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Maass T, Ssebyatika G, Brückner M, Breckwoldt L, Krey T, Mallagaray A, Peters T, Frank M, Creutznacher R. Binding of Glycans to the SARS CoV-2 Spike Protein, an Open Question: NMR Data on Binding Site Localization, Affinity, and Selectivity. Chemistry 2022; 28:e202202614. [PMID: 36161798 PMCID: PMC9537997 DOI: 10.1002/chem.202202614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022]
Abstract
We have used NMR experiments to explore the binding of selected glycans and glycomimetics to the SARS CoV-2 spike glycoprotein (S-protein) and to its receptor binding domain (RBD). STD NMR experiments confirm the binding of sialoglycans to the S-protein of the prototypic Wuhan strain virus and yield dissociation constants in the millimolar range. The absence of STD effects for sialoglycans in the presence of the Omicron/BA.1 S-protein reflects a loss of binding as a result of S-protein evolution. Likewise, no STD effects are observed for the deletion mutant Δ143-145 of the Wuhan S-protein, thus supporting localization of the binding site in the N-terminal domain (NTD). The glycomimetics Oseltamivir and Zanamivir bind weakly to the S-protein of both virus strains. Binding of blood group antigens to the Wuhan S-protein cannot be confirmed by STD NMR. Using 1 H,15 N TROSY HSQC-based chemical shift perturbation (CSP) experiments, we excluded binding of any of the ligands studied to the RBD of the Wuhan S-protein. Our results put reported data on glycan binding into perspective and shed new light on the potential role of glycan-binding to the S-protein.
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Affiliation(s)
- Thorben Maass
- University of Lübeck: Universitat zu LubeckInstitute of Chemistry and MetabolomicsGERMANY
| | - George Ssebyatika
- University of Lübeck: Universitat zu LubeckInstitute of BiochemistryGERMANY
| | - Marlene Brückner
- University of Lübeck: Universitat zu LubeckInstitute of Chemistry and MetabolomicsGERMANY
| | - Lea Breckwoldt
- University of Lübeck: Universitat zu LubeckInstitute of Chemistry and MetabolomicsGERMANY
| | - Thomas Krey
- University of Lübeck: Universitat zu LubeckInstitute of BiochemistryGERMANY
| | - Alvaro Mallagaray
- University of Lübeck: Universitat zu LubeckInstitute of Chemistry and MetabolomicsGERMANY
| | - Thomas Peters
- Institute for Chemistry and MetabolomicsUniversität zu LübeckRatzeburger Allee 16023562LübeckGERMANY
| | | | - Robert Creutznacher
- University of Lübeck: Universitat zu LubeckInstitute of Chemistry and MetabolomicsGERMANY
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2
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Islam MK, Dhondt B, Syed P, Khan M, Gidwani K, Webber J, Hendrix A, Jenster G, Lamminen T, Boström PJ, Pettersson K, Lamminmäki U, Leivo J. Integrins are enriched on aberrantly fucosylated tumour-derived urinary extracellular vesicles. JOURNAL OF EXTRACELLULAR BIOLOGY 2022; 1:e64. [PMID: 38939212 PMCID: PMC11080809 DOI: 10.1002/jex2.64] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/30/2022] [Accepted: 09/19/2022] [Indexed: 06/29/2024]
Abstract
Urinary extracellular vesicles (uEVs) are enriched with glycosylated proteins which have been extensively studied as putative biomarkers of urological cancers. Here, we characterized the glycosylation and integrin profile of EVs derived from urological cancer cell lines. We used fluorescent europium-doped nanoparticles coated with lectins and antibodies to identify a biomarker combination consisting of integrin subunit alpha 3 (ITGA3) and fucose. In addition, we used the same cancer cell line-derived EVs as analytical standards to assess the sensitivity of the ITGA3-UEA assay. The clinical performance of the ITGA3-UEA assay was analysed using urine samples of various urological pathologies including diagnostically challenging benign prostatic hyperplasia (BPH), prostate cancer (PCa) and bladder cancer (BlCa). The assay can significantly discriminate BlCa from all other patient groups: PCa (9.2-fold; p = 0.00038), BPH (5.5-fold; p = 0.004) and healthy individuals (and 23-fold; p = 0.0001). Our results demonstrate that aberrantly fucosylated uEVs and integrin ITGA3 can be detected with fucose-specific lectin UEA in a simple bioaffinity assay for the detection of BlCa directly from unprocessed urine.
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Affiliation(s)
- Md. Khirul Islam
- Department of Life TechnologiesDivision of BiotechnologyUniversity of TurkuTurkuFinland
- InFLAMES Research Flagship CenterUniversity of TurkuTurkuFinland
| | - Bert Dhondt
- Department of UrologyGhent University HospitalGhentBelgium
- Laboratory for Experimental Cancer ResearchDepartment of Human Structure and RepairGhent UniversityGhentBelgium
- Cancer Research InstituteGhent UniversityGhentBelgium
| | | | - Misba Khan
- Department of Life TechnologiesDivision of BiotechnologyUniversity of TurkuTurkuFinland
| | - Kamlesh Gidwani
- Department of Life TechnologiesDivision of BiotechnologyUniversity of TurkuTurkuFinland
| | - Jason Webber
- Institute of Life Science 1Swansea University Medical SchoolSwanseaUK
| | - An Hendrix
- Laboratory for Experimental Cancer ResearchDepartment of Human Structure and RepairGhent UniversityGhentBelgium
- Cancer Research InstituteGhent UniversityGhentBelgium
| | - Guido Jenster
- Department of UrologyErasmus MCRotterdamThe Netherlands
| | - Tarja Lamminen
- Department of UrologyTurku University Hospital and University of TurkuTurkuFinland
| | - Peter J. Boström
- Department of UrologyTurku University Hospital and University of TurkuTurkuFinland
| | - Kim Pettersson
- Department of Life TechnologiesDivision of BiotechnologyUniversity of TurkuTurkuFinland
| | - Urpo Lamminmäki
- Department of Life TechnologiesDivision of BiotechnologyUniversity of TurkuTurkuFinland
- InFLAMES Research Flagship CenterUniversity of TurkuTurkuFinland
| | - Janne Leivo
- Department of Life TechnologiesDivision of BiotechnologyUniversity of TurkuTurkuFinland
- InFLAMES Research Flagship CenterUniversity of TurkuTurkuFinland
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3
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Di Carluccio C, Forgione MC, Martini S, Berti F, Molinaro A, Marchetti R, Silipo A. Investigation of protein-ligand complexes by ligand-based NMR methods. Carbohydr Res 2021; 503:108313. [PMID: 33865181 DOI: 10.1016/j.carres.2021.108313] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 11/20/2022]
Abstract
Molecular recognition is at the base of all biological events and its knowledge at atomic level is pivotal in the development of new drug design approaches. NMR spectroscopy is one of the most widely used technique to detect and characterize transient ligand-receptor interactions in solution. In particular, ligand-based NMR approaches, including NOE-based NMR techniques, diffusion experiments and relaxation methods, are excellent tools to investigate how ligands interact with their receptors. Here we describe the key structural information that can be achieved on binding processes thanks to the combined used of advanced NMR and computational methods. Saturation Transfer Difference NMR (STD-NMR), WaterLOGSY, diffusion- and relaxation-based experiments, together with tr-NOE techniques allow, indeed, to investigate the ligand behavior when bound to a receptor, determining, among others, the epitope map of the ligand and its bioactive conformation. The combination of these NMR techniques with computational methods, including docking, molecular dynamics and CORCEMA-ST analysis, permits to define and validate an accurate 3D model of protein-ligand complexes.
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Affiliation(s)
- Cristina Di Carluccio
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126, Napoli, Italy
| | - Maria Concetta Forgione
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126, Napoli, Italy; GSK, Via Fiorentina 1, 53100, Siena, Italy
| | | | | | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126, Napoli, Italy
| | - Roberta Marchetti
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126, Napoli, Italy.
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126, Napoli, Italy; CNR, Institute for Polymers, Composites and Biomaterials, IPCB ss, Catania, Italy.
