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Chaloupecká E, Kurfiřt M, Červenková Šťastná L, Karban J, Dračínský M. Exploring long-range fluorine-carbon J-coupling for conformational analysis of deoxyfluorinated disaccharides: A combined computational and NMR study. Bioorg Chem 2024; 147:107388. [PMID: 38678775 DOI: 10.1016/j.bioorg.2024.107388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
In this study, we investigated the potential of long-range fluorine-carbon J-coupling for determining the structures of deoxyfluorinated disaccharides. Three disaccharides, previously synthesized as potential galectin inhibitors, exhibited through-space fluorine-carbon J-couplings. In our independent conformational analysis of these disaccharide derivatives, we employed a combination of density functional theory (DFT) calculations and nuclear magnetic resonance (NMR) experiments. By comparing the calculated nuclear shieldings with the experimental carbon chemical shifts, we were able to identify the most probable conformers for each compound. A model comprising fluoromethane and methane molecules was used to study the relationship between molecular arrangements and intermolecular through-space J-coupling. Our study demonstrates the important effect of internuclear distance and molecular orientation on the magnitude of fluorine-carbon coupling. The experimental values for the fluorine-carbon through-space couplings (TSCs) of the disaccharides corresponded with values calculated for the most probable conformers identified by the conformational analysis. These results unlock the broader application of fluorine-carbon TSCs as powerful tools for conformational analysis of flexible molecules, offering valuable insights for future structural investigations.
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Affiliation(s)
- Ema Chaloupecká
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Martin Kurfiřt
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, 165 00 Prague 6, Czech Republic; University of Chemistry and Technology, Technická 3, 166 28 Prague 6, Czech Republic
| | - Lucie Červenková Šťastná
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, 165 00 Prague 6, Czech Republic
| | - Jindřich Karban
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, 165 00 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic.
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2
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Charvati E, Sun H. Potential Energy Surfaces Sampled in Cremer-Pople Coordinates and Represented by Common Force Field Functionals for Small Cyclic Molecules. J Phys Chem A 2023; 127:2646-2663. [PMID: 36893434 DOI: 10.1021/acs.jpca.3c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The complex conformations of the cyclic moieties impact the physical and chemical properties of molecules. In this work, we chose 22 molecules of four-, five-, and six-membered rings and performed a thorough conformational sampling using Cremer-Pople coordinates. With consideration of symmetries, we obtained a total of 1504 conformational structures for four-membered, 5576 for five-membered, and 13509 for six-membered rings. All well-known and many less well-known conformers for each molecule were identified. We represented the potential energy surfaces (PESs) by fitting the data to common analytical force field (FF) functional forms. We found that the general features of PESs can be described by the essential FF functional forms; however, the accuracy of representation can be improved remarkably by including the torsion-bond and torsion-angle coupling terms. The best fit yields R-squared (R2) values close to 1.0 and mean absolute errors in energy less than 0.3 kcal/mol.
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Affiliation(s)
- Evangelia Charvati
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai Sun
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Structure and Conformation Study of the O-Antigen from the Lipopolysaccharide of Cupriavidus Metallidurans CH34. POLYSACCHARIDES 2022. [DOI: 10.3390/polysaccharides3010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cupriavidus metallidurans is a Gram-negative bacterium that has attracted the attention of the scientific community since its discovery back in 1976. It was initially studied as a model organism for bioremediation processes due to its ability to survive in heavy metal-rich environments. However, in recent years, there is evidence that this bacterium can be a potential pathogen for humans. How C. metallidurans can survive in such different environments is unknown and prompted the following work. Its great adaptability could be explained by the structural and conformational studies of the O-antigen portion of the lipopolysaccharide, the main constituent of the outer membrane of Gram-negative bacteria, which is the one in direct contact with the external environment. Therefore, a combination of chemical and spectroscopic analyses was used to define the O-antigen structure, disclosing that it is a polysaccharide constituted of a linear tetrasaccharide repeating unit that does not resemble other structures already reported for bacteria: [4)-α-d-GalNAc-(1→3)-α-d-Qui2NAc4NHBA-(1→3)-α-l-Rha-(1→3)-α-l-Rha-(1→]. Interestingly, the molecular dynamics studies revealed that the three-dimensional structure of the O-antigen is highly flexible: it might adopt three different right-handed helix conformations described by a two, three, or four-fold symmetry. This conformational behavior could represent the reason behind the survival of C. metallidurans in different environments.
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4
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Xiang Y, Tang YH, Liu H, Lin G, Sun H. Predicting Single-Substance Phase Diagrams: A Kernel Approach on Graph Representations of Molecules. J Phys Chem A 2021; 125:4488-4497. [PMID: 33999627 DOI: 10.1021/acs.jpca.1c02391] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This work presents a Gaussian process regression (GPR) model on top of a novel graph representation of chemical molecules that predicts thermodynamic properties of pure substances in single, double, and triple phases. A transferable molecular graph representation is proposed as the input for a marginalized graph kernel, which is the major component of the covariance function in our GPR models. Radial basis function kernels of temperature and pressure are also incorporated into the covariance function when necessary. We predicted three types of representative properties of pure substances in single, double, and triple phases, i.e., critical temperature, vapor-liquid equilibrium (VLE) density, and pressure-temperature density. The accuracy of the models is nearly identical to the precision of the experimental measurements. Moreover, the reliability of our predictions can be quantified on a per-sample basis using the posterior uncertainty of the GPR model. We compare our model against Morgan fingerprints and a graph neural network to further demonstrate the advantage of the proposed method.
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Affiliation(s)
- Yan Xiang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu-Hang Tang
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hongyi Liu
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guang Lin
- Department of Mathematics & School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Huai Sun
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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5
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Marchetti R, Bedini E, Gully D, Lanzetta R, Giraud E, Molinaro A, Silipo A. Rhodopseudomonas palustris Strain CGA009 Produces an O-Antigen Built up by a C-4-Branched Monosaccharide: Structural and Conformational Studies. Org Lett 2018; 20:3656-3660. [PMID: 29874087 DOI: 10.1021/acs.orglett.8b01439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, the analysis of the peculiar homopolymeric O-chain, isolated from the lipopolysaccharide (LPS) of Rhodopseudomonas palustris strain CGA009, is reported. The O-chain is built up of a novel 4-C-branched sugar (12-deoxy-4- C-(d- altro-5,7,8,9-tetrahydroxyhexyl))-3- O-methyl-d-galactopyranose)) whose structure, absolute configuration, and conformational features were deduced by 2D NMR spectroscopy, optical rotation measurements, and molecular dynamics simulations.
