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Kozmon S, Matuška R, Spiwok V, Koča J. Three-dimensional potential energy surface of selected carbohydrates' CH/π dispersion interactions calculated by high-level quantum mechanical methods. Chemistry 2011; 17:5680-90. [PMID: 21480404 DOI: 10.1002/chem.201002876] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Indexed: 11/10/2022]
Abstract
In this study we present the first systematic computational three-dimensional scan of carbohydrate hydrophobic patches for the ability to interact through CH/π dispersion interactions. The carbohydrates β-d-glucopyranose, β-d-mannopyranose and α-l-fucopyranose were studied in a complex with a benzene molecule, which served as a model of the CH/π interaction in carbohydrate/protein complexes. The 3D relaxed scans were performed at the SCC-DFTB-D level with 3 757 grid points for both carbohydrate hydrophobic sides. The interaction energy of all grid points was recalculated at the DFT-D BP/def2-TZVPP level. The results obtained clearly show highly delimited and separated areas around each CH group, with an interaction energy up to -5.40 kcal mol(-1) . The results also show that with increasing H⋅⋅⋅π distance these delimited areas merge and form one larger region, which covers all hydrogen atoms on that specific carbohydrate side. Simultaneously, the interaction becomes weaker with an energy of -2.5 kcal mol(-1) . All local energy minima were optimized at the DFT-D BP/def2-TZVPP level and the interaction energies of these complexes were refined by use of the high-level ab initio computation at the CCSD(T)/CBS level. Results obtained from the optimization suggest that the CH group hydrogen atoms are not equivalent and the interaction energy at the CCSD(T)/CBS level range from -3.54 to -5.40 kcal mol(-1) . These results also reveal that the optimal H⋅⋅⋅π distance for the CH/π dispersion interaction is approximately (2.310±0.030) Å, and the angle defined as carbon-hydrogen-benzene geometrical centre is (180±30)°. These results reveal that whereas the dispersion interactions with the lowest interaction energies are quite strictly located in space, the slightly higher interaction energy regions adopt a much larger space.
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Affiliation(s)
- Stanislav Kozmon
- National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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Ardá A, Cañada FJ, Nativi C, Francesconi O, Gabrielli G, Ienco A, Jiménez-Barbero J, Roelens S. Chiral Diaminopyrrolic Receptors for Selective Recognition of Mannosides, Part 2: A 3D View of the Recognition Modes by X-ray, NMR Spectroscopy, and Molecular Modeling. Chemistry 2011; 17:4821-9. [DOI: 10.1002/chem.201002872] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 11/29/2011] [Indexed: 11/12/2022]
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53
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Takahashi O, Kohno Y, Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem Rev 2011; 110:6049-76. [PMID: 20550180 DOI: 10.1021/cr100072x] [Citation(s) in RCA: 447] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
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Mazik M, Geffert C. 8-Hydroxyquinoline as a building block for artificial receptors: binding preferences in the recognition of glycopyranosides. Org Biomol Chem 2011; 9:2319-26. [DOI: 10.1039/c0ob00960a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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55
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Mazik M, Sonnenberg C. Isopropylamino and Isobutylamino Groups as Recognition Sites for Carbohydrates: Acyclic Receptors with Enhanced Binding Affinity toward β-Galactosides. J Org Chem 2010; 75:6416-23. [DOI: 10.1021/jo100982x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Monika Mazik
- Institut für Organische Chemie der Technischen Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Claudia Sonnenberg
- Institut für Organische Chemie der Technischen Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
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Vacas T, Corzana F, Jiménez-Osés G, González C, Gómez AM, Bastida A, Revuelta J, Asensio JL. Role of Aromatic Rings in the Molecular Recognition of Aminoglycoside Antibiotics: Implications for Drug Design. J Am Chem Soc 2010; 132:12074-90. [DOI: 10.1021/ja1046439] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tatiana Vacas
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Francisco Corzana
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Gonzalo Jiménez-Osés
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Carlos González
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Ana M. Gómez
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Agatha Bastida
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Julia Revuelta
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
| | - Juan Luis Asensio
- Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain, Departamento de Química, Universidad de La Rioja, UA-CSIC, Logroño, Spain, Departamento de Química Orgánica y Química Física. Universidad de Zaragoza-CSIC, Zaragoza, Spain, and Instituto de Química Física Rocasolano (CSIC), Madrid, Spain
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57