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Specific Norovirus Interaction with Lewis x and Lewis a on Human Intestinal Inflammatory Mucosa during Refractory Inflammatory Bowel Disease. mSphere 2021; 6:6/1/e01185-20. [PMID: 33441404 PMCID: PMC7845605 DOI: 10.1128/msphere.01185-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), are progressive diseases affecting millions of people each year. Flare-ups during IBD result in severe mucosal alterations of the small intestine (in CD) and in the colon and rectum (in CD and UC). Inflammatory bowel disease (IBD), which includes Crohn’s disease (CD) and ulcerative colitis (UC), is related to immunological and microbial factors, with the possible implication of enteric viruses. We characterized the interaction between human noroviruses (HuNoVs) and blood group antigens in refractory CD and UC using HuNoV virus-like particles (VLPs) and histological tissues. Immunohistochemistry was conducted on inflammatory tissue samples from the small intestine, colon, and rectum in 15 CD and 9 UC patients. Analysis of the regenerative mucosa of the colon and rectum revealed strong expression of sialylated Lewis a (sLea) and Lewis x (sLex) antigens and HuNoV VLP binding in the absence of ABO antigen expression in both UC and CD. Competition experiments using sialidase, lectins, and monoclonal antibodies demonstrated that HuNoV attachment mostly involved Lea and, to a lesser extent, Lex moieties on regenerative mucosa in both UC and CD. Further studies will be required to understand the implications of specific HuNoV binding to regenerative mucosa in refractory IBD. IMPORTANCE Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), are progressive diseases affecting millions of people each year. Flare-ups during IBD result in severe mucosal alterations of the small intestine (in CD) and in the colon and rectum (in CD and UC). Immunohistochemical analysis of CD and UC samples showed strong expression of known tumoral markers sialyl Lewis a (CA19.9) and sialyl Lewis x (CD15s) antigens on colonic and rectal regenerative mucosa, concurrent with strong human norovirus (HuNov) VLP GII.4 affinity. Sialidase treatment and competition experiments using histo-blood group antigen (HBGA)-specific monoclonal antibodies and lectins clearly demonstrated the implication of the Lewis a moiety and, to a lesser extent, the Lewis x moiety in HuNov recognition in regenerative mucosa of CD and UC tissues. Further studies are required to explore the possible implications of enteric viruses in the impairment of epithelial repair and dysregulation of inflammatory pathways during severe IBD.
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Jegatheeswaran S, Asnani A, Forman A, Hendel JL, Moore CJ, Nejatie A, Wang A, Wang JW, Auzanneau FI. Recognition of Dimeric Lewis X by Anti-Dimeric Le x Antibody SH2. Vaccines (Basel) 2020; 8:vaccines8030538. [PMID: 32957489 PMCID: PMC7563222 DOI: 10.3390/vaccines8030538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 11/16/2022] Open
Abstract
The carbohydrate antigen dimeric Lewis X (DimLex), which accumulates in colonic and liver adenocarcinomas, is a valuable target to develop anti-cancer therapeutics. Using the native DimLex antigen as a vaccine would elicit an autoimmune response against the Lex antigen found on normal, healthy cells. Thus, we aim to study the immunogenic potential of DimLex and search internal epitopes displayed by DimLex that remain to be recognized by anti-DimLex monoclonal antibodies (mAbs) but no longer possess epitopes recognized by anti-Lex mAbs. In this context, we attempted to map the epitope recognized by anti-DimLex mAb SH2 by titrations and competitive inhibition experiments using oligosaccharide fragments of DimLex as well as Lex analogues. We compare our results with that reported for anti-Lex mAb SH1 and anti-polymeric Lex mAbs 1G5F6 and 291-2G3-A. While SH1 recognizes an epitope localized to the non-reducing end Lex trisaccharide, SH2, 1G5F6, and 291-2G3-A have greater affinity for DimLex conjugates than for Lex conjugates. We show, however, that the Lex trisaccharide is still an important recognition element for SH2, which (like 1G5F6 and 291-2G3-A) makes contacts with all three sugar units of Lex. In contrast to mAb SH1, anti-polymeric Lex mAbs make contact with the GlcNAc acetamido group, suggesting that epitopes extend further from the non-reducing end Lex. Results with SH2 show that this epitope is only recognized when DimLex is presented by glycoconjugates. We have reported that DimLex adopts two conformations around the β-d-GlcNAc-(1→3)-d-Gal bond connecting the Lex trisaccharides. We propose that only one of these conformations is recognized by SH2 and that this conformation is favored when the hexasaccharide is presented as part of a glycoconjugate such as DimLex-bovine serum albumin (DimLex-BSA). Proper presentation of the oligosaccharide candidate via conjugation to a protein or lipid is essential for the design of an anti-cancer vaccine or immunotherapeutic based on DimLex.
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Affiliation(s)
- Sinthuja Jegatheeswaran
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Immunology Department, University of Toronto, 1 King’s College Circle, Toronto, ON M5S-1A8, Canada
| | - Ari Asnani
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Department of Chemistry, Universitas Jenderal Soedirman, Purwokerto, Jawa Tengah 53123, Indonesia
| | - Adam Forman
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S-3H6, Canada
| | - Jenifer L. Hendel
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Research and Development, Ludger Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14-3EB, UK
| | - Christopher J. Moore
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Quality Control, SteriMax Inc., 2770 Portland Dr, Oakville, ON L6H-6R4, Canada
| | - Ali Nejatie
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada
| | - An Wang
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- SGS-CSTC Standards Technical Services Co., Ltd. 4/F, 4th Building, 889 Yishan Road, Xuhui District, Shanghai 200233, China
| | - Jo-Wen Wang
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- IQVIA, QuintilesIMS, Clinical Research, 10188 Telesis Ct #400, San Diego, CA 92121, USA
| | - France-Isabelle Auzanneau
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Correspondence:
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6
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2D Saturation Transfer Difference NMR for Determination of Protein Binding Sites on RNA Guanine Quadruplexes. Methods Mol Biol 2020. [PMID: 32681509 DOI: 10.1007/978-1-0716-0680-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Saturation transfer difference (STD) NMR is a technique that provides information on the intermolecular interfaces of heterogenous complexes by cross-saturation from one molecule to the other. In this case, selective saturation of protein protons is applied, and the cross-relaxation to the RNA sample results in a reduction of the peak intensities in the measured H1-H1 NOESY spectrum. This allows for a relatively rapid and simple method of identifying the protein binding interface of an RNA with assigned chemical shift data.
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Tvaroška I, Selvaraj C, Koča J. Selectins-The Two Dr. Jekyll and Mr. Hyde Faces of Adhesion Molecules-A Review. Molecules 2020; 25:molecules25122835. [PMID: 32575485 PMCID: PMC7355470 DOI: 10.3390/molecules25122835] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/27/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Selectins belong to a group of adhesion molecules that fulfill an essential role in immune and inflammatory responses and tissue healing. Selectins are glycoproteins that decode the information carried by glycan structures, and non-covalent interactions of selectins with these glycan structures mediate biological processes. The sialylated and fucosylated tetrasaccharide sLex is an essential glycan recognized by selectins. Several glycosyltransferases are responsible for the biosynthesis of the sLex tetrasaccharide. Selectins are involved in a sequence of interactions of circulated leukocytes with endothelial cells in the blood called the adhesion cascade. Recently, it has become evident that cancer cells utilize a similar adhesion cascade to promote metastases. However, like Dr. Jekyll and Mr. Hyde’s two faces, selectins also contribute to tissue destruction during some infections and inflammatory diseases. The most prominent function of selectins is associated with the initial stage of the leukocyte adhesion cascade, in which selectin binding enables tethering and rolling. The first adhesive event occurs through specific non-covalent interactions between selectins and their ligands, with glycans functioning as an interface between leukocytes or cancer cells and the endothelium. Targeting these interactions remains a principal strategy aimed at developing new therapies for the treatment of immune and inflammatory disorders and cancer. In this review, we will survey the significant contributions to and the current status of the understanding of the structure of selectins and the role of selectins in various biological processes. The potential of selectins and their ligands as therapeutic targets in chronic and acute inflammatory diseases and cancer will also be discussed. We will emphasize the structural characteristic of selectins and the catalytic mechanisms of glycosyltransferases involved in the biosynthesis of glycan recognition determinants. Furthermore, recent achievements in the synthesis of selectin inhibitors will be reviewed with a focus on the various strategies used for the development of glycosyltransferase inhibitors, including substrate analog inhibitors and transition state analog inhibitors, which are based on knowledge of the catalytic mechanism.