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Affiliation(s)
- Roberta Marchetti
- Dipartimento di Scienze Chimiche , Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II , Via Cintia 4 , I-80126 Napoli , Italy
| | - Emiliano Bedini
- Dipartimento di Scienze Chimiche , Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II , Via Cintia 4 , I-80126 Napoli , Italy
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) , UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J - Campus de Baillarguet , Montpellier 34398 Cedex 5 , France
| | - Rosa Lanzetta
- Dipartimento di Scienze Chimiche , Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II , Via Cintia 4 , I-80126 Napoli , Italy
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) , UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J - Campus de Baillarguet , Montpellier 34398 Cedex 5 , France
| | - Antonio Molinaro
- 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
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6
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Lacetera A, Berbís MÁ, Nurisso A, Jiménez-Barbero J, Martín-Santamaría S. Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactions. COMPUTATIONAL TOOLS FOR CHEMICAL BIOLOGY 2017. [DOI: 10.1039/9781788010139-00145] [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
Molecular modelling provides a major impact in the field of glycosciences, helping in the characterisation of the molecular basis of the recognition between lectins from pathogens and human glycoconjugates, and in the design of glycocompounds with anti-infectious properties. The conformational properties of oligosaccharides are complex, and therefore, the simulation of these properties is a challenging task. Indeed, the development of suitable force fields is required for the proper simulation of important problems in glycobiology, such as the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics, including O-linkages in oligo- and polysaccharides, and N- and O-linkages in glycoproteins. The computational description of representative examples is discussed, herein, related to biologically active oligosaccharides and their interaction with lectins and other proteins, and the new routes open for the design of glycocompounds with promising biological activities.
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Affiliation(s)
- Alessandra Lacetera
- Center for Biological Research CIB-CSIC. Ramiro de Maeztu, 9 28040-Madrid Spain
| | - M. Álvaro Berbís
- Center for Biological Research CIB-CSIC. Ramiro de Maeztu, 9 28040-Madrid Spain
| | - Alessandra Nurisso
- School of Pharmaceutical Sciences University of Geneva, University of Lausanne, Rue Michel Servet 1 CH-1211 Geneva 4 Switzerland
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7
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Vidal P, Jiménez-Barbero J, Espinosa JF. Conformational flexibility around the Gal-β-(1 → 3)-Glc linkage: Experimental evidence for the existence of the anti-ψ conformation in aqueous solution. Carbohydr Res 2016; 433:36-40. [PMID: 27434833 DOI: 10.1016/j.carres.2016.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/24/2016] [Accepted: 06/26/2016] [Indexed: 10/21/2022]
Abstract
NOE-based analysis of the disaccharide β-Gal-(1 → 3)-β-Glc-OMe (1), especially a diagnostic Gal1-Glc4 NOE detected in a HSQC-NOESY spectrum, reveals the existence of the anti-ψ conformer in aqueous solution in addition to the major syn conformer. This result provides experimental proof of conformational flexibility around the aglyconic bond of β-(1 → 3) disaccharides, in contrast to previous studies that suggested that the flexibility around this linkage was restricted to the syn conformational region.
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Affiliation(s)
- Paloma Vidal
- Discovery Chemistry Research and Technologies, Centro de Investigación Lilly, Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | | | - Juan F Espinosa
- Discovery Chemistry Research and Technologies, Centro de Investigación Lilly, Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain.
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8
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De Felice A, Silipo A, Scherlach K, Ross C, Hertweck C, Molinaro A. Structural and Conformational Study of the O-Antigenic Portion of the Lipopolysaccharide Isolated fromBurkholderia gladiolipv.cocovenenans. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Structural and conformational study of the O-polysaccharide produced by the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris strain BisA53. Carbohydr Polym 2014; 114:384-391. [DOI: 10.1016/j.carbpol.2014.08.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 11/20/2022]
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10
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Canales Á, Mallagaray Á, Berbís MÁ, Navarro-Vázquez A, Domínguez G, Cañada FJ, André S, Gabius HJ, Pérez-Castells J, Jiménez-Barbero J. Lanthanide-Chelating Carbohydrate Conjugates Are Useful Tools To Characterize Carbohydrate Conformation in Solution and Sensitive Sensors to Detect Carbohydrate–Protein Interactions. J Am Chem Soc 2014; 136:8011-7. [DOI: 10.1021/ja502406x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ángeles Canales
- Department
of Química Orgánica I, Fac. C.C. Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n 28040, Madrid, Spain
| | - Álvaro Mallagaray
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - M. Álvaro Berbís
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Armando Navarro-Vázquez
- Department
of Química Orgánica, Universidade de Vigo, Campus Universitario
Vigo, 36310, Pontevedra, Spain
| | - Gema Domínguez
- Faculty
of De Farmacia, Department of Química, Universidad CEU San Pablo, Urb. Montepríncipe, ctra. Boadilla del Monte, 28668, Madrid, Spain
| | - F. Javier Cañada
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Sabine André
- Institute
of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians University, 80539, Munich, Germany
| | - Hans-Joachim Gabius
- Institute
of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians University, 80539, Munich, Germany
| | - Javier Pérez-Castells
- Faculty
of De Farmacia, Department of Química, Universidad CEU San Pablo, Urb. Montepríncipe, ctra. Boadilla del Monte, 28668, Madrid, Spain
| | - Jesús Jiménez-Barbero
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
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11
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Solís D, Bovin NV, Davis AP, Jiménez-Barbero J, Romero A, Roy R, Smetana K, Gabius HJ. A guide into glycosciences: How chemistry, biochemistry and biology cooperate to crack the sugar code. Biochim Biophys Acta Gen Subj 2014; 1850:186-235. [PMID: 24685397 DOI: 10.1016/j.bbagen.2014.03.016] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 01/17/2023]
Abstract
BACKGROUND The most demanding challenge in research on molecular aspects within the flow of biological information is posed by the complex carbohydrates (glycan part of cellular glycoconjugates). How the 'message' encoded in carbohydrate 'letters' is 'read' and 'translated' can only be unraveled by interdisciplinary efforts. SCOPE OF REVIEW This review provides a didactic step-by-step survey of the concept of the sugar code and the way strategic combination of experimental approaches characterizes structure-function relationships, with resources for teaching. MAJOR CONCLUSIONS The unsurpassed coding capacity of glycans is an ideal platform for generating a broad range of molecular 'messages'. Structural and functional analyses of complex carbohydrates have been made possible by advances in chemical synthesis, rendering production of oligosaccharides, glycoclusters and neoglycoconjugates possible. This availability facilitates to test the glycans as ligands for natural sugar receptors (lectins). Their interaction is a means to turn sugar-encoded information into cellular effects. Glycan/lectin structures and their spatial modes of presentation underlie the exquisite specificity of the endogenous lectins in counterreceptor selection, that is, to home in on certain cellular glycoproteins or glycolipids. GENERAL SIGNIFICANCE Understanding how sugar-encoded 'messages' are 'read' and 'translated' by lectins provides insights into fundamental mechanisms of life, with potential for medical applications.