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Chávez MI, Vila-Perelló M, Cañada FJ, Andreu D, Jiménez-Barbero J. Effect of a serine-to-aspartate replacement on the recognition of chitin oligosaccharides by truncated hevein. A 3D view by using NMR. Carbohydr Res 2010; 345:1461-8. [DOI: 10.1016/j.carres.2010.02.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 02/11/2010] [Accepted: 02/20/2010] [Indexed: 11/24/2022]
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Kumirska J, Czerwicka M, Kaczyński Z, Bychowska A, Brzozowski K, Thöming J, Stepnowski P. Application of spectroscopic methods for structural analysis of chitin and chitosan. Mar Drugs 2010; 8:1567-636. [PMID: 20559489 PMCID: PMC2885081 DOI: 10.3390/md8051567] [Citation(s) in RCA: 525] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 03/30/2010] [Accepted: 04/27/2010] [Indexed: 12/22/2022] Open
Abstract
Chitin, the second most important natural polymer in the world, and its N-deacetylated derivative chitosan, have been identified as versatile biopolymers for a broad range of applications in medicine, agriculture and the food industry. Two of the main reasons for this are firstly the unique chemical, physicochemical and biological properties of chitin and chitosan, and secondly the unlimited supply of raw materials for their production. These polymers exhibit widely differing physicochemical properties depending on the chitin source and the conditions of chitosan production. The presence of reactive functional groups as well as the polysaccharide nature of these biopolymers enables them to undergo diverse chemical modifications. A complete chemical and physicochemical characterization of chitin, chitosan and their derivatives is not possible without using spectroscopic techniques. This review focuses on the application of spectroscopic methods for the structural analysis of these compounds.
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Affiliation(s)
- Jolanta Kumirska
- Faculty of Chemistry, University of Gdansk, Sobieskiego 18/19, PL-80-952 Gdansk, Poland; E-Mails:
(M.C.);
(Z.K.);
(A.B.);
(K.B.);
(P.S.)
| | - Małgorzata Czerwicka
- Faculty of Chemistry, University of Gdansk, Sobieskiego 18/19, PL-80-952 Gdansk, Poland; E-Mails:
(M.C.);
(Z.K.);
(A.B.);
(K.B.);
(P.S.)
| | - Zbigniew Kaczyński
- Faculty of Chemistry, University of Gdansk, Sobieskiego 18/19, PL-80-952 Gdansk, Poland; E-Mails:
(M.C.);
(Z.K.);
(A.B.);
(K.B.);
(P.S.)
| | - Anna Bychowska
- Faculty of Chemistry, University of Gdansk, Sobieskiego 18/19, PL-80-952 Gdansk, Poland; E-Mails:
(M.C.);
(Z.K.);
(A.B.);
(K.B.);
(P.S.)
| | - Krzysztof Brzozowski
- Faculty of Chemistry, University of Gdansk, Sobieskiego 18/19, PL-80-952 Gdansk, Poland; E-Mails:
(M.C.);
(Z.K.);
(A.B.);
(K.B.);
(P.S.)
| | - Jorg Thöming
- UFT-Centre for Environmental Research and Sustainable Technology, University of Bremen, Leobener Straße UFT, D-28359 Bremen, Germany; E-Mail:
(J.T.)
| | - Piotr Stepnowski
- Faculty of Chemistry, University of Gdansk, Sobieskiego 18/19, PL-80-952 Gdansk, Poland; E-Mails:
(M.C.);
(Z.K.);
(A.B.);
(K.B.);
(P.S.)
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Kumar RM, Elango M, Subramanian V. Carbohydrate-Aromatic Interactions: The Role of Curvature on XH···π Interactions. J Phys Chem A 2010; 114:4313-24. [DOI: 10.1021/jp907547f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. Mahesh Kumar
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - M. Elango
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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60
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Mazik M, Hartmann A. Recognition properties of receptors consisting of imidazole and indole recognition units towards carbohydrates. Beilstein J Org Chem 2010; 6:9. [PMID: 20485591 PMCID: PMC2871371 DOI: 10.3762/bjoc.6.9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 01/19/2010] [Indexed: 11/25/2022] Open
Abstract
Compounds 4 and 5, including both 4(5)-substituted imidazole or 3-substituted indole units as the entities used in nature, and 2-aminopyridine group as a heterocyclic analogue of the asparagine/glutamine primary amide side chain, were prepared and their binding properties towards carbohydrates were studied. The design of these receptors was inspired by the binding motifs observed in the crystal structures of protein-carbohydrate complexes. ¹H NMR spectroscopic titrations in competitive and non-competitive media as well as binding studies in two-phase systems, such as dissolution of solid carbohydrates in apolar media, revealed both highly effective recognition of neutral carbohydrates and interesting binding preferences of these acyclic compounds. Compared to the previously described acyclic receptors, compounds 4 and 5 showed significantly increased binding affinity towards β-galactoside. Both receptors display high β- vs. α-anomer binding preferences in the recognition of glycosides. It has been shown that both hydrogen bonding and interactions of the carbohydrate CH units with the aromatic rings of the receptors contribute to the stabilization of the receptor-carbohydrate complexes. The molecular modeling calculations, synthesis and binding properties of 4 and 5 towards selected carbohydrates are described and compared with those of the previously described receptors.
