy-AMP1 was expressed in Escherichia coli and purified to study the role of chitin-binding domain. The mutants of Cy-AMP1 lost chitin-binding ability completely, and its antifungal activity was markedly decreased in comparison with native Cy-AMP1. However, the antimicrobial activities of the mutant peptides are nearly identical to that of native one. It was suggested that the chitin-binding domain plays an essential role in antifungal, but not antimicrobial, activity of Cy-AMP1.
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Affiliation(s)
- Seiya Yokoyama
- Department of Applied Biological Chemistry, The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
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Sugawara K, Kawai M, Hirabayashi G, Kuramitz H. Sensitivity of a glassy carbon electrode covered with a chitin film improved by the addition of carbon powder. ANAL SCI 2009; 25:105-8. [PMID: 19139582 DOI: 10.2116/analsci.25.105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The redox activity of a chitin film on a glassy carbon electrode was remarkably improved by the addition of carbon powder to the film in the detection of ascorbic acid, flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide (NADH). Although oxidation of ascorbic acid using the electrode with the chitin film did not give an appreciable voltametric response, the addition of carbon powder to the film greatly improved its activity up to a 95% level of the bare carbon electrode. For FAD and NADH, an increase in each oxidation peak was observed in a similar manner. The improvement was due to electron mediation of the carbon powder contained in the film. Thus, the electrode effectively recovers the sensitivity for some biological molecules, and thus becomes a powerful device to monitor reactions between biological molecules. Because both carbon and chitin are materials with high biocompatibility, the film can be considered as cell scaffolds. Furthermore, the film immobilized on the plate has a possibility as an electrode in itself.
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Affiliation(s)
- Kazuharu Sugawara
- Faculty of Education, Gunma University, Maebashi, Gunma 371-8510, Japan.
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44
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Jayaraman N. Multivalent ligand presentation as a central concept to study intricate carbohydrate–protein interactions. Chem Soc Rev 2009; 38:3463-83. [DOI: 10.1039/b815961k] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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45
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Ribeiro JP, Bacchi S, Dell'Anna G, Morando M, Cañada FJ, Cozzi F, Jiménez-Barbero J. A Combined NMR, Computational, and HPLC Study of the Inclusion of Aromatic and Fluoroaromatic Compounds in Cyclodextrins as a Model for Studying Carbohydrate-Aromatic Interactions. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800585] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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46
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Vandenbussche S, Díaz D, Fernández-Alonso MC, Pan W, Vincent SP, Cuevas G, Cañada FJ, Jiménez-Barbero J, Bartik K. Aromatic-carbohydrate interactions: an NMR and computational study of model systems. Chemistry 2008; 14:7570-8. [PMID: 18481803 DOI: 10.1002/chem.200800247] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The interactions of simple carbohydrates with aromatic moieties have been investigated experimentally by NMR spectroscopy. The analysis of the changes in the chemical shifts of the sugar proton signals induced upon addition of aromatic entities has been interpreted in terms of interaction geometries. Phenol and aromatic amino acids (phenylalanine, tyrosine, tryptophan) have been used. The observed sugar-aromatic interactions depend on the chemical nature of the sugar, and thus on the stereochemistries of the different carbon atoms, and also on the solvent. A preliminary study of the solvation state of a model monosaccharide (methyl beta-galactopyranoside) in aqueous solution, both alone and in the presence of benzene and phenol, has also been carried out by monitoring of intermolecular homonuclear solvent-sugar and aromatic-sugar NOEs. These experimental results have been compared with those obtained by density functional theory methods and molecular mechanics calculations.