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Affiliation(s)
- Dolores Solís
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 07110 Bunyola, Mallorca, Illes Baleares, Spain.
| | - Nicolai V Bovin
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho-Maklaya 16/10, 117871 GSP-7, V-437, Moscow, Russian Federation.
| | - Anthony P Davis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - Antonio Romero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - René Roy
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada.
| | - Karel Smetana
- Charles University, 1st Faculty of Medicine, Institute of Anatomy, U nemocnice 3, 128 00 Prague 2, Czech Republic.
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 München, Germany.
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12
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Hayafune M, Berisio R, Marchetti R, Silipo A, Kayama M, Desaki Y, Arima S, Squeglia F, Ruggiero A, Tokuyasu K, Molinaro A, Kaku H, Shibuya N. Chitin-induced activation of immune signaling by the rice receptor CEBiP relies on a unique sandwich-type dimerization. Proc Natl Acad Sci U S A 2014; 111:E404-13. [PMID: 24395781 PMCID: PMC3903257 DOI: 10.1073/pnas.1312099111] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Perception of microbe-associated molecular patterns (MAMPs) through pattern recognition receptors (PRRs) triggers various defense responses in plants. This MAMP-triggered immunity plays a major role in the plant resistance against various pathogens. To clarify the molecular basis of the specific recognition of chitin oligosaccharides by the rice PRR, CEBiP (chitin-elicitor binding protein), as well as the formation and activation of the receptor complex, biochemical, NMR spectroscopic, and computational studies were performed. Deletion and domain-swapping experiments showed that the central lysine motif in the ectodomain of CEBiP is essential for the binding of chitin oligosaccharides. Epitope mapping by NMR spectroscopy indicated the preferential binding of longer-chain chitin oligosaccharides, such as heptamer-octamer, to CEBiP, and also the importance of N-acetyl groups for the binding. Molecular modeling/docking studies clarified the molecular interaction between CEBiP and chitin oligosaccharides and indicated the importance of Ile122 in the central lysine motif region for ligand binding, a notion supported by site-directed mutagenesis. Based on these results, it was indicated that two CEBiP molecules simultaneously bind to one chitin oligosaccharide from the opposite side, resulting in the dimerization of CEBiP. The model was further supported by the observations that the addition of (GlcNAc)8 induced dimerization of the ectodomain of CEBiP in vitro, and the dimerization and (GlcNAc)8-induced reactive oxygen generation were also inhibited by a unique oligosaccharide, (GlcNβ1,4GlcNAc)4, which is supposed to have N-acetyl groups only on one side of the molecule. Based on these observations, we proposed a hypothetical model for the ligand-induced activation of a receptor complex, involving both CEBiP and Oryza sativa chitin-elicitor receptor kinase-1.
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Affiliation(s)
- Masahiro Hayafune
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, National Research Council, I-80134 Naples, Italy
| | - Roberta Marchetti
- Department of Chemical Sciences, Universita di Napoli Federico II, I-80126 Naples, Italy; and
| | - Alba Silipo
- Department of Chemical Sciences, Universita di Napoli Federico II, I-80126 Naples, Italy; and
| | - Miyu Kayama
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Yoshitake Desaki
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Sakiko Arima
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, National Research Council, I-80134 Naples, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, National Research Council, I-80134 Naples, Italy
| | - Ken Tokuyasu
- Food Resource Division, National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan
| | - Antonio Molinaro
- Department of Chemical Sciences, Universita di Napoli Federico II, I-80126 Naples, Italy; and
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
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13
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Abstract
Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).
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Affiliation(s)
- Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV - EHU), Apartado 644, 48940, Bilbao, Spain,
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14
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Li Y, Liu X, Chen D, Wei Z, Liu B. Predicting the preferred conformations of luteolin-4'-O-β-D-glucoside in gas phase: a comparison of two computational approaches. J Mol Model 2013; 19:3619-26. [PMID: 23748558 DOI: 10.1007/s00894-013-1894-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 05/19/2013] [Indexed: 10/26/2022]
Abstract
A tree-step computational approach has been applied to determine the lowest-energy conformers of luteolin-4'-O-β-D-glucoside (L4'G). Fifty-seven starting structures of the L4'G have been built, and then by performing with density functional theory (DFT) optimizations and second-order Møller-Plesset (MP2) calculations, the preferred conformations of L4'G are predicted. In order to test the accuracy of the computational approach, a hybrid Monte-Carlo multiple minimum (MCMM)/quantum mechanical (QM) approach is applied to determine the favorable conformers of L4'G. The alternative classification is employed to put similar conformations into the same catalogue according to the dihedral angles among the luteolin rings, glycosidic dihedral angles, and the orientations of hydroxyl and hydroxymethyl groups. The low-energy conformations are located after the optimizations at the HF/6-31G(d) and B3LYP/6-311+G(d) levels. Compared with the hybrid MCMM/QM approach, the tree-step computational approach not only remains accurate but also saves a lot of computing resources.