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Affiliation(s)
- Igor Tvaroška
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovak Republic
- Correspondence: (I.T.); (J.K.); Tel.: +421-948-535-601 (I.T.); +420-731-682-606 (J.K.)
| | - Chandrabose Selvaraj
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Jaroslav Koča
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- Correspondence: (I.T.); (J.K.); Tel.: +421-948-535-601 (I.T.); +420-731-682-606 (J.K.)
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Jegatheeswaran S, Auzanneau FI. Recognition of Lewis X by Anti-Le x Monoclonal Antibody IG5F6. THE JOURNAL OF IMMUNOLOGY 2019; 203:3037-3044. [PMID: 31666308 DOI: 10.4049/jimmunol.1900806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/22/2019] [Indexed: 11/19/2022]
Abstract
mAbs directed toward the Lewis X (Lex) determinant have been shown to display different specificities, depending on the presentation of Lex to the immune system. Of interest is the murine anti-Lex mAb IG5F6, generated against the O chain polysaccharide of Helicobacter pylori that contains polymeric Lex structures. The mAb was found to have a higher affinity for polymeric Lex over monomeric Lex In this study, we explore the recognition of monomeric Lex by IG5F6 using a panel of Lex analogues in which N-acetyl-d-glucosamine, l-fucose, or d-galactose (D-Gal) are replaced with d-glucose and/or l-rhamnose. Our studies show that all analogues were weaker inhibitors than the Lex Ag, indicating that all three residues are essential in the recognition of Lex by mAb IG5F6. We explored the involvement of 4″-OH of d-Gal in the binding with IG5F6 using a panel of 4″-modified Lex analogues. Although the 4″-OH is only involved in a weak polar interaction, we conclude that the D-Gal residue in Lex is primarily involved in aromatic stacking interactions with the Ab binding site. We compared these results to our work with mAb SH1. Although stacking interactions between D-Gal and an aromatic residue was also suggested for SH1, an H-bond involving the 4″-OH was identified that is not found in the binding of IG5F6 to Lex Thus, anti-Lex mAbs SH1 and IG5F6 bind to Lex in different manners, even though the hydrophobic patch displayed by the β-galactoside in Lex is essential in both cases for their binding to Lex.
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9
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Suzuki T, Yanaka S, Watanabe T, Yan G, Satoh T, Yagi H, Yamaguchi T, Kato K. Remodeling of the Oligosaccharide Conformational Space in the Prebound State To Improve Lectin-Binding Affinity. Biochemistry 2019; 59:3180-3185. [PMID: 31553574 DOI: 10.1021/acs.biochem.9b00594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We developed an approach to improve the lectin-binding affinity of an oligosaccharide by remodeling its conformational space in the precomplexed state. To develop this approach, we used a Lewis X-containing oligosaccharide interacting with RSL as a model system. Using an experimentally validated molecular dynamics simulation, we designed a Lewis X analogue with an increased population of conformational species that were originally very minor but exclusively accessible to the target lectin without steric hindrance by modifying the nonreducing terminal galactose, which does not directly contact the lectin in the complex. This Lewis X mimetic showed 17 times higher affinity for the lectin than the native counterpart. Our approach, complementing the lectin-bound-state optimizations, offers an alternative strategy to create high-affinity oligosaccharides by increasing populations of on-pathway metastable conformers.
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Affiliation(s)
- Tatsuya Suzuki
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.,School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Tokio Watanabe
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Gengwei Yan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Japan
| | - Tadashi Satoh
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Hirokazu Yagi
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Takumi Yamaguchi
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.,School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.,School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
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10
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Ishida T. Computational analysis of carbohydrate recognition based on hybrid QM/MM modeling: a case study of norovirus capsid protein in complex with Lewis antigen. Phys Chem Chem Phys 2018; 20:4652-4665. [PMID: 29372731 DOI: 10.1039/c7cp07701g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Norovirus is a major pathogen of nonbacterial acute gastroenteritis in humans and animals. Carbohydrate recognition between norovirus capsid proteins and Lewis antigens is considered to play a critical role in initiating infection of eukaryotic cells. In this article, we first report a detailed atomistic simulation study of the norovirus capsid protein in complex with the Lewis antigen based on ab initio QM/MM combined with MD-FEP simulations. To understand the mechanistic details of ligand binding, we analyzed and compared the carbohydrate recognition mechanism of the wild-type P domain protein with a mutant protein. Small structural differences between two capsid proteins are observed on the weak interaction site of residue 389, which is located on the solvent exposed surface of the P domain. To further clarify affinity differences in ligand binding, we directly evaluated free energy changes of the ligand binding process. Although the mutant protein loses its interaction energy with the Lewis antigen, this small amount of energy penalty is compensated for by an increase in the solvation stability, which is induced by structural reorganization at the ligand binding site on the protein surface. As a sum of these opposite energy components, the mutant P domain obtains a slightly enhanced binding affinity for the Lewis antigen. The present computational study clearly demonstrated that a detailed free energy balance of the interaction energy between the capsid protein and the surrounding aqueous solvent is the mechanistic basis of carbohydrate recognition in the norovirus capsid protein.
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Affiliation(s)
- Toyokazu Ishida
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, 305-8568, Japan.
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11
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Alibay I, Burusco KK, Bruce NJ, Bryce RA. Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics. J Phys Chem B 2018; 122:2462-2474. [PMID: 29419301 DOI: 10.1021/acs.jpcb.7b09841] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free-energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling, and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 μs trajectories; these simulations find a predominance of closed conformer and a range of low-occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the 4C1 form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 μs unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.
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Affiliation(s)
- Irfan Alibay
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
| | - Kepa K Burusco
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
| | - Neil J Bruce
- Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35 , Heidelberg 69118 , Germany
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
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12
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Structure and Interactions of A Host Defense Antimicrobial Peptide Thanatin in Lipopolysaccharide Micelles Reveal Mechanism of Bacterial Cell Agglutination. Sci Rep 2017; 7:17795. [PMID: 29259246 PMCID: PMC5736615 DOI: 10.1038/s41598-017-18102-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/05/2017] [Indexed: 12/15/2022] Open
Abstract
Host defense cationic Antimicrobial Peptides (AMPs) can kill microorganisms including bacteria, viruses and fungi using various modes of action. The negatively charged bacterial membranes serve as a key target for many AMPs. Bacterial cell death by membrane permeabilization has been well perceived. A number of cationic AMPs kill bacteria by cell agglutination which is a distinctly different mode of action compared to membrane pore formation. However, mechanism of cell agglutinating AMPs is poorly understood. The outer membrane lipopolysaccharide (LPS) or the cell-wall peptidoglycans are targeted by AMPs as a key step in agglutination process. Here, we report the first atomic-resolution structure of thanatin, a cell agglutinating AMP, in complex with LPS micelle by solution NMR. The structure of thanatin in complex with LPS, revealed four stranded antiparallel β-sheet in a ‘head-tail’ dimeric topology. By contrast, thanatin in free solution assumed an antiparallel β-hairpin conformation. Dimeric structure of thanatin displayed higher hydrophobicity and cationicity with sites of LPS interactions. MD simulations and biophysical interactions analyses provided mode of LPS recognition and perturbation of LPS micelle structures. Mechanistic insights of bacterial cell agglutination obtained in this study can be utilized to develop antibiotics of alternative mode of action.