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Affiliation(s)
- Monika Mazik
- Institut für Organische Chemie der Technischen Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.
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61
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Raju RK, Hillier IH, Burton NA, Vincent MA, Doudou S, Bryce RA. The effects of perfluorination on carbohydrate–π interactions: computational studies of the interaction of benzene and hexafluorobenzene with fucose and cyclodextrin. Phys Chem Chem Phys 2010; 12:7959-67. [DOI: 10.1039/c002058c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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62
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Kövér KE, Szilágyi L, Batta G, Uhrín D, Jiménez-Barbero J. Biomolecular Recognition by Oligosaccharides and Glycopeptides: The NMR Point of View. COMPREHENSIVE NATURAL PRODUCTS II 2010:197-246. [DOI: 10.1016/b978-008045382-8.00193-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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63
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Ardá A, Venturi C, Nativi C, Francesconi O, Cañada FJ, Jiménez-Barbero J, Roelens S. Selective Recognition of β-Mannosides by Synthetic Tripodal Receptors: A 3D View of the Recognition Mode by NMR. European J Org Chem 2009. [DOI: 10.1002/ejoc.200901024] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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64
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Carrillo R, López-Rodríguez M, Martín V, Martín T. Quantification of a CH-π Interaction Responsible for Chiral Discrimination and Evaluation of Its Contribution to Enantioselectivity. Angew Chem Int Ed Engl 2009; 48:7803-8. [DOI: 10.1002/anie.200903281] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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65
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Carrillo R, López-Rodríguez M, Martín V, Martín T. Quantification of a CH-π Interaction Responsible for Chiral Discrimination and Evaluation of Its Contribution to Enantioselectivity. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903281] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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66
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Walker DB, Joshi G, Davis AP. Progress in biomimetic carbohydrate recognition. Cell Mol Life Sci 2009; 66:3177-91. [PMID: 19582369 PMCID: PMC11115563 DOI: 10.1007/s00018-009-0081-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 06/12/2009] [Accepted: 06/18/2009] [Indexed: 11/29/2022]
Abstract
The importance of carbohydrate recognition in biology, and the unusual challenges involved, have lead to great interest in mimicking saccharide-binding proteins such as lectins. In this review, we discuss the design of artificial carbohydrate receptors, focusing on those which work under natural (i.e. aqueous) conditions. The problem is intrinsically difficult because of the similarity between substrate (carbohydrate) and solvent (water) and, accordingly, progress has been slow. However, recent developments suggest that solutions can be found. In particular, the "temple" family of carbohydrate receptors show good affinities and excellent selectivities for certain all-equatorial substrates. One example is selective for O-linked beta-N-acetylglucosamine (GlcNAc, as in the O-GlcNAc protein modification), while another is specific for beta-cellobiosyl and closely related disaccharides. Both show roughly millimolar affinities, matching the strength of some lectin-carbohydrate interactions.
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Affiliation(s)
- D. Barney Walker
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS UK
| | - Gururaj Joshi
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS UK
| | - Anthony P. Davis
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS UK
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67
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Mazik M, Hartmann A, Jones P. Highly Effective Recognition of Carbohydrates by Phenanthroline-Based Receptors: α- versus β-Anomer Binding Preference. Chemistry 2009; 15:9147-59. [DOI: 10.1002/chem.200900664] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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68
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Jiménez-Barbero J, L. Asensio J, Cuevas G, Canales A, Fernández-Alonso MC, Javier Cañada F. Conformational insights on the molecular recognition processes of carbohydrate molecules by proteins and enzymes: A 3D view by using NMR. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420600598103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Abstract
Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.
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Affiliation(s)
- Hans-Jörg Schneider
- Organische Chemie, Universität des Saarlandes, 66041 Saarbrücken, Deutschland.