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Affiliation(s)
- Yongzhi Li
- Institute of Photo Biophysics, Physics and Electronics Department, Henan University, 475004, Kaifeng, China
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15
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Chen D, Yao Y, Wei Z, Zhang S, Tu P, Liu B, Dong M. Determining the structural preferences of dimannosides through the linkage constraint and hydrogen-bonded network. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Silipo A, Larsbrink J, Marchetti R, Lanzetta R, Brumer H, Molinaro A. NMR spectroscopic analysis reveals extensive binding interactions of complex xyloglucan oligosaccharides with the Cellvibrio japonicus glycoside hydrolase family 31 α-xylosidase. Chemistry 2012; 18:13395-404. [PMID: 22961810 DOI: 10.1002/chem.201200488] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 06/13/2012] [Indexed: 01/23/2023]
Abstract
The study of the interaction of glycoside hydrolases with their substrates is fundamental to diverse applications in medicine, food and feed production, and biomass-resource utilization. Recent molecular modeling of the α-xylosidase CjXyl31A from the soil saprophyte Cellvibrio japonicus, together with protein crystallography and enzyme-kinetic analysis, has suggested that an appended PA14 protein domain, unique among glycoside hydrolase family 31 members, may confer specificity for large oligosaccharide fragments of the ubiquitous plant polysaccharide xyloglucan (J. Larsbrink, A. Izumi, F.M. Ibatullin, A. Nakhai, H.J. Gilbert, G.J. Davies, H. Brumer, Biochem. J. 2011, 436, 567-580). In the present study, a combination of NMR spectroscopic techniques, including saturation transfer difference (STD) and transfer NOE (TR-NOE) spectroscopy, was used to reveal extensive interactions between CjXyl31A active-site variants and xyloglucan hexa- and heptasaccharides. The data specifically indicate that the enzyme recognizes the entire cello-tetraosyl backbone of the substrate and product in positive enzyme subsites and makes further significant interactions with internal pendant α-(1→6)-linked xylosyl units. As such, the present analysis provides an important rationalization of previous kinetic data on CjXyl31A and unique insight into the role of the PA14 domain, which was not otherwise obtainable by protein crystallography.
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Affiliation(s)
- Alba Silipo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli, Italy.
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Manzano VE, Uhrig ML, Varela O. Convenient synthesis of 4-thiolactose, 3,4-dithiolactose and related thiooligosaccharides and disulfides. Inhibitory activity of the glycomimetics against a β-galactosidase. Org Biomol Chem 2012; 10:8884-94. [DOI: 10.1039/c2ob26388b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Passos Ó, Fernandes PA, Ramos MJ. QM/MM Study of the Catalytic Mechanism of GalNAc Removal from GM2 Ganglioside Catalyzed by Human β-HexosaminidaseA. J Phys Chem B 2011; 115:14751-9. [DOI: 10.1021/jp205826n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Óscar Passos
- Requimte, Faculty of Sciences, Porto University, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal
| | | | - Maria João Ramos
- Requimte, Faculty of Sciences, Porto University, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal
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Conformational preferences in diglycosyl disulfides: NMR and molecular modeling studies. Carbohydr Res 2011; 346:2612-21. [DOI: 10.1016/j.carres.2011.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 07/05/2011] [Accepted: 07/12/2011] [Indexed: 11/20/2022]
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20
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Pincu M, Cocinero EJ, Mayorkas N, Brauer B, Davis BG, Gerber RB, Simons JP. Isotopic Hydration of Cellobiose: Vibrational Spectroscopy and Dynamical Simulations. J Phys Chem A 2011; 115:9498-509. [DOI: 10.1021/jp112109p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Madeleine Pincu
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Emilio J. Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, (UPV − EHU), Apartado 644, E-48940, Bilbao, Spain
| | - Nitzan Mayorkas
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Brina Brauer
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Benjamin G. Davis
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, U.K
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - John P. Simons
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, U.K
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Momany FA, Schnupf U. DFTMD studies of β-cellobiose: conformational preference using implicit solvent. Carbohydr Res 2011; 346:619-30. [PMID: 21333280 DOI: 10.1016/j.carres.2011.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 01/04/2011] [Accepted: 01/06/2011] [Indexed: 10/18/2022]
Abstract
Previous DFT in vacuo studies on the conformational preferences for cellobiose showed that upon optimization the φ(H)-anti conformations were of lower energy than the syn forms. Upon optimization using an implicit solvation method, COSMO, the syn or observed form was still not predicted to be of lower energy than the φ(H)-anti form, even though optimization after addition of several explicit water molecules did show a relative energy difference favoring the syn form. In order to examine the predictive ability of COSMO on this carbohydrate, constant energy dynamics, DFTMD, simulations were carried out on low energy syn and φ(H)-anti conformations with and without COSMO included during the dynamics. The resulting analysis confirmed that when COSMO is included in the dynamics, the syn conformations become energetically favored over the φ(H)-anti forms suggesting that both solvent and entropy play roles in dictating the solution conformation of cellobiose. Analysis of the dynamic runs includes distributions of selected dihedral angles versus time, conformational transitions, and populations of some quasi-planar, boat, skew forms during the simulations.
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Affiliation(s)
- F A Momany
- Plant Polymer Research, USDA, ARS, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, IL 61604, USA.
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22
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Silipo A, Molinaro A, Molteni M, Rossetti C, Parrilli M, Lanzetta R. Full Structural Characterization of an Extracellular Polysaccharide Produced by the Freshwater Cyanobacterium Oscillatoria planktothrix FP1. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000749] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Brás NF, Fernandes PA, Ramos MJ. QM/MM Studies on the β-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions. J Chem Theory Comput 2010; 6:421-33. [DOI: 10.1021/ct900530f] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Natércia F. Brás
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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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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Cocinero EJ, Gamblin DP, Davis BG, Simons JP. The building blocks of cellulose: the intrinsic conformational structures of cellobiose, its epimer, lactose, and their singly hydrated complexes. J Am Chem Soc 2009; 131:11117-23. [PMID: 19722675 DOI: 10.1021/ja903322w] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A combination of vibrational spectroscopy conducted under molecular beam conditions and quantum chemical calculation has established the intrinsic three-dimensional structures of the cellulose disaccharide and, focusing on the critical beta1,4-linkage at the nonreducing end of the growing cellulose polymer, its C-4' epimer. Left to their own devices they both adopt a cis (anti-phi/syn-psi) glycosidic configuration, supported in the epimer by strong, cooperative inter-ring hydrogen bonding. In the cellulose disaccharide, however, where the OH-4'(Glc) group is equatorial, the cooperativity is reduced and the corresponding inter-ring hydrogen bonding is relatively weak. The cis conformational preference is still retained in their singly hydrated complexes. In the cellulose disaccharide insertion of the water molecule at the favored binding site between OH-4' and the neighboring hydroxyl group OH-6' promotes a structural reorganization to create a configuration that parallels that of its unhydrated epimer and greatly strengthens the inter-ring hydrogen bonding. In the C-4' epimer, the axial orientation of OH-4' blocks this binding site and the bound water molecule simply adds on at the end of the (OH-O)(n) chain, which has a negligible effect on the (already strong) inter-ring bonding. The implications of these results are discussed with respect to the structure and insolubility of native cellulose polymers.