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13
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Jassam SA, Maherally Z, Smith JR, Ashkan K, Roncaroli F, Fillmore HL, Pilkington GJ. CD15s/CD62E Interaction Mediates the Adhesion of Non-Small Cell Lung Cancer Cells on Brain Endothelial Cells: Implications for Cerebral Metastasis. Int J Mol Sci 2017; 18:ijms18071474. [PMID: 28698503 PMCID: PMC5535965 DOI: 10.3390/ijms18071474] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 01/29/2023] Open
Abstract
Expression of the cell adhesion molecule (CAM), Sialyl Lewis X (CD15s) correlates with cancer metastasis, while expression of E-selectin (CD62E) is stimulated by TNF-α. CD15s/CD62E interaction plays a key role in the homing process of circulating leukocytes. We investigated the heterophilic interaction of CD15s and CD62E in brain metastasis-related cancer cell adhesion. CD15s and CD62E were characterised in human brain endothelium (hCMEC/D3), primary non-small cell lung cancer (NSCLC) (COR-L105 and A549) and metastatic NSCLC (SEBTA-001 and NCI-H1299) using immunocytochemistry, Western blotting, flow cytometry and immunohistochemistry in human brain tissue sections. TNF-α (25 pg/mL) stimulated extracellular expression of CD62E while adhesion assays, under both static and physiological flow live-cell conditions, explored the effect of CD15s-mAb immunoblocking on adhesion of cancer cell–brain endothelium. CD15s was faintly expressed on hCMEC/D3, while high levels were observed on primary NSCLC cells with expression highest on metastatic NSCLC cells (p < 0.001). CD62E was highly expressed on hCMEC/D3 cells activated with TNF-α, with lower levels on primary and metastatic NSCLC cells. CD15s and CD62E were expressed on lung metastatic brain biopsies. CD15s/CD62E interaction was localised at adhesion sites of cancer cell–brain endothelium. CD15s immunoblocking significantly decreased cancer cell adhesion to brain endothelium under static and shear stress conditions (p < 0.001), highlighting the role of CD15s–CD62E interaction in brain metastasis.
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Affiliation(s)
- Samah A Jassam
- Brain Tumour Research Centre, Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK.
| | - Zaynah Maherally
- Brain Tumour Research Centre, Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK.
| | - James R Smith
- Brain Tumour Research Centre, Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK.
| | - Keyoumars Ashkan
- Neuro-Surgery, King's College Hospital, Denmark Hill, London SE5 9RS, UK.
| | - Federico Roncaroli
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, Oxford Road, Manchester M13 9PT, UK.
| | - Helen L Fillmore
- Brain Tumour Research Centre, Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK.
| | - Geoffrey J Pilkington
- Brain Tumour Research Centre, Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK.
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14
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Rissanen S, Grzybek M, Orłowski A, Róg T, Cramariuc O, Levental I, Eggeling C, Sezgin E, Vattulainen I. Phase Partitioning of GM1 and Its Bodipy-Labeled Analog Determine Their Different Binding to Cholera Toxin. Front Physiol 2017; 8:252. [PMID: 28536532 PMCID: PMC5422513 DOI: 10.3389/fphys.2017.00252] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/10/2017] [Indexed: 12/19/2022] Open
Abstract
Driven by interactions between lipids and proteins, biological membranes display lateral heterogeneity that manifests itself in a mosaic of liquid-ordered (Lo) or raft, and liquid-disordered (Ld) or non-raft domains with a wide range of different properties and compositions. In giant plasma membrane vesicles and giant unilamellar vesicles, specific binding of Cholera Toxin (CTxB) to GM1 glycolipids is a commonly used strategy to label raft domains or Lo membrane environments. However, these studies often use acyl-chain labeled bodipy-GM1 (bdGM1), whose headgroup accessibility and membrane order or phase partitioning may differ from those of GM1, rendering the interpretation of CTxB binding data quite problematic. To unravel the molecular basis of CTxB binding to GM1 and bdGM1, we explored the partitioning and the headgroup presentation of these gangliosides in the Lo and Ld phases using atomistic molecular dynamics simulations complemented by CTxB binding experiments. The conformation of both GM1 and bdGM1 was shown to be largely similar in the Lo and Ld phases. However, bdGM1 showed reduction in receptor availability when reconstituted into synthetic bilayer mixtures, highlighting that membrane phase partitioning of the gangliosides plays a considerable role in CTxB binding. Our results suggest that the CTxB binding is predominately modulated by the partitioning of the receptor to an appropriate membrane phase. Further, given that the Lo and Ld partitioning of bdGM1 differs from those of GM1, usage of bdGM1 for studying GM1 behavior in cells can lead to invalid interpretation of experimental data.
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Affiliation(s)
- Sami Rissanen
- Department of Physics, Tampere University of TechnologyTampere, Finland
| | - Michal Grzybek
- Paul Langerhans Institute Dresden of the Helmholtz Centre Munich at the University Clinic Carl Gustav Carus, TU DresdenDresden, Germany.,German Center for Diabetes ResearchNeuherberg, Germany
| | - Adam Orłowski
- Department of Physics, Tampere University of TechnologyTampere, Finland.,Department of Physics and Energy, University of LimerickLimerick, Ireland
| | - Tomasz Róg
- Department of Physics, Tampere University of TechnologyTampere, Finland.,Department of Physics, University of HelsinkiHelsinki, Finland
| | - Oana Cramariuc
- Department of Physics, Tampere University of TechnologyTampere, Finland
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, University of Texas Health Science CenterHouston, TX, USA
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxford, UK
| | - Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxford, UK
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of TechnologyTampere, Finland.,Department of Physics, University of HelsinkiHelsinki, Finland.,MEMPHYS-Center for Biomembrane Physics, University of Southern DenmarkOdense, Denmark
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15
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Improved cancer specificity in PSA assay using Aleuria aurantia lectin coated Eu-nanoparticles for detection. Clin Biochem 2017; 50:54-61. [DOI: 10.1016/j.clinbiochem.2016.06.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/17/2016] [Accepted: 06/19/2016] [Indexed: 01/02/2023]
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16
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Topin J, Lelimousin M, Arnaud J, Audfray A, Pérez S, Varrot A, Imberty A. The Hidden Conformation of Lewis x, a Human Histo-Blood Group Antigen, Is a Determinant for Recognition by Pathogen Lectins. ACS Chem Biol 2016; 11:2011-20. [PMID: 27198630 DOI: 10.1021/acschembio.6b00333] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histo-blood group epitopes are fucosylated branched oligosaccharides with well-defined conformations in solution that are recognized by receptors, such as lectins from pathogens. We report here the results of a series of experimental and computational endeavors revealing the unusual distortion of histo-blood group antigens by bacterial and fungal lectins. The Lewis x trisaccharide adopts a rigid closed conformation in solution, while crystallography and molecular dynamics reveal several higher energy open conformations when bound to the Ralstonia solanacearum lectin, which is in agreement with thermodynamic and kinetic measurements. Extensive molecular dynamics simulations confirm rare transient Le(x) openings in solution, frequently assisted by distortion of the central N-acetyl-glucosamine ring. Additional directed molecular dynamic trajectories revealed the role of a conserved tryptophan residue in guiding the fucose into the binding site. Our findings show that conformational adaptation of oligosaccharides is of paramount importance in cell recognition and should be considered when designing anti-infective glyco-compounds.
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Affiliation(s)
- Jérémie Topin
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Mickaël Lelimousin
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Julie Arnaud
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Aymeric Audfray
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Serge Pérez
- DPM UMR5063, Université Grenoble Alpes, and CNRS, BP 53, 38041 Grenoble cedex 9, France
| | - Annabelle Varrot
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Anne Imberty
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
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17
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Biophysical characterization of laforin–carbohydrate interaction. Biochem J 2016; 473:335-45. [DOI: 10.1042/bj20141555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 11/17/2015] [Indexed: 11/17/2022]
Abstract
Laforin, a key regulator of glycogen metabolism, is a low-affinity glycan binder. In the present work, we thoroughly biophysically characterized its glycan interaction.
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18
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Blaum BS, Frank M, Walker RC, Neu U, Stehle T. Complement Factor H and Simian Virus 40 bind the GM1 ganglioside in distinct conformations. Glycobiology 2015; 26:532-9. [PMID: 26715202 DOI: 10.1093/glycob/cwv170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/22/2015] [Indexed: 11/13/2022] Open
Abstract
Mammalian cell surfaces are decorated with a variety of glycan chains that orchestrate development and defense and are exploited by pathogens for cellular attachment and entry. While glycosidic linkages are, in principle, flexible, the conformational space that a given glycan can sample is subject to spatial and electrostatic restrictions imposed by its overall chemical structure. Here, we show how the glycan moiety of the GM1 ganglioside, a branched, monosialylated pentasaccharide that serves as a ligand for various proteins, undergoes differential conformational selection in its interactions with different lectins. Using STD NMR and X-ray crystallography, we found that the innate immune regulator complement Factor H (FH) binds a previously not reported GM1 conformation that is not compatible with the GM1-binding sites of other structurally characterized GM1-binding lectins such as the Simian Virus 40 (SV40) capsid. Molecular dynamics simulations of the free glycan in explicit solvent on the 10 μs timescale reveal that the FH-bound conformation nevertheless corresponds to a minimum in the Gibbs free energy plot. In contrast to the GM1 conformation recognized by SV40, the FH-bound GM1 conformation is associated with poor NOE restraints, explaining how it escaped(1)H-(1)H NOE-restrained modeling in the past and highlighting the necessity for ensemble representations of glycan structures.