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70
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Tsuzuki S, Uchimaru T, Mikami M. Magnitude and nature of carbohydrate-aromatic interactions: ab initio calculations of fucose-benzene complex. J Phys Chem B 2009; 113:5617-21. [PMID: 19331351 DOI: 10.1021/jp8093726] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The stable geometries of fucose-benzene complex and the stabilization energies by formation of the complex (E(form)) were studied by ab initio molecular orbital calculations. The benzene ring has close contact with an O-H or C-H bond of fucose in the optimized geometries (OH/pi hydrogen-bonded structures and CH/pi contact structures). The E(form) calculated for the most stable OH/pi hydrogen-bonded structure was -5.1 kcal/mol. The E(form) calculated for the most stable CH/pi contact structure was -4.5 kcal/mol, which shows that significant attraction exists between the nonpolar surface of fucose and a benzene. The E(form) is close to the interaction energies in typical hydrogen-bonded complexes. A few nearly isoenergetic CH/pi contact structures were found by the calculations, which suggests that the directionality of the carbohydrate-aromatic interaction is weak. The dispersion interaction is the major source of the attraction in the complex. The electrostatic contributions to the attraction are relatively small. Although the size of the interaction energy is not largely different from that of typical hydrogen bonds, the nature of the carbohydrate-aromatic interaction, which is sometimes denoted as a CH/pi hydrogen bond, is completely different from that of typical hydrogen bonds, which have strong directionality due to the strong electrostatic interactions.
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Affiliation(s)
- Seiji Tsuzuki
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan.
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Mazik M, Buthe AC. Recognition properties of receptors based on dimesitylmethane-derived core: Di- vs. monosaccharide preference. Org Biomol Chem 2009; 7:2063-71. [DOI: 10.1039/b901173k] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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73
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Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/π hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009. [DOI: 10.1039/b902318f] [Citation(s) in RCA: 481] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Cerqueira NMFSA, Bras NF, Fernandes PA, Ramos MJ. MADAMM: A multistaged docking with an automated molecular modeling protocol. Proteins 2009; 74:192-206. [DOI: 10.1002/prot.22146] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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75
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Ribeiro JP, Bacchi S, Dell'Anna G, Morando M, Cañada FJ, Cozzi F, Jiménez-Barbero J. A Combined NMR, Computational, and HPLC Study of the Inclusion of Aromatic and Fluoroaromatic Compounds in Cyclodextrins as a Model for Studying Carbohydrate-Aromatic Interactions. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800585] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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76
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Vandenbussche S, Díaz D, Fernández-Alonso MC, Pan W, Vincent SP, Cuevas G, Cañada FJ, Jiménez-Barbero J, Bartik K. Aromatic-carbohydrate interactions: an NMR and computational study of model systems. Chemistry 2008; 14:7570-8. [PMID: 18481803 DOI: 10.1002/chem.200800247] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The interactions of simple carbohydrates with aromatic moieties have been investigated experimentally by NMR spectroscopy. The analysis of the changes in the chemical shifts of the sugar proton signals induced upon addition of aromatic entities has been interpreted in terms of interaction geometries. Phenol and aromatic amino acids (phenylalanine, tyrosine, tryptophan) have been used. The observed sugar-aromatic interactions depend on the chemical nature of the sugar, and thus on the stereochemistries of the different carbon atoms, and also on the solvent. A preliminary study of the solvation state of a model monosaccharide (methyl beta-galactopyranoside) in aqueous solution, both alone and in the presence of benzene and phenol, has also been carried out by monitoring of intermolecular homonuclear solvent-sugar and aromatic-sugar NOEs. These experimental results have been compared with those obtained by density functional theory methods and molecular mechanics calculations.
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Affiliation(s)
- Sophie Vandenbussche
- Molecular & Biomolecular Engineering, Université Libre de Bruxelles, Brussels, Belgium
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77
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Laughrey ZR, Kiehna SE, Riemen AJ, Waters ML. Carbohydrate-pi interactions: what are they worth? J Am Chem Soc 2008; 130:14625-33. [PMID: 18844354 DOI: 10.1021/ja803960x] [Citation(s) in RCA: 169] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein-carbohydrate interactions play an important role in many biologically important processes. The recognition is mediated by a number of noncovalent interactions, including an interaction between the alpha-face of the carbohydrate and the aromatic side chain of the protein. To elucidate this interaction, it has been studied in the context of a beta-hairpin in aqueous solution, in which the interaction can be investigated in the absence of other cooperative noncovalent interactions. In this beta-hairpin system, both the aromatic side chain and the carbohydrate were varied in an effort to gain greater insight into the driving force and magnitude of the carbohydrate-pi interaction. The magnitude of the interaction was found to vary from -0.5 to -0.8 kcal/mol, depending on the nature of the aromatic ring and the carbohydrate. Replacement of the aromatic ring with an aliphatic group resulted in a decrease in interaction energy to -0.1 kcal/mol, providing evidence for the contribution of CH-pi interactions to the driving force. These findings demonstrate the significance of carbohydrate-pi interactions within biological systems and also their utility as a molecular recognition element in designed systems.