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Affiliation(s)
- Emilio J Cocinero
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
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Ieranò T, Silipo A, Cescutti P, Leone MR, Rizzo R, Lanzetta R, Parrilli M, Molinaro A. Structural Study and Conformational Behavior of the Two Different Lipopolysaccharide O-Antigens Produced by the Cystic Fibrosis PathogenBurkholderia multivorans. Chemistry 2009; 15:7156-66. [DOI: 10.1002/chem.200900647] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Santos JI, Carvalho de Souza A, Cañada FJ, Martín-Santamaría S, Kamerling JP, Jiménez-Barbero J. Assessing carbohydrate-carbohydrate interactions by NMR spectroscopy: the trisaccharide epitope from the marine sponge Microciona prolifera. Chembiochem 2009; 10:511-9. [PMID: 19123195 DOI: 10.1002/cbic.200800548] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
WEAK RECOGNITION PROCESSES: Weak calcium-mediated carbohydrate-carbohydrate interactions have been detected by DOSY and TRNOESY NMR methods by employing a gold glyconanoparticle as a multivalent system. In addition, 3D models of trisaccharide-Ca(II)-trisaccharide complexes based on results from molecular dynamics simulations are proposed. Diffusion-ordered NMR spectroscopy (DOSY-NMR) and TR-NOESY-NMR experiments are used to detect ligand binding to macromolecular receptors. These techniques have been applied to detect weak carbohydrate-carbohydrate self-recognition in solution, making use of sugar-decorated gold nanoparticles as the "macromolecule" and the same carbohydrate as the ligand. Changes in the diffusion coefficient of the free carbohydrate in the presence of the glyconanoparticle (only with Ca(II) ions in the sample solution), as well as changes in the sign of the sugar NOE peaks--positive for the free sugar (in the presence or absence of Ca(II)) and negative for the sugar only in the simultaneous presence of the glyconanoparticle and Ca(II) ions--have been taken as proof of weak Ca(II)-mediated carbohydrate-carbohydrate interactions in solution. Although different methods such as SPR, TEM, and AFM have been used in the past to detect carbohydrate-carbohydrate interactions with the aid of gold nanoparticles and gold selfassembled monolayers, they are restricted to high-affinity ranges. The methods used in this study allow expansion of the number of techniques to tackle this relevant biological problem, also for approaching ligand-receptor interactions below the high-affinity range. Additionally, 3D models of trisaccharide-Ca(II)-trisaccharide complexes based on results from molecular dynamics simulations are proposed.
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28
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Docking and molecular dynamics studies on the stereoselectivity in the enzymatic synthesis of carbohydrates. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0507-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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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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31
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Silipo A, Zhang Z, Cañada FJ, Molinaro A, Linhardt RJ, Jiménez-Barbero J. Conformational analysis of a dermatan sulfate-derived tetrasaccharide by NMR, molecular modeling, and residual dipolar couplings. Chembiochem 2008; 9:240-52. [PMID: 18072186 PMCID: PMC4135520 DOI: 10.1002/cbic.200700400] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Indexed: 11/08/2022]
Abstract
The solution conformation behavior of a dermatan-derived tetrasaccharide--Delta HexA-(1-->3)-GalNAc4S-beta-(1-->4)-IdoA-alpha-(1-->3)-red-GalNAc4S (S is a sulfate group)--has been explored by means of NMR spectroscopy, especially by NOE-based conformational analysis. The tetrasaccharide was present as four species, two of which are chemically different in the anomeric orientation of the reducing 2-deoxy-2-acetamido-galactose (red-GalNAc) residue, while the other two are the result of different conformations of the iduronic acid (IdoA) unit. The two alpha-beta-interconverting anomers were present in a 0.6:1 ratio. Ring conformations have been defined by analysis of (3)J(H,H) coupling constants and interresidual NOE contacts. Both 2-deoxy-2-acetamido-galactose (GalNAc) residues were found in the (4)C(1) chair conformation, the unsaturated uronic acid (Delta-Hex A) adopts a strongly predominant half-chair (1)H(2) conformation, while the IdoA residue exists either in the (1)C(4) chair or in the (2)S(0) skewed boat geometries, in a 4:1 ratio. There is a moderate flexibility of Phi and Psi torsions as suggested by nuclear Overhauser effects (NOEs), molecular modeling (MM), and molecular dynamics (MD) studies. This was further investigated by residual dipolar couplings (RDCs). One-bond C--H RDCs ((1)D(C,H)) and long-range H-H ((3)D(H,H)) RDCs were measured for the tetrasaccharide in a phage solution and interpreted in combination with restrained MD simulation. The RDC-derived data substantially confirmed the validity of the conformer distribution resulting from the NOE-derived simulations, but allowed an improved definition of the conformational behavior of the oligosaccharides in solution. In summary, the data show a moderate flexibility of the four tetrasaccharide species at the central glycosidic linkage. Differences in the shapes of species with the IdoA in skew and in chair conformations and in the distribution of the sulfate groups have also been highlighted.