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Affiliation(s)
- Bärbel S Blaum
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen 72076, Germany
| | - Martin Frank
- Biognos AB, Generatorsgatan 1, Gothenburg 41705, Sweden
| | - Ross C Walker
- San Diego Supercomputer Center and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ursula Neu
- Max-Planck-Institute of Colloids and Interfaces, Potsdam 14476, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen 72076, Germany Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37212, USA
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19
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Ardá A, Canales A, Cañada FJ, Jiménez-Barbero J. Carbohydrate–Protein Interactions: A 3D View by NMR. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00001] [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
NMR spectroscopy is a key tool for carbohydrate research. In studies with complex oligosaccharides there are limits to the amount of relevant structural information provided by these observables due to problems of signal overlapping, strong coupling and/or the scarcity of the key NOE information. Thus, there is an increasing need for additional parameters with structural information, such as residual dipolar couplings (RDCs), paramagnetic relaxation enhancements (PREs) or pseudo contact shifts (PCSs). Carbohydrates are rather flexible molecules. Therefore, NMR observables do not always correlate with a single conformer but with an ensemble of low free-energy conformers that can be accessed by thermal fluctuations. Depending on the system under study, different NMR approaches can be followed to characterize protein–carbohydrate interactions: the standard methodologies can usually be classified as “ligand-based” or “receptor-based”. The selection of the proper methodology is usually determined by the size of the receptor, the dissociation constant of the complex (KD), the availability of the labelled protein (15N, 13C) and the access to soluble receptors at enough concentration for NMR measurements.
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Affiliation(s)
- Ana Ardá
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Angeles Canales
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - F. Javier Cañada
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edif. 801A-1 48160 Derio-Bizkaia Spain
- Ikerbasque, Basque Foundation for Science Bilbao Spain
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20
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Jackson TA, Robertson V, Auzanneau FI. Evidence for Two Populated Conformations for the Dimeric LeX and LeALeX Tumor-Associated Carbohydrate Antigens. J Med Chem 2014; 57:817-27. [DOI: 10.1021/jm401576x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Trudy A. Jackson
- Department of Chemistry, University of Guelph, Guelph, Ontario, N1G2W1, Canada
| | - Valerie Robertson
- Department of Chemistry, University of Guelph, Guelph, Ontario, N1G2W1, Canada
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21
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Moore CJ, Auzanneau FI. Understanding the Recognition of Lewis X by Anti-Lex Monoclonal Antibodies. J Med Chem 2013; 56:8183-90. [DOI: 10.1021/jm401304h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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22
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Kratz EM, Waszkiewicz N, Kałuża A, Szajda SD, Zalewska-Szajda B, Szulc A, Zwierz K, Ferens-Sieczkowska M. Glycosylation Changes in the Salivary Glycoproteins of Alcohol-Dependent Patients: A Pilot Study. Alcohol Alcohol 2013; 49:23-30. [DOI: 10.1093/alcalc/agt152] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Matsuoka K, Yamaguchi H, Kohzu T, Sakamoto JI, Koyama T, Hatano K, Yamamoto S, Mori T, Hatanaka K. Convenient assembly of trimeric Lex determinants using carbosilane scaffolds by means of Huisgen cycloaddition. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mata L, Avenoza A, Busto JH, Corzana F, Peregrina JM. Quaternary Chiral β2,2-Amino Acids with Pyridinium and Imidazolium Substituents. Chemistry 2012; 18:15822-30. [DOI: 10.1002/chem.201202096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 11/07/2022]
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25
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Moore CJ, Auzanneau FI. Synthesis of 4" manipulated Lewis X trisaccharide analogues. Beilstein J Org Chem 2012; 8:1134-43. [PMID: 23019441 PMCID: PMC3458731 DOI: 10.3762/bjoc.8.126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/29/2012] [Indexed: 11/25/2022] Open
Abstract
Three analogues of the Lex trisaccharide antigen (β-D-Galp(1→4)[α-L-Fucp(1→3)]-D-GlcNAcp) in which the galactosyl residue is modified at O-4 as a methyloxy, deoxychloro or deoxyfluoro, were synthesized. We first report the preparation of the modified 4-OMe, 4-Cl and 4-F trichloroacetimidate galactosyl donors and then report their use in the glycosylation of an N-acetylglucosamine glycosyl acceptor. Thus, we observed that the reactivity of these donors towards the BF3·OEt2-promoted glycosylation at O-4 of the N-acetylglucosamine glycosyl acceptors followed the ranking 4-F > 4-OAc ≈ 4-OMe > 4-Cl. The resulting disaccharides were deprotected at O-3 of the glucosamine residue and fucosylated, giving access to the desired protected Lex analogues. One-step global deprotection (Na/NH3) of the protected 4”-methoxy analogue, and two-step deprotections (removal of a p-methoxybenzyl with DDQ, then Zemplén deacylation) of the 4”-deoxychloro and 4”-deoxyfluoro protected Lex analogues gave the desired compounds in good yields.
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Affiliation(s)
- Christopher J Moore
- Department of Chemistry, University of Guelph, 50 Stone Rd. East, Guelph, Ontario, N1G 2W1, Canada
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26
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Auzanneau FI, Jackson TA, Liao L. Stochastic searches and NMR experiments on four Lewis A analogues: NMR experiments support some flexibility around the fucosidic bond. Bioorg Med Chem 2012; 20:5085-93. [PMID: 22867708 DOI: 10.1016/j.bmc.2012.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/04/2012] [Accepted: 07/10/2012] [Indexed: 11/29/2022]
Abstract
We have compared the conformational behavior of three Le(a) analogues with that of Le(a) using stochastic searches (MOE2005) and selective ROESY experiments. In the analogues either or both the β-d-Gal and α-l-Fuc residues were replaced by β-d-Glc and α-l-Rha units, respectively. All compounds showed similar behavior and even though four conformational families were identified, the calculations and NMR experiments support that the 'stacked conformation' known for Le(a) is predominant for all analogues. Interestingly, ROESY showed a correlation between H-1 Fuc/Rha and H-3 GlcNAc which, although small, could be seen in all analogues. For two compounds, the corresponding distance was measured and found to be shorter (∼3.7Å) than that found in the global minimum (4.5Å). While one published study suggests some motion around the fucosidic bond, this constitutes the first experimental evidence supporting such flexibility. Our MD simulation (Amber10/Glycam06) on Le(a) was in full agreement with previous studies which described a rigid conformation for this branched trisaccharide. Thus, NMR seems to indicate that these dynamic studies are underestimating flexibility around the fucosidic bond.
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27
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Rodríguez F, Somovilla VJ, Corzana F, Busto JH, Avenoza A, Peregrina PJM. Cyclohexane Ring as a Tool to Select the Presentation of the Carbohydrate Moiety in Glycosyl Amino Acids. Chemistry 2012; 18:5096-104. [DOI: 10.1002/chem.201103089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 01/19/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Fernando Rodríguez
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, UA‐CSI, Madre de Dios, 51, 26006 Logroño (Spain), Fax: (+34) 941‐299‐621
| | - Víctor J. Somovilla
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, UA‐CSI, Madre de Dios, 51, 26006 Logroño (Spain), Fax: (+34) 941‐299‐621
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, UA‐CSI, Madre de Dios, 51, 26006 Logroño (Spain), Fax: (+34) 941‐299‐621
| | - Jesús H. Busto
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, UA‐CSI, Madre de Dios, 51, 26006 Logroño (Spain), Fax: (+34) 941‐299‐621
| | - Alberto Avenoza
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, UA‐CSI, Madre de Dios, 51, 26006 Logroño (Spain), Fax: (+34) 941‐299‐621
| | - Prof Jesús M. Peregrina
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, UA‐CSI, Madre de Dios, 51, 26006 Logroño (Spain), Fax: (+34) 941‐299‐621
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28
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Tanaka H, Kawai T, Adachi Y, Hanashima S, Yamaguchi Y, Ohno N, Takahashi T. Synthesis of β(1,3) oligoglucans exhibiting a Dectin-1 binding affinity and their biological evaluation. Bioorg Med Chem 2012; 20:3898-914. [PMID: 22578491 DOI: 10.1016/j.bmc.2012.04.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 04/06/2012] [Accepted: 04/07/2012] [Indexed: 02/07/2023]
Abstract
In this report, we describe the synthesis and biological evaluation of β(1,3) oligosaccharides that contain an aminoalkyl group and their biological evaluation. A 2,3 diol glycoside with a 4,6 benzylidene protecting group was used as an effective glycosyl acceptor for the synthesis of some β(1,3) linked glycosides. The use of a combination of a linear tetrasaccharide and a branched pentasaccharide as glycosyl donors led to the preparation of β(1,3) linear octa- to hexadecasaccharides and branched nona- to heptadecasaccharides in good total yields. Measurements of the competitive effects of the oligosaccharides on the binding of a soluble form of Dectin-1 to a solid-supported Schizophyllan (SPG) revealed that the branched heptadecasaccharide and the linear hexadecasaccharides also have binding activity for Dectin-1. In addition, the two oligosaccharides, both of which contain a β(1,3) hexadecasaccharide backbone, exhibited agonist activity in a luciferase-assisted NF-κB assay. STD-NMR analyses of complexes of Dectin-1 and the linear hexadecasaccharides clearly indicate Dectin-1 specifically recognizes the sugar part of the oligosaccharides and not the aminoalkyl chain.