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Affiliation(s)
- Zachary R Laughrey
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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78
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Mazik M, Hartmann A. Phenanthroline Unit as a Building Block for Carbohydrate Receptors. J Org Chem 2008; 73:7444-50. [DOI: 10.1021/jo8005842] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Monika Mazik
- Institut für Organische Chemie der Technischen Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Andrè Hartmann
- Institut für Organische Chemie der Technischen Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
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79
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Bérubé M, Dowlut M, Hall DG. Benzoboroxoles as Efficient Glycopyranoside-Binding Agents in Physiological Conditions: Structure and Selectivity of Complex Formation. J Org Chem 2008; 73:6471-9. [DOI: 10.1021/jo800788s] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marie Bérubé
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Meenakshi Dowlut
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Dennis G. Hall
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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80
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Sato H, Fukae K, Kajihara Y. 2D Selective-TOCSY–DQFCOSY and HSQC–TOCSY NMR experiments for assignment of a homogeneous asparagine-linked triantennary complex type undecasaccharide. Carbohydr Res 2008; 343:1333-45. [DOI: 10.1016/j.carres.2008.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Revised: 02/22/2008] [Accepted: 03/03/2008] [Indexed: 11/25/2022]
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81
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82
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Viegas A, Brás NF, Cerqueira NMFSA, Fernandes PA, Prates JAM, Fontes CMGA, Bruix M, Romão MJ, Carvalho AL, Ramos MJ, Macedo AL, Cabrita EJ. Molecular determinants of ligand specificity in family 11 carbohydrate binding modules - an NMR, X-ray crystallography and computational chemistry approach. FEBS J 2008; 275:2524-35. [DOI: 10.1111/j.1742-4658.2008.06401.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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83
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Mazik M, Kuschel M. Highly Effective Acyclic Carbohydrate Receptors Consisting of Aminopyridine, Imidazole, and Indole Recognition Units. Chemistry 2008; 14:2405-19. [DOI: 10.1002/chem.200701269] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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84
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Mazik M, Kuschel M. Amide, Amino, Hydroxy and Aminopyridine Groups as Building Blocks for Carbohydrate Receptors. European J Org Chem 2008. [DOI: 10.1002/ejoc.200701097] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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85
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Bautista-Ibañez L, Ramírez-Gualito K, Quiroz-García B, Rojas-Aguilar A, Cuevas G. Calorimetric measurement of the CH/pi interaction involved in the molecular recognition of saccharides by aromatic compounds. J Org Chem 2008; 73:849-57. [PMID: 18173283 DOI: 10.1021/jo701926r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Can a benzene molecule differentiate between two isomeric carbohydrates? It is generally accepted that two factors govern molecular recognition: complementarity and preorganization. Preorganization requires the presence of cavities for positioning the host's groups of complementary nature to those of the guest. This study shows that, in fact, groups should be complementary to recognize each other (for the case presented here, it is controlled by the CH/pi interaction) but preorganization is not essential. Since weak interactions have their origin in dispersion forces, they also have impact on the enthalpic term of the free energy, so it was considered that their participation can be demonstrated by measuring the energy involved. For recognition to happen, two conditions must be satisfied: specificity and associated stabilizing energy. In this study we evaluated the heat of dissolution of different carbohydrates such as methyl 2,3,4,6-tetra-O-methyl-alpha-d-mannopyranoside and methyl 2,3,4,6-tetra-O-methyl-beta-d-galactopyranoside using different aromatic solvents. The solvation enthalpies in benzene were -78.8 +/- 3.9 and -88.7 +/- 5.5 kJ mol(-1) for each carbohydrate, respectively; and these values yielded a CH/pi energy of interaction of 9.9 kJ mol(-1). In addition, NMR studies of the effect of the addition of benzene to chloroform solutions of the two carbohydrates showed that benzene specifically interacts with the hydrogen atoms of the pyranose ring at positions 3, 4, and 5 located on the alpha face of the methyl-beta-galactoside, so it is, in fact, able to recognize it. Thus, the interactions between carbohydrates and the aromatic residues of proteins occur in the absence of the confinement generated by the protein structure. By experimentally measuring the energy associated with this interaction and comparing it to theoretical calculations, it was also possible to unequivocally determine the existence of CH/pi interactions between carbohydrates and proteins.