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Affiliation(s)
- Alba Silipo
- Centro de Investigaciones Biològicas, CSIC, Ramiro de Maeztu 9,28040 Madrid (Spain)
- Dipartimento di Chimica Organica e Biochimica Università di Napoli “Federico II” Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli (Italy)
| | - Zhenqing Zhang
- Departments of Chemistry and Chemical Biology, Biology, and Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180 (USA)
| | - F. Javier Cañada
- Centro de Investigaciones Biològicas, CSIC, Ramiro de Maeztu 9,28040 Madrid (Spain)
| | - Antonio Molinaro
- Dipartimento di Chimica Organica e Biochimica Università di Napoli “Federico II” Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli (Italy)
| | - Robert J. Linhardt
- Departments of Chemistry and Chemical Biology, Biology, and Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180 (USA)
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Leone S, De Castro C, Parrilli M, Baldi F, Lanzetta R. Structure of the Iron-Binding Exopolysaccharide Produced Anaerobically by the Gram-Negative BacteriumKlebsiella oxytoca BAS-10. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700302] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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García-Aparicio V, Sollogoub M, Blériot Y, Colliou V, André S, Asensio JL, Cañada FJ, Gabius HJ, Sinaÿ P, Jiménez-Barbero J. The conformation of the C-glycosyl analogue of N-acetyl-lactosamine in the free state and bound to a toxic plant agglutinin and human adhesion/growth-regulatory galectin-1. Carbohydr Res 2007; 342:1918-28. [PMID: 17408600 DOI: 10.1016/j.carres.2007.02.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 02/19/2007] [Accepted: 02/21/2007] [Indexed: 11/21/2022]
Abstract
The conformational behavior of the C-glycoside analogue of N-acetyl-lactosamine, beta-C-Gal-(1-->4)-beta-GlcNAc-OMe, 1, has been studied using a combination of molecular mechanics calculations and NMR spectroscopy (J and NOE data). It is shown that the C-disaccharide populates three distinctive conformational families in solution, the major one being the anti-psi conformation. Of note, this conformation is only marginally populated for the O-disaccharide. Due to its conspicuous role in the regulation of adhesion, growth and tissue invasion of tumors and its avid binding to N-acetyl-lactosamine human, galectin-1 was tested as a receptor. This endogenous lectin recognizes a local minimum of 1, the syn-PhiPsi conformer, and thus a conformational selection process is correlated with the molecular recognition event.
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Affiliation(s)
- Víctor García-Aparicio
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS 8642, 24, rue Lhomond, 75231 Paris Cedex 05, France
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Corzana F, Cuesta I, Freire F, Revuelta J, Torrado M, Bastida A, Jiménez-Barbero J, Asensio JL. The Pattern of Distribution of Amino Groups Modulates the Structure and Dynamics of Natural Aminoglycosides: Implications for RNA Recognition. J Am Chem Soc 2007; 129:2849-65. [PMID: 17298063 DOI: 10.1021/ja066348x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aminoglycosides are clinically relevant antibiotics that participate in a large variety of molecular recognition processes involving different RNA and protein receptors. The 3-D structures of these policationic oligosaccharides play a key role in RNA binding and therefore determine their biological activity. Herein, we show that the particular NH2/NH3(+)/OH distribution within the antibiotic scaffold modulates the oligosaccharide conformation and flexibility. In particular, those polar groups flanking the glycosidic linkages have a significant influence on the antibiotic structure. A careful NMR/theoretical analysis of different natural aminoglycosides, their fragments, and synthetic derivatives proves that both hydrogen bonding and charge-charge repulsive interactions are at the origin of this effect. Current strategies to obtain new aminoglycoside derivatives are mainly focused on the optimization of the direct ligand/receptor contacts. Our results strongly suggest that the particular location of the NH2/NH3(+)/OH groups within the antibiotics can also modulate their RNA binding properties by affecting the conformational preferences and inherent flexibility of these drugs. This fact should also be carefully considered in the design of new antibiotics with improved activity.
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Affiliation(s)
- Francisco Corzana
- Contribution from the Instituto de Química OrgAnica General and Centro de Investigaciones Biológicas (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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Mari S, Cañada FJ, Jiménez-Barbero J, Bernardi A, Marcou G, Motto I, Velter I, Nicotra F, La Ferla B. Synthesis and Conformational Analysis of Galactose-Derived Bicyclic Scaffolds. European J Org Chem 2006. [DOI: 10.1002/ejoc.200501012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Corsaro MM, De Castro C, Naldi T, Parrilli M, Tomás JM, Regué M. 1H and 13C NMR characterization and secondary structure of the K2 polysaccharide of Klebsiella pneumoniae strain 52145. Carbohydr Res 2005; 340:2212-7. [PMID: 16054607 DOI: 10.1016/j.carres.2005.07.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Revised: 07/11/2005] [Accepted: 07/12/2005] [Indexed: 11/27/2022]
Abstract
The complete (1)H and (13)C NMR characterization of the tetrasaccharide repeating unit from the K2 polysaccharide of Klebsiella pneumoniae strain 52145 is reported. [chemical structure] In addition a model for its secondary structure was suggested on the basis of dynamic and molecular calculations.
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Affiliation(s)
- Maria Michela Corsaro
- Dipartimento di Chimica Organica e Biochimica Università Federico II di Napoli, Italy.
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Simons JP, Jockusch RA, ÇarÇabal P, Hünig I, Kroemer RT, Macleod NA, Snoek LC. Sugars in the gas phase. Spectroscopy, conformation, hydration, co-operativity and selectivity. INT REV PHYS CHEM 2005. [DOI: 10.1080/01442350500415107] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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Martín-Pastor M, Canales A, Corzana F, Asensio JL, Jiménez-Barbero J. Limited Flexibility of Lactose Detected from Residual Dipolar Couplings Using Molecular Dynamics Simulations and Steric Alignment Methods. J Am Chem Soc 2005; 127:3589-95. [PMID: 15755180 DOI: 10.1021/ja043445m] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conformational flexibility of lactose in solution has been investigated by residual dipolar couplings (RDCs). One-bond carbon-proton and proton-proton coupling constants have been measured in two oriented media and interpreted in combination with molecular dynamics simulations (MD). Two different approaches, known as PALES (Zweckstetter et al., J. Am. Chem. Soc. 2000, 122, 3791-3792) and TRAMITE (Azurmendi et al., J. Am. Chem. Soc. 2002, 124, 2426-2427), have been used to determine the alignment tensor from a shape-induced alignment model with the oriented medium. The steric alignment of the structures from several MD trajectories has provided ensemble averaged RDCs that have been compared with the experimental ones. The obtained results reveal the almost exclusive presence of a major low energy region defined as syn-phi/syn-psi (> 97%), for which sampling occurs in a dynamic manner. This result satisfactorily agrees with that determined by standard NOE-based methods.