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Affiliation(s)
- Hiroshi Tanaka
- Department of Applied Chemistry, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1-S1-35 Ookayama, Meguro, Tokyo 152-8552, Japan.
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29
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Bergström M, Åström E, Påhlsson P, Ohlson S. Elucidating the selectivity of recombinant forms of Aleuria aurantia lectin using weak affinity chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 885-886:66-72. [DOI: 10.1016/j.jchromb.2011.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 12/08/2011] [Accepted: 12/14/2011] [Indexed: 12/30/2022]
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30
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Fiege B, Rademacher C, Cartmell J, Kitov PI, Parra F, Peters T. Molecular Details of the Recognition of Blood Group Antigens by a Human Norovirus as Determined by STD NMR Spectroscopy. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105719] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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31
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Fiege B, Rademacher C, Cartmell J, Kitov PI, Parra F, Peters T. Molecular details of the recognition of blood group antigens by a human norovirus as determined by STD NMR spectroscopy. Angew Chem Int Ed Engl 2011; 51:928-32. [PMID: 22170811 DOI: 10.1002/anie.201105719] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Indexed: 01/26/2023]
Affiliation(s)
- Brigitte Fiege
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
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32
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Bhunia A, Bhattacharjya S. Mapping residue-specific contacts of polymyxin B with lipopolysaccharide by saturation transfer difference NMR: insights into outer-membrane disruption and endotoxin neutralization. Biopolymers 2011; 96:273-87. [PMID: 20683937 DOI: 10.1002/bip.21530] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
High-resolution interactions studies of molecules with lipopolysaccharide (LPS) or endotoxin are important for health, diseases and environment. LPS is the major constituent of the outer layer of the outer membrane of the gram-negative bacteria. LPS provides an efficient barrier against permeation of variety of compounds including antibacterial agents and antimicrobial peptides. In the intensive care units, LPS is known for the fatal septic shock syndromes. Because of LPS toxicity, high affinity LPS sensors are sought-after for the assessment of the quality of water and pharmaceutical products. Therefore, elucidation of binding epitopes of LPS interacting molecules would be vital for the development of antimicrobial, antiendotoxic molecules. Polymyxin B (PMB), an antibacterial cyclic lipo-peptide, is well known for its LPS sequestering and neutralizing activities. Here, we have used saturation transfer difference (STD) NMR methods for characterizing interactions of PMB with LPS from E. coli 0111:B4 and P. aeruginosa. The dissociation constants of the LPS-PMB complexes were obtained from concentration dependent STD studies. Further a detailed epitope mapping of PMB has been carried out in E. coli 0111:B4 LPS micelles. Experiments including one-dimensional 1H STD, two-dimensional 1H-1H STD-TOCSY and naturalabundance 13C-1H STD-HSQC, are performed to determine the site(s) of interactions of PMB with endotoxin at atomic resolution. Our studies reveal that the hydrophobic sidechains of PMB including a part of the N-terminus lipidic tail demonstrate close contacts with LPS. In contrast, cyclic backbone structure of PMB has the lowest STD effects suggesting a rather loose association with endotoxin.
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Affiliation(s)
- Anirban Bhunia
- Biomolecular NMR and Drug Discovery Laboratory, School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore 637551
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33
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Bhunia A, Saravanan R, Mohanram H, Mangoni ML, Bhattacharjya S. NMR structures and interactions of temporin-1Tl and temporin-1Tb with lipopolysaccharide micelles: mechanistic insights into outer membrane permeabilization and synergistic activity. J Biol Chem 2011; 286:24394-406. [PMID: 21586570 PMCID: PMC3129218 DOI: 10.1074/jbc.m110.189662] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 04/27/2011] [Indexed: 11/06/2022] Open
Abstract
Temporins are a group of closely related short antimicrobial peptides from frog skin. Lipopolysaccharide (LPS), the major constituent of the outer membrane of gram-negative bacteria, plays important roles in the activity of temporins. Earlier studies have found that LPS induces oligomerization of temporin-1Tb (TB) thus preventing its translocation across the outer membrane and, as a result, reduces its activity on gram-negative bacteria. On the other hand, temporin-1Tl (TL) exhibits higher activity, presumably because of lack of such oligomerization. A synergistic mechanism was proposed, involving TL and TB in overcoming the LPS-mediated barrier. Here, to gain insights into interactions of TL and TB within LPS, we investigated the structures and interactions of TL, TB, and TL+TB in LPS micelles, using NMR and fluorescence spectroscopy. In the context of LPS, TL assumes a novel antiparallel dimeric helical structure sustained by intimate packing between aromatic-aromatic and aromatic-aliphatic residues. By contrast, independent TB has populations of helical and aggregated conformations in LPS. The LPS-induced aggregated states of TB are largely destabilized in the presence of TL. Saturation transfer difference NMR studies have delineated residues of TL and TB in close contact with LPS and enhanced interactions of these two peptides with LPS, when combined together. Fluorescence resonance energy transfer and (31)P NMR have pointed out the proximity of TL and TB in LPS and conformational changes of LPS, respectively. Importantly, these results provide the first structural insights into the mode of action and synergism of antimicrobial peptides at the level of the LPS-outer membrane.
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Affiliation(s)
- Anirban Bhunia
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore 637551 and
| | - Rathi Saravanan
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore 637551 and
| | - Harini Mohanram
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore 637551 and
| | - Maria L. Mangoni
- the Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche Universita‘ La Sapienza, Piazzale Aldo Moro, 5-00185 Roma, Italy
| | - Surajit Bhattacharjya
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore 637551 and
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34
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Calle LP, Cañada FJ, Jiménez-Barbero J. Application of NMR methods to the study of the interaction of natural products with biomolecular receptors. Nat Prod Rep 2011; 28:1118-25. [DOI: 10.1039/c0np00071j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Olausson J, Åström E, Jonsson BH, Tibell LAE, Påhlsson P. Production and characterization of a monomeric form and a single-site form of Aleuria aurantia lectin. Glycobiology 2010; 21:34-44. [DOI: 10.1093/glycob/cwq129] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Singh RS, Bhari R, Kaur HP. Mushroom lectins: current status and future perspectives. Crit Rev Biotechnol 2010; 30:99-126. [PMID: 20105049 DOI: 10.3109/07388550903365048] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Lectins are nonimmune proteins or glycoproteins that bind specifically to cell surface carbohydrates, culminating in cell agglutination. These are known to play key roles in host defense system and also in metastasis. Many new sources have been explored for the occurrence of lectins during the last few years. Numerous novel lectins with unique specificities and exploitable properties have been discovered. Mushrooms have attracted a number of researchers in food and pharmaceuticals. Many species have long been used in traditional Chinese medicines or functional foods in Japan and other Asian countries. A number of bioactive constituents have been isolated from mushrooms including polysaccharides, polysaccharopeptides, polysaccharide-protein complexes, proteases, ribonucleases, ribosome inactivating proteins, antifungal proteins, immunomodulatory proteins, enzymes, lectins, etc. Mushroom lectins are endowed with mitogenic, antiproliferative, antitumor, antiviral, and immune stimulating potential. In this review, an attempt has been made to collate the information on mushroom lectins, their blood group and sugar specificities, with an emphasis on their biomedical potential and future perspectives.