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Affiliation(s)
- Lorena Bautista-Ibañez
- Instituto de Química, Universidad Nacional Autónoma de México, Apdo. Postal 70213, 04510, CoyoacAn, México, D.F., México
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86
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Mazik M, Buthe AC. Highly effective receptors showing di- vs. monosaccharide preference. Org Biomol Chem 2008; 6:1558-68. [DOI: 10.1039/b719212f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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87
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On the role of aromatic-sugar interactions in the molecular recognition of carbohydrates: A 3D view by using NMR. PURE APPL CHEM 2008. [DOI: 10.1351/pac200880081827] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This revision describes an up-to-date review of our efforts to investigate the interaction of carbohydrates with aromatic moieties at different levels of complexity. Protein-sugar interactions have been studied using NMR experiments on a variety of hevein/chitooligosaccharide systems. In addition, NMR and computational methods have also been used to evaluate the interaction of simple aromatic entities with simple monosaccharides. In between, the stacking features of aromatic-containing glycomolecules have also been described by using an analogous experimental-theoretical approach.
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88
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IR-Spectral Signatures of Aromatic–Sugar Complexes: Probing Carbohydrate–Protein Interactions. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200605116] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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89
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Screen J, Stanca-Kaposta EC, Gamblin DP, Liu B, Macleod NA, Snoek LC, Davis BG, Simons JP. IR-Spectral Signatures of Aromatic–Sugar Complexes: Probing Carbohydrate–Protein Interactions. Angew Chem Int Ed Engl 2007; 46:3644-8. [PMID: 17385782 DOI: 10.1002/anie.200605116] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- James Screen
- Department of Chemistry, University of Oxford, OX1 3QZ, UK
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90
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McFeeters RL, Xiong C, O'Keefe BR, Bokesch HR, McMahon JB, Ratner DM, Castelli R, Seeberger PH, Byrd RA. The novel fold of scytovirin reveals a new twist for antiviral entry inhibitors. J Mol Biol 2007; 369:451-61. [PMID: 17434526 PMCID: PMC2696897 DOI: 10.1016/j.jmb.2007.03.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 03/06/2007] [Accepted: 03/13/2007] [Indexed: 11/20/2022]
Abstract
The solution structure of the potent 95 residue anti-HIV protein scytovirin has been determined and two carbohydrate-binding sites have been identified. This unique protein, containing five structurally important disulfide bonds, demonstrates a novel fold with no elements of extended regular secondary structure. Scytovirin contains two 39 residue sequence repeats, differing in only three amino acid residues, and each repeat has primary sequence similarity to chitin binding proteins. Both sequence repeats form similarly structured domains, with the exception of one region. The result is two carbohydrate-binding sites with substantially different affinities. The unusual fold clusters aromatic residues in both sites, suggesting a binding mechanism similar to other known hevein-like carbohydrate-binding proteins but differing in carbohydrate specificity. Scytovirin, originally isolated from the cyanobacterium Scytonema varium, holds potential as an HIV entry inhibitor for both therapeutic and prophylactic anti-HIV applications. The high-resolution structural studies reported are an important initial step in unlocking the therapeutic potential of scytovirin.
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Affiliation(s)
- Robert. L. McFeeters
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Changyun Xiong
- Molecular Targets Development Program, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Barry R. O'Keefe
- Molecular Targets Development Program, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Heidi R. Bokesch
- Molecular Targets Development Program, National Cancer Institute, Frederick, MD, 21702-1201, USA
- SAIC-Frederick, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - James B. McMahon
- Molecular Targets Development Program, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Daniel M. Ratner
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA
| | | | - Peter H. Seeberger
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139 USA
| | - R. Andrew Byrd
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, 21702-1201, USA
- Author to whom correspondence should be sent
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91
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Terraneo G, Potenza D, Canales A, Jiménez-Barbero J, Baldridge KK, Bernardi A. A Simple Model System for the Study of Carbohydrate−Aromatic Interactions. J Am Chem Soc 2007; 129:2890-900. [PMID: 17309255 DOI: 10.1021/ja066633g] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular scaffold was identified which enables the establishment of intramolecular interactions between a monosaccharide and a nearby phenyl ring. A group of molecules containing four different monosaccharides (glucose, galactose, N-acetyl-glucosamine, and N-acetyl-galactosamine) was synthesized and used to investigate the extent and nature of this carbohydrate-arene interaction, as well as the effect on the overall 3D structure of the molecules involved. The sugar-aromatic distance was evaluated by rigorous NMR studies supported by molecular modeling and found to be constant throughout the series, independent of the nature of the sugar and of the conformational behavior of the fragment connecting the two elements. Ab initio calculations at the B3LYP/DZV(2d,p) level of theory enable the analysis of the electronic nature of the interaction. The study shows that, given the opportunity, persistent intramolecular aromatic-sugar interactions can be established and can significantly influence overall molecular shape and energetics. These results have important implications in the design of structural mimics of oligosaccharides.