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The conformational behaviour of α,β-trehalose-like disaccharides and their C-glycosyl, imino-C-glycosyl and carbagalactose analogues depends on the chemical nature of the modification: an NMR investigation. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2004.11.072] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Jockusch RA, Kroemer RT, Talbot FO, Snoek LC, Carçabal P, Simons JP, Havenith M, Bakker JM, Compagnon I, Meijer G, von Helden G. Probing the Glycosidic Linkage: UV and IR Ion-Dip Spectroscopy of a Lactoside. J Am Chem Soc 2004; 126:5709-14. [PMID: 15125663 DOI: 10.1021/ja031679k] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The beta(1-->4) glycosidic linkage found in lactose is a prevalent structural motif in many carbohydrates and glycoconjugates. Using UV and IR ion-dip spectroscopies to probe benzyl lactoside isolated in the gas phase, we find that the disaccharide unit adopts only a single, rigid structure. Its fully resolved infrared ion-dip spectrum is in excellent agreement with that of the global minimum structure computed ab initio. This has glycosidic torsion angles of phi(H) (H1-C1-O-C4') approximately 180 degrees and psi(H) (C1-O-C4'-H4') approximately 0 degrees which correspond to a rotation of approximately 150 degrees about the glycosidic bond compared to the accepted solution-phase conformation. We discuss the biological implications of this discovery and the generality of the strategies employed in making it.
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Affiliation(s)
- Rebecca A Jockusch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, Oxford OX1 3QZ, United Kingdom
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Siebert HC, Jiménez-Barbero J, André S, Kaltner H, Gabius HJ. Describing topology of bound ligand by transferred nuclear Overhauser effect spectroscopy and molecular modeling. Methods Enzymol 2003; 362:417-34. [PMID: 12968380 DOI: 10.1016/s0076-6879(03)01029-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Hans-Christian Siebert
- Institute of Physiological Chemistry, Ludwig-Maximilians University, Veterinarstrasse 13, Munich D-80539, Germany
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Watts J, Jiménez-Barbero J, Poveda A, Grindley TB. Control of disaccharide conformation by π-stacking. CAN J CHEM 2003. [DOI: 10.1139/v03-062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The conformations of a series of derivatives of the disaccharide α-L-fucopyranosyl-(1[Formula: see text]3)-2-acetamido-2-deoxy-D-glucopyranoside, part of the Lex determinant, were studied by molecular modelling using the MM3* forcefield and by 1H NMR spectroscopy. Unusually shielded O-benzyl protons were observed in the 1H NMR spectrum of phenyl 2,3,4-tri-O-benzyl-α-L-fucopyranosyl-(1[Formula: see text]3)-2-deoxy-2-phthalimido-1-thio-α-D-glucopyranoside and assigned to the 2-O-benzyl group. This observation was explained by a shift in the population of the conformational mixture present about the glycosidic linkage from the positive Ψ region in the unsubstituted disaccharide to the negative Ψ region induced by π-stacking between the phthalimide and the 2-O-benzyl phenyl ring. The experimental nuclear Overhauser enhancements confirm the accuracy of the calculations.Key words: disaccharide, conformation, π-stacking, Lex determinant, NOE measurements, MM3 calculations.
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Strati GL, Willett JL, Momany FA. Ab initio computational study of beta-cellobiose conformers using B3LYP/6-311++G**. Carbohydr Res 2002; 337:1833-49. [PMID: 12431885 DOI: 10.1016/s0008-6215(02)00267-7] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The molecular structure of 27 conformers of beta-cellobiose were studied in vacuo through gradient geometry optimization using B3LYP density functionals and the 6-311++G** basis set. The conformationally dependent geometry changes and energies were explored as well as the hydrogen-bonding network. The lowest electronic energy structures found were not those suggested from available crystallographic and NMR solution data, where the glycosidic dihedral angles fall in the region (phi, psi) approximately (40 degrees, -20 degrees ). Rather, 'flipped' conformations in which the dihedral angles are in the range (phi, psi) approximately (180 degrees, 0 degrees ) are energetically more stable by approximately 2.5 kcal/mol over the 'experimentally accepted' structure. Further, when the vibrational free energy, deltaG, obtained from the calculated frequencies, is compared throughout the series, structures with (phi, psi) in the experimentally observed range still have higher free energy ( approximately 2.0 kcal/mol) than 'flipped' forms. The range of bridging dihedral angles of the 'normal' conformers, resulting from the variance in the phi dihedral is larger than that found in the 'flipped' forms. Due to this large flat energy surface for the normal conformations, we surmise that the summation of populations of these conformations will favor the 'normal' conformations, although evidence suggests that polar solvent effects may play the dominant role in providing stability for the 'normal' forms. Even though some empirical studies previously found the 'flipped' conformations to be lowest in energy, these studies have been generally discredited because they were in disagreement with experimental results. Most of the DFT/ab initio conformations reported here have not been reported previously in the ab initio literature, in part because the use of less rigorous theoretical methods, i.e. smaller basis sets, have given results in general agreement with experimental data, that is, they energetically favored the 'normal' forms. These are the first DFT/ab initio calculations at this level of theory, apparently because of the length and difficulty of carrying out optimizations at these high levels.
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Affiliation(s)
- Gina L Strati
- Plant Polymer Research, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University St., Peoria, IL 61604, USA
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Jimenez-Barbero J, Castro C, Evidente A, Molinaro A, Parrilli M, Surico G. Structural Determination of the O-Specific Chain of the Lipopolysaccharide fromPseudomonas cichorii. European J Org Chem 2002. [DOI: 10.1002/1099-0690(200206)2002:11<1770::aid-ejoc1770>3.0.co;2-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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García-Herrero A, Montero E, Muñoz JL, Espinosa JF, Vián A, García JL, Asensio JL, Cañada FJ, Jiménez-Barbero J. Conformational selection of glycomimetics at enzyme catalytic sites: experimental demonstration of the binding of distinct high-energy distorted conformations of C-, S-, and O-glycosides by E. Coli beta-galactosidases. J Am Chem Soc 2002; 124:4804-10. [PMID: 11971730 DOI: 10.1021/ja0122445] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We show that the conformational features of the molecular complexes of E. coli beta-galactosidase and O-glycosides may differ from those formed with closely related compounds in their chemical nature, such as C- and S-glycosyl analogues. In the particular case presented here, NMR and ab initio quantum mechanical results show that the 3D-shapes of the ligand/inhibitor within the enzyme binding site depend on the chemical nature of the compounds. In fact, they depend on the relative size of the stereoelectronic barriers for chair deformation or for rotation around Phi glycosidic linkage.