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Affiliation(s)
- Sophie Vandenbussche
- Molecular & Biomolecular Engineering, Université Libre de Bruxelles, Brussels, Belgium
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47
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Laughrey ZR, Kiehna SE, Riemen AJ, Waters ML. Carbohydrate-pi interactions: what are they worth? J Am Chem Soc 2008; 130:14625-33. [PMID: 18844354 DOI: 10.1021/ja803960x] [Citation(s) in RCA: 169] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein-carbohydrate interactions play an important role in many biologically important processes. The recognition is mediated by a number of noncovalent interactions, including an interaction between the alpha-face of the carbohydrate and the aromatic side chain of the protein. To elucidate this interaction, it has been studied in the context of a beta-hairpin in aqueous solution, in which the interaction can be investigated in the absence of other cooperative noncovalent interactions. In this beta-hairpin system, both the aromatic side chain and the carbohydrate were varied in an effort to gain greater insight into the driving force and magnitude of the carbohydrate-pi interaction. The magnitude of the interaction was found to vary from -0.5 to -0.8 kcal/mol, depending on the nature of the aromatic ring and the carbohydrate. Replacement of the aromatic ring with an aliphatic group resulted in a decrease in interaction energy to -0.1 kcal/mol, providing evidence for the contribution of CH-pi interactions to the driving force. These findings demonstrate the significance of carbohydrate-pi interactions within biological systems and also their utility as a molecular recognition element in designed systems.
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Affiliation(s)
- Zachary R Laughrey
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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48
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On the role of aromatic-sugar interactions in the molecular recognition of carbohydrates: A 3D view by using NMR. PURE APPL CHEM 2008. [DOI: 10.1351/pac200880081827] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This revision describes an up-to-date review of our efforts to investigate the interaction of carbohydrates with aromatic moieties at different levels of complexity. Protein-sugar interactions have been studied using NMR experiments on a variety of hevein/chitooligosaccharide systems. In addition, NMR and computational methods have also been used to evaluate the interaction of simple aromatic entities with simple monosaccharides. In between, the stacking features of aromatic-containing glycomolecules have also been described by using an analogous experimental-theoretical approach.
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Ferrand Y, Crump MP, Davis AP. A Synthetic Lectin Analog for Biomimetic Disaccharide Recognition. Science 2007; 318:619-22. [DOI: 10.1126/science.1148735] [Citation(s) in RCA: 286] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Carbohydrate recognition is biologically important but intrinsically challenging, for both nature and host-guest chemists. Saccharides are complex, subtly variable, and camouflaged by hydroxyl groups that hinder discrimination between substrate and water. We have developed a rational strategy for the biomimetic recognition of carbohydrates with all-equatorial stereochemistry (β-glucose, analogs, and homologs) and have now applied it to disaccharides such as cellobiose. Our synthetic receptor showed good affinities, not unlike those of some lectins (carbohydrate-binding proteins). Binding was demonstrated by nuclear magnetic resonance, induced circular dichroism, fluorescence spectroscopy, and calorimetry, all methods giving self-consistent results. Selectivity for the target substrates was exceptional; minor changes to disaccharide structure (for instance, cellobiose to lactose) caused almost complete suppression of complex formation.
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Chávez MI, Andreu C, Vidal P, Aboitiz N, Freire F, Groves P, Asensio JL, Asensio G, Muraki M, Cañada FJ, Jiménez-Barbero J. On the importance of carbohydrate-aromatic interactions for the molecular recognition of oligosaccharides by proteins: NMR studies of the structure and binding affinity of AcAMP2-like peptides with non-natural naphthyl and fluoroaromatic residues. Chemistry 2006; 11:7060-74. [PMID: 16220560 DOI: 10.1002/chem.200500367] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The specific interaction of a variety of modified hevein domains to chitooligosaccharides has been studied by NMR spectroscopy in order to assess the importance of aromatic-carbohydrate interactions for the molecular recognition of neutral sugars. These mutant AcAMP2-like peptides, which have 4-fluoro-phenylalanine, tryptophan, or 2-naphthylalanine at the key interacting positions, have been prepared by solid-phase synthesis. Their three-dimensional structures, when bound to the chitin-derived trisaccharide, have been deduced by NMR spectroscopy. By using DYANA and restrained molecular dynamics simulations with the AMBER 5.0 force field, the three-dimensional structures of the protein-sugar complexes have been obtained. The thermodynamic analysis of the interactions that occur upon complex formation have also been carried out. Regarding binding affinity, the obtained data have permitted the deduction that the larger the aromatic group, the higher the association constant and the binding enthalpy. In all cases, entropy opposes binding. In contrast, deactivation of the aromatic rings by attaching fluorine atoms decreases the binding affinity, with a concomitant decrease in enthalpy. The role of the chemical nature of the aromatic ring for establishing sugar contacts has been thus evaluated.
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Affiliation(s)
- M Isabel Chávez
- Department of Protein Structure and Function, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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