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Affiliation(s)
- Giancarlo Terraneo
- Universita' di Milano, Dipartimento di Chimica Organica e Industriale e Centro di Eccellenza CISI, via Venezian 21, 20133 Milano, Italy
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92
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Kiehna SE, Laughrey ZR, Waters ML. Evaluation of a carbohydrate–π interaction in a peptide model system. Chem Commun (Camb) 2007:4026-8. [PMID: 17912404 DOI: 10.1039/b711431a] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A carbohydrate-pi interaction contributes -0.8 kcal mol(-1) to the stabilization of a beta-hairpin peptide.
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Affiliation(s)
- Sarah E Kiehna
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, NC 27599, USA
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93
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Stanca-Kaposta EC, Gamblin DP, Screen J, Liu B, Snoek LC, Davis BG, Simons JP. Carbohydrate molecular recognition: a spectroscopic investigation of carbohydrate–aromatic interactions. Phys Chem Chem Phys 2007; 9:4444-51. [PMID: 17690769 DOI: 10.1039/b704792d] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The physical basis of carbohydrate molecular recognition at aromatic protein binding sites is explored by creating molecular complexes between a series of selected monosaccharides and toluene (as a truncated model for phenylalanine). They are formed at low temperatures under molecular beam conditions, and detected and characterized through mass-selected, infrared ion depletion spectroscopy-a strategy which exploits the extraordinary sensitivity of their vibrational signatures to the local hydrogen-bonded environment of their OH groups. The trial set of carbohydrates, alpha- and beta-anomers of glucose, galactose and fucose, reflects ligand fragments in naturally occurring protein-carbohydrate complexes and also allows an investigation of the effect of systematic structural changes, including the shape and extent of 'apolar' patches on the pyranose ring, removal of the OH on the exocyclic hydroxymethyl group, and removal of the aglycon. Bound complexes invariably form, establishing the general existence of intrinsic intermolecular potential minima. In most of the cases explored, comparison between recorded and computed vibrational spectra of the bound and free carbohydrates in the absence of solvent water molecules reveal that dispersion forces involving CH-pi interactions, which promote little if any distortion of the bound carbohydrate, predominate although complexes bound through specific OH-pi hydrogen-bonded interactions have also been identified. Since the complexes form at low temperatures in the absence of water, entropic contributions associated with the reorganization of surrounding water molecules, the essence of the proposed 'hydrophobic interaction', cannot contribute and other modes of binding drive the recognition of sugars by aromatic residues. Excitingly, some of the proposed structures mirror those found in naturally occurring protein-carbohydrate binding sites.
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Affiliation(s)
- E Cristina Stanca-Kaposta
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, UK
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94
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Manikandan K, Bhardwaj A, Gupta N, Lokanath NK, Ghosh A, Reddy VS, Ramakumar S. Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions. Protein Sci 2006; 15:1951-60. [PMID: 16823036 PMCID: PMC2242578 DOI: 10.1110/ps.062220206] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Crystal structures are known for several glycosyl hydrolase family 10 (GH10) xylanases. However, none of them is from an alkalophilic organism that can grow in alkaline conditions. We have determined the crystal structures at 2.2 Angstroms of a GH10 extracellular endoxylanase (BSX) from an alkalophilic Bacillus sp. NG-27, for the native and the complex enzyme with xylosaccharides. The industrially important enzyme is optimally active and stable at 343 K and at a pH of 8.4. Comparison of the structure of BSX with those of other thermostable GH10 xylanases optimally active at acidic or close to neutral pH showed that the solvent-exposed acidic amino acids, Asp and Glu, are markedly enhanced in BSX, while solvent-exposed Asn was noticeably depleted. The BSX crystal structure when compared with putative three-dimensional homology models of other extracellular alkalophilic GH10 xylanases from alkalophilic organisms suggests that a protein surface rich in acidic residues may be an important feature common to these alkali thermostable enzymes. A comparison of the surface features of BSX and of halophilic proteins allowed us to predict the activity of BSX at high salt concentrations, which we verified through experiments. This offered us important lessons in the polyextremophilicity of proteins, where understanding the structural features of a protein stable in one set of extreme conditions provided clues about the activity of the protein in other extreme conditions. The work brings to the fore the role of the nature and composition of solvent-exposed residues in the adaptation of enzymes to polyextreme conditions, as in BSX.