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Affiliation(s)
- Alicia García-Herrero
- Department Bioorganic Chemistry, Instituto Quimica Organica, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
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Alonso-Plaza JM, Canales MA, Jiménez M, Roldán JL, García-Herrero A, Iturrino L, Asensio JL, Cañada FJ, Romero A, Siebert HC, André S, Solís D, Gabius HJ, Jiménez-Barbero J. NMR investigations of protein-carbohydrate interactions: insights into the topology of the bound conformation of a lactose isomer and beta-galactosyl xyloses to mistletoe lectin and galectin-1. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1568:225-36. [PMID: 11786229 DOI: 10.1016/s0304-4165(01)00224-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A hallmark of oligosaccharides is their often limited spatial flexibility, allowing them to access a distinct set of conformers in solution. Viewing each individual or even the complete ensemble of conformations as potential binding partner(s) for lectins in protein-carbohydrate interactions, it is pertinent to address the question on the characteristics of bound state conformation(s) in solution. Also, it is possible that entering the lectin's binding site distorts the low-energy topology of a glycosidic linkage. As a step to delineate the strategy of ligand selection for galactosides, a common physiological docking point, we have performed a NMR study on two non-homologous lectins showing identical monosaccharide specificity. Thus, the conformation of lactose analogues bound to bovine heart galectin-1 and to mistletoe lectin in solution has been determined by transferred nuclear Overhauser effect measurements. It is demonstrated that the lectins select the syn conformation of lactose and various structural analogues (Galbeta(1-->4)Xyl, Galbeta(1-->3)Xyl, Galbeta(1-->2)Xyl, and Galbeta(1-->3)Glc) from the ensemble of presented conformations. No evidence for conformational distortion was obtained. Docking of the analogues to the modeled binding sites furnishes explanations, in structural terms, for exclusive recognition of the syn conformer despite the non-homologous design of the binding sites.
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Höög C, Landersjö C, Widmalm G. Oligosaccharides display both rigidity and high flexibility in water as determined by 13C NMR relaxation and 1H,1H NOE spectroscopy: evidence of anti-phi and anti-psi torsions in the same glycosidic linkage. Chemistry 2001; 7:3069-77. [PMID: 11495434 DOI: 10.1002/1521-3765(20010716)7:14<3069::aid-chem3069>3.0.co;2-a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The trisaccharide beta-D-Glcp-(1-->2)-beta-D-Glcp-(1-->3)-alpha-D-Glcp-OMe has been investigated by molecular dynamics (MD) simulations and NMR experiments in water. 13C spin-lattice (T1) and spin-spin (T2) relaxation times, together with 1H,13C NOE data were measured at two magnetic field strengths (9.4 and 14.1 T) in a 277 K D2O solution. Relaxation data interpreted by means of the model-free formalism revealed a rigid (S2 approximately 0.9) oligosaccharide tumbling in solution. 1H,1H Cross-relaxation rates were determined at 600 MHz by 1D DPFGSE NOESY and T-ROESY experiments, which provided high quality data and subsequently proton-proton distances within the trisaccharide. The presence of anti conformers at both torsions of a glycosidic linkage is demonstrated for the first time. MD simulations were carried out to facilitate analysis of the NOE data. In total, 15 simulations-starting from five different conformational states--were performed, with production runs of up to 10 ns, resulting in 83 ns of oligosaccharide dynamics in water. anti Conformers were populated to different degrees in the simulations, especially at the phi2 torsion angle. By combining the results from the NOE experiments and the MD simulations, the anti conformers at the (1-->2)-linkage were quantified as 7% anti-phi2 and 2% anti-psi2, revealing a highly flexible trisaccharide in which large conformational changes occur. From the MD simulations, interresidue hydrogen bonding, from HO2" to O2 or O3, was significantly populated (approximately 40%) in both of the anti conformational states. The contentious issue over rigidity versus flexibility in oligosaccharides has thus been thoroughly examined, showing that the dynamics should be taken into account for a relevant description of the molecular system.
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Affiliation(s)
- C Höög
- Department of Organic Chemistry, Arrhenius Laboratory Stockholm University, Sweden
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Jiménez-Barbero J, Espinosa JF, Asensio JL, Cañada FJ, Poveda A. The conformation of C-glycosyl compounds. Adv Carbohydr Chem Biochem 2001; 56:235-84. [PMID: 11039113 DOI: 10.1016/s0065-2318(01)56006-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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Montero E, García-Herrero A, Asensio J, Hirai K, Ogawa S, Santoyo-González F, Cañada F, Jiménez-Barbero J. The Conformational Behaviour of Non-Hydrolizable Lactose Analogues: The Thioglycoside, Carbaglycoside, and Carba-Iminoglycoside Cases. European J Org Chem 2000. [DOI: 10.1002/(sici)1099-0690(200005)2000:10<1945::aid-ejoc1945>3.0.co;2-g] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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50
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Martin-Pastor M, Bush CA. The use of NMR residual dipolar couplings in aqueous dilute liquid crystalline medium for conformational studies of complex oligosaccharides. Carbohydr Res 2000; 323:147-55. [PMID: 10782296 DOI: 10.1016/s0008-6215(99)00237-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
C-H dipolar coupling values were measured for a natural-abundance sample of the pentasaccharide beta-D-Galp-(1-->3)-[alpha-L-Fucp-(1-->4)]-beta-D-GlcNAcp-(1 -->3)-beta-D- Galp-(1-->4)-beta-D-Glcp ('lacto-N-fucopentaose 2') (LNF-2), in a 7.5% solution of dimyristoyl phosphatidylcholine-dihexanoyl phosphatidylcholine bicelle liquid crystals oriented in the NMR magnetic field. Interpretation of the dipolar coupling data and NOE confirms the conformational model for the Lewis(a) trisaccharide epitope based on NOE, molecular dynamics simulations, and scalar coupling data and provided new structural information for the remaining residues of the pentasaccharide. Since residual dipolar coupling provides information on long-range order, it is a valuable complement to other types of NMR data such as NOE and scalar coupling for exploring conformations of complex oligosaccharides.
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Affiliation(s)
- M Martin-Pastor
- Department of Chemistry and Biochemistry, University of Maryland-Baltimore County 21250, USA
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