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Affiliation(s)
- Ram Sarup Singh
- Carbohydrate and Protein Biotechnology Laboratory, Department of Biotechnology, Punjabi University, Patiala, Punjab, India.
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Ishida T. Computational modeling of carbohydrate-recognition process in E-selectin complex: structural mapping of sialyl Lewis X onto ab initio QM/MM free energy surface. J Phys Chem B 2010; 114:3950-64. [PMID: 20078087 DOI: 10.1021/jp905872t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To advance our knowledge of carbohydrate recognition by lectins, we propose a systematic computational modeling strategy to identify complex sugar-chain conformations on the reduced free energy surface (FES). We selected the complex of E-selectin with sialyl Lewis X (denoted E-selectin/SLe(x) complex) as a first target molecule. First, we introduced the reduced 2D-FES that characterizes conformational changes in carbohydrate structure as well as the degree of solvation stability of the carbohydrate ligand, and evaluated the overall free energy profile by classical molecular dynamics simulation combined with ab initio QM/MM energy corrections. Second, we mapped flexible carbohydrate structures onto the reduced QM/MM 2D-FES, and identified the details of molecular interactions between each monosaccharide component and the amino acid residues at the carbohydrate-recognition domain. Finally, we confirmed the validity of our modeling strategy by evaluating the chemical shielding tensor by ab initio QM/MM-GIAO computations for several QM/MM-refined geometries sampled from the minimum free energy region in the 2D-FES, and compared this theoretical averaging data with the experimental 1D-NMR profile. The model clearly shows that the binding geometries of the E-selectin/SLe(x) complex are determined not by one single, rigid carbohydrate structure but rather by the sum of averaged conformations fluctuating around the minimum free energy region. For the E-selectin/SLe(x) complex, the major molecular interactions are hydrogen bonds between Fuc and the Ca(2+) binding site in the carbohydrate-recognition domain, and Gal is important in determining the ligand specificity.
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Affiliation(s)
- Toyokazu Ishida
- Research Institute for Computational Sciences, 1-1-1 Umezono, Tsukuba, 305-8568, Japan.
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38
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Corzana F, Busto JH, García de Luis M, Fernández-Tejada A, Rodríguez F, Jiménez-Barbero J, Avenoza A, Peregrina JM. Dynamics and Hydration Properties of Small Antifreeze-Like Glycopeptides Containing Non-Natural Amino Acids. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000375] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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39
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Fernández-Tejada A, Corzana F, Busto JH, Avenoza A, Peregrina JM. Conformational effects of the non-natural alpha-methylserine on small peptides and glycopeptides. J Org Chem 2010; 74:9305-13. [PMID: 19924838 DOI: 10.1021/jo901988w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis and the conformational analysis in aqueous solution of a peptide and a glycopeptide containing the sequence threonine-alanine-alanine (Thr-Ala-Ala) are reported. Furthermore, the threonine residue has been replaced by the quaternary amino acid alpha-methylserine (MeSer) and their corresponding non-natural peptide and glycopeptide are also studied. The conformational analysis in aqueous solution combines NOEs and coupling constants data with Molecular Dynamics (MD) simulations with time-averaged restraints. The study reveals that the beta-O-glycosylation produces a remarkable and completely different effect on the backbone of the peptide derived from Thr and MeSer. In the former, the beta-O-glycosylation is responsible for the experimentally observed shift from extended conformations (peptide) to folded ones (glycopeptide). In contrast, the beta-O-glycosylation of the MeSer-containing peptide, which clearly shows two main conformations in aqueous solution [extended ones (70%) and beta-turn (30%)], causes a high degree of flexibility for the backbone.
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Affiliation(s)
- Alberto Fernández-Tejada
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Sintesis Química, Grupo de Sintesis Química de La Rioja, UA-CSIC, 26006 Logroño, Spain
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40
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Bhunia A, Domadia PN, Torres J, Hallock KJ, Ramamoorthy A, Bhattacharjya S. NMR structure of pardaxin, a pore-forming antimicrobial peptide, in lipopolysaccharide micelles: mechanism of outer membrane permeabilization. J Biol Chem 2010; 285:3883-3895. [PMID: 19959835 PMCID: PMC2823531 DOI: 10.1074/jbc.m109.065672] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Revised: 11/02/2009] [Indexed: 11/06/2022] Open
Abstract
Lipopolysaccharide (LPS), the major constituent of the outer membrane of Gram-negative bacteria, is an important element against permeability of bactericidal agents, including antimicrobial peptides. However, structural determinants of antimicrobial peptides for LPS recognition are not clearly understood. Pardaxins (Pa1, Pa2, Pa3, and Pa4) are a group of pore-forming bactericidal peptides found in the mucous glands of sole fishes. Despite having a low net positive charge, pardaxins contain a broad spectrum of antibacterial activities. To elucidate the structural basis of LPS interactions of pardaxins, herein, we report the first three-dimensional structure of Pa4 bound to LPS micelles. The binding kinetics of Pa4 with LPS is estimated using [(15)N-Leu-19] relaxation dispersion NMR experiments. LPS/Pa4 interactions are further characterized by a number of biophysical methods, including isothermal titration calorimetry, (31)P NMR, saturation transfer difference NMR, dynamic light scattering, and IR spectroscopy. In the LPS-Pa4 complex, Pa4 adopts a unique helix-turn-helix conformation resembling a "horseshoe." Interestingly, the LPS-bound structure of Pa4 shows striking differences with the structures determined in lipid micelles or organic solvents. Saturation transfer difference NMR identifies residues of Pa4 that are intimately associated with LPS micelles. Collectively, our results provide mechanistic insights into the outer membrane permeabilization by pardaxin.
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Affiliation(s)
- Anirban Bhunia
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and
| | - Prerna N Domadia
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and
| | - Jaume Torres
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and
| | - Kevin J Hallock
- the Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Ayyalusamy Ramamoorthy
- the Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055.
| | - Surajit Bhattacharjya
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and.
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41
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Fernández-Tejada A, Corzana F, Busto JH, Jiménez-Osés G, Jiménez-Barbero J, Avenoza A, Peregrina JM. Insights into the geometrical features underlying beta-O-GlcNAc glycosylation: water pockets drastically modulate the interactions between the carbohydrate and the peptide backbone. Chemistry 2009; 15:7297-301. [PMID: 19544521 DOI: 10.1002/chem.200901204] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alberto Fernández-Tejada
- Departamento de Química, Universidad de La Rioja, UA-CSIC. Madre de Dios 51, 26006 Logroño, La Rioja, Spain
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42
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Harris LG, Schofield WCE, Doores KJ, Davis BG, Badyal JPS. Rewritable glycochips. J Am Chem Soc 2009; 131:7755-61. [PMID: 19438244 DOI: 10.1021/ja901294r] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe microarraying of carbohydrates for protein screening using either disulfide bridge or Schiff base imine immobilization chemistries on plasmachemical deposited functional nanolayers. The commonly observed issue of nonspecific background binding of proteins is overcome by spotting carbohydrates through a protein-resistant overlayer yielding spatially localized interaction with a reactive functional underlayer.