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95
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Kawatkar SP, Kuntz DA, Woods RJ, Rose DR, Boons GJ. Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions. J Am Chem Soc 2006; 128:8310-9. [PMID: 16787095 PMCID: PMC2553320 DOI: 10.1021/ja061216p] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The X-ray crystal structures of mannose trimming enzyme drosophila Golgi alpha-mannosidase II (dGMII) complexed with the inhibitors mannostatin A (1) and an N-benzyl analogue (2) have been determined. Molecular dynamics simulations and NMR studies have shown that the five-membered ring of mannostatin A is rather flexible occupying pseudorotational itineraries between 2T3 and 5E, and 2T3 and 4E. In the bound state, mannostatin A adopts a 2T1 twist envelope conformation, which is not significantly populated in solution. Possible conformations of the mannosyl oxacarbenium ion and an enzyme-linked intermediate have been compared to the conformation of mannostatin A in the cocrystal structure with dGMII. It has been found that mannostatin A best mimics the covalent linked mannosyl intermediate, which adopts a 1S5 skew boat conformation. The thiomethyl group, which is critical for high affinity, superimposes with the C-6 hydroxyl of the covalent linked intermediate. This functionality is able to make a number of additional polar and nonpolar interactions increasing the affinity for dGMII. Furthermore, the X-ray structures show that the environment surrounding the thiomethyl group of 1 is remarkably similar to the arrangements around the methionine residues in the protein. Collectively, our studies contradict the long held view that potent inhibitors of glycosidases must mimic an oxacarbenium ion like transition state.
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Affiliation(s)
- Sameer P. Kawatkar
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602
| | - Douglas A Kuntz
- Ontario Cancer Institute, University of Toronto, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602
| | - David R. Rose
- Ontario Cancer Institute, University of Toronto, 101 College St., Toronto, Ontario, Canada M5G 1L7
- Department of Medical Biophysics, University of Toronto, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602
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96
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Yu F, Prestegard JH. Structural monitoring of oligosaccharides through 13C enrichment and NMR observation of acetyl groups. Biophys J 2006; 91:1952-9. [PMID: 16782783 PMCID: PMC1544292 DOI: 10.1529/biophysj.105.079913] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Structural characterization of biomolecules by NMR methods frequently requires the enrichment of magnetically active isotopes at particular molecular sites. Introduction is usually achieved biosynthetically through the use of bacterial cultures grown on isotopically enriched media, but for certain types of molecules-cell-surface carbohydrates of mammalian origin, for example-this is not practical. Here we explore a means of introducing 13C-enriched sites, postisolation in natural carbohydrate products, and illustrate an ability to acquire sufficient information to select appropriate conformational models from among energetically allowed sets. The application presented involves replacement of native N-acetyl groups with 13C-labeled acetyl groups in a simple disaccharide derivative, (GlcNAc)2-OBu, or O-butyl-chitobiose. The assignment of the two acetyl groups introduced is based on a novel combination of NMR and mass spectrometry data. Structural information is obtained from chemical shift anisotropy offsets of 13C carbonyl resonances and 13C-13C dipolar couplings between the labeled methyl and carbonyl carbons of the acetyl groups. Although the application is to a relatively simple system, it lays the groundwork for application to biologically important complex carbohydrate systems.
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Affiliation(s)
- Fei Yu
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
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97
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Jiménez-Barbero J, Javier Cañada F, Asensio JL, Aboitiz N, Vidal P, Canales A, Groves P, Gabius HJ, Siebert HC. Hevein Domains: An Attractive Model to Study Carbohydrate–Protein Interactions at Atomic Resolution. Adv Carbohydr Chem Biochem 2006; 60:303-54. [PMID: 16750446 DOI: 10.1016/s0065-2318(06)60007-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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