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Affiliation(s)
- L G Harris
- Department of Chemistry, Science Laboratories, Durham University, Durham DH1 3LE, UK
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43
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Matsuoka K, Kohzu T, Hakumura T, Koyama T, Hatano K, Terunuma D. Synthetic construction of a Lex determinant via gabriel amine synthesis and the glycopolymer involving highly clustered Lex residues. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.03.099] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Fernández-Tejada A, Corzana F, Busto JH, Avenoza A, Peregrina JM. Stabilizing unusual conformations in small peptides and glucopeptides using a hydroxylated cyclobutane amino acid. Org Biomol Chem 2009; 7:2885-93. [DOI: 10.1039/b907091p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Matsumura K, Higashida K, Hata Y, Kominami J, Nakamura-Tsuruta S, Hirabayashi J. Comparative analysis of oligosaccharide specificities of fucose-specific lectins from Aspergillus oryzae and Aleuria aurantia using frontal affinity chromatography. Anal Biochem 2008; 386:217-21. [PMID: 19109923 DOI: 10.1016/j.ab.2008.11.044] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2008] [Revised: 11/20/2008] [Accepted: 11/26/2008] [Indexed: 11/17/2022]
Abstract
Aleuria aurantia lectin (AAL) is widely used to estimate the extent of alpha1,6-fucosylated oligosaccharides and to fractionate glycoproteins for the detection of specific biomarkers for developmental antigens. Our previous studies have shown that Aspergillus oryzae lectin (AOL) reflects the extent of alpha1,6-fucosylation more clearly than AAL. However, the subtle specificities of these lectins to fucose linked to oligosaccharides through the 2-, 3-, 4-, or 6-position remain unclear, because large amounts of oligosaccharides are required for the systematic comparative analysis using surface plasmon resonance. Here we show a direct comparison of the dissociation constants (K(d)) of AOL and AAL using 113 pyridylaminated oligosaccharides with frontal affinity chromatography. As a result, AOL showed a similar specificity as AAL in terms of the high affinity for alpha1,6-fucosylated oligosaccharides, for smaller fucosylated oligosaccharides, and for oligosaccharides fucosylated at the reducing terminal core GlcNAc. On the other hand, AOL showed 2.9-6.2 times higher affinity constants (K(a)) for alpha1,6-fucosylated oligosaccharides than AAL and only AAL additionally recognized oligosaccharides which were alpha1,3-fucosylated at the reducing terminal GlcNAc. These results explain why AOL reflects the extent of alpha1,6-fucosylation on glycoproteins more clearly than AAL. This systematic comparative analysis made from a quantitative viewpoint enabled a clear physical interpretation of these fucose-specific lectins with multivalent fucose-binding sites.
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Affiliation(s)
- Kengo Matsumura
- Research Institute, Gekkeikan Sake Co. Ltd., 300 Katahara-cho, Fushimi-ku, Kyoto 612-8361, Japan.
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46
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Becker BA, Larive CK. Probing the Binding of Propranolol Enantiomers to α1-Acid Glycoprotein with Ligand-Detected NMR Experiments. J Phys Chem B 2008; 112:13581-7. [DOI: 10.1021/jp8060366] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bridget A. Becker
- Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - Cynthia K. Larive
- Department of Chemistry, University of California, Riverside, Riverside, California 92521
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47
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Fernández-Tejada A, Corzana F, Busto JH, Jiménez-Osés G, Peregrina JM, Avenoza A. Non-natural amino acids as modulating agents of the conformational space of model glycopeptides. Chemistry 2008; 14:7042-58. [PMID: 18604849 DOI: 10.1002/chem.200800460] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The synthesis and conformational analysis in aqueous solution of different alpha-methyl-alpha-amino acid diamides, derived from serine, threonine, beta-hydroxycyclobutane-alpha-amino acids, and their corresponding model beta-O-glucopeptides, are reported. The study reveals that the presence of an alpha-methyl group forces the model peptides to adopt helix-like conformations. These folded conformations are especially significant for cyclobutane derivatives. Interestingly, this feature was also observed in the corresponding model glucopeptides, thus indicating that the alpha-methyl group and not the beta-O-glucosylation process largely determines the conformational preference of the backbone in these structures. On the other hand, atypical conformations of the glycosidic linkage were experimentally determined. Therefore, when a methyl group was located at the Cbeta atom with an R configuration, the glycosidic linkage was rather rigid. Nevertheless, when the S configuration was displayed, a significant degree of flexibility was observed for the glycosidic linkage, thus showing both alternate and eclipsed conformations of the psi(s) dihedral angle. In addition, some derivatives exhibited an unusual value for the phi(s) angle, which was far from a value of -60 degrees expected for a conventional beta-O-glycosidic linkage. In this sense, the different conformations exhibited by these molecules could be a useful tool in obtaining systems with conformational preferences "à la carte".
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48
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Detection of a high affinity binding site in recombinant Aleuria aurantia lectin. Glycoconj J 2008; 25:753-62. [PMID: 18493851 DOI: 10.1007/s10719-008-9135-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 04/02/2008] [Accepted: 04/03/2008] [Indexed: 10/22/2022]
Abstract
Lectins are carbohydrate binding proteins that are involved in many recognition events at molecular and cellular levels. Lectin-oligosaccharide interactions are generally considered to be of weak affinity, however some mushroom lectins have unusually high binding affinity towards oligosaccharides with K (d) values in the micromolar range. This would make mushroom lectins ideal candidates to study protein-carbohydrate interactions. In the present study we investigated the properties of a recombinant form of the mushroom lectin Aleuria aurantia (AAL). AAL is a fucose-binding lectin composed of two identical 312-amino acid subunits. Each subunit contains five binding sites for fucose. We found that one of the binding sites in rAAL had unusually high affinities towards fucose and fucose-containing oligosaccharides with K (d) values in the nanomolar range. This site could bind to oligosaccharides with fucose linked alpha1-2, alpha1-3 or alpha1-4, but in contrast to the other binding sites in AAL it could not bind oligosaccharides with alpha1-6 linked fucose. This binding site is not detected in native AAL (nAAL) one possible explanation may be that this site is blocked with free fucose in nAAL. Recombinant AAL was produced in E. coli as a His-tagged protein, and purified in a one-step procedure. The resulting protein was analyzed by electrophoresis, enzyme-linked lectin assay and circular dichroism spectroscopy, and compared to nAAL. Binding properties were measured using tryptophan fluorescence and surface plasmon resonance. Removal of the His-tag did not alter the binding properties of recombinant AAL in the enzyme-linked lectin assay. Our study forms a basis for understanding the AAL-oligosaccharide interaction and for using molecular techniques to design lectins with novel specificities and high binding affinities towards oligosaccharides.
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Revuelta J, Vacas T, Torrado M, Corzana F, Gonzalez C, Jiménez-Barbero J, Menendez M, Bastida A, Asensio JL. NMR-based analysis of aminoglycoside recognition by the resistance enzyme ANT(4'): the pattern of OH/NH3(+) substitution determines the preferred antibiotic binding mode and is critical for drug inactivation. J Am Chem Soc 2008; 130:5086-103. [PMID: 18366171 DOI: 10.1021/ja076835s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The most significant mechanism of bacterial resistance to aminoglycosides is the enzymatic inactivation of the drug. Herein, we analyze several key aspects of the aminoglycoside recognition by the resistance enzyme ANT(4') from Staphylococcus aureus, employing NMR complemented with site-directed mutagenesis experiments and measurements of the enzymatic activity on newly synthesized kanamycin derivatives. From a methodological perspective, this analysis provides the first example reported for the use of transferred NOE (trNOE) experiments in the analysis of complex molecular recognition processes, characterized by the existence of simultaneous binding events of the ligand to different regions of a protein receptor. The obtained results show that, in favorable cases, these overlapping binding processes can be isolated employing site-directed mutagenesis and then independently analyzed. From a molecular recognition perspective, this work conclusively shows that the enzyme ANT(4') displays a wide tolerance to conformational variations in the drug. Thus, according to the NMR data, kanamycin-A I/II linkage exhibits an unusual anti-Psi orientation in the ternary complex, which is in qualitative agreement with the previously reported crystallographic complex. In contrast, closely related, kanamycin-B is recognized by the enzyme in the syn-type arrangement for both glycosidic bonds. This observation together with the enzymatic activity displayed by ANT(4') against several synthetic kanamycin derivatives strongly suggests that the spatial distribution of positive charges within the aminoglycoside scaffold is the key feature that governs its preferred binding mode to the protein catalytic region and also the regioselectivity of the adenylation reaction. In contrast, the global shape of the antibiotic does not seem to be a critical factor. This feature represents a qualitative difference between the target A-site RNA and the resistance enzyme ANT(4') as aminoglycoside receptors.
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Affiliation(s)
- Julia Revuelta
- Instituto de Química Orgánica General (CSIC), Madrid 28006, Spain
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Moreno FBMB, de Oliveira TM, Martil DE, Viçoti MM, Bezerra GA, Abrego JRB, Cavada BS, Filgueira de Azevedo W. Identification of a new quaternary association for legume lectins. J Struct Biol 2008; 161:133-43. [DOI: 10.1016/j.jsb.2007.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 09/27/2007] [Accepted: 10/04/2007] [Indexed: 10/22/2022]
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