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Stortz CA, Sarotti AM. Exhaustive exploration of the conformational landscape of mono- and disubstituted five-membered rings by DFT and MP2 calculations. RSC Adv 2019; 9:24134-24145. [PMID: 35527879 PMCID: PMC9069843 DOI: 10.1039/c9ra03524a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/18/2019] [Indexed: 11/21/2022] Open
Abstract
The conformational landscape of 22 different non, mono-, and disubstituted compounds with a five-membered ring was thoroughly explored by ab initio (MP2) and DFT (B3LYP and M06-2X) methods with the 6-311+G** basis set. Our results showed that the conformational preference of these compounds was governed mainly by the specific characteristics of the substituents, with a minor influence of the level of theory employed. After a detailed analysis of the computational data, we found an interesting preference of the electronegative substituents to take pseudo-axial positions, whereas alkyl groups preferred adopting the pseudo-equatorial locations. Such preferences were pronounced with MP2 and M06-2X and underestimated by B3LYP. Despite each level of theory affording different landscapes in many cases, as a general trend, we noticed that M06-2X afforded much higher correlation with the MP2 results than B3LYP. The conformational landscape of 22 different non, mono-, and disubstituted compounds with a five-membered ring was thoroughly explored by ab initio (MP2) and DFT (B3LYP and M06-2X) methods with the 6-311+G** basis set.![]()
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Affiliation(s)
- Carlos A. Stortz
- Universidad de Buenos Aires
- Facultad de Ciencias Exactas
- Departamento de Química Orgánica
- Centro de Investigaciones en Hidratos de Carbono (CIHIDECAR)
- 1428 Buenos Aires
| | - Ariel M. Sarotti
- Instituto de Química Rosario (CONICET)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- Rosario 2000
- Argentina
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He S, Zhao H, Guo X, Xu X, Zhou X, Liu J, Xing Z, Ye L, Jiang L, Chen Q, He Y. The Readout of Base-Pair Information in Adenine-Thymine α-D-Arabinonucleosides. Chemistry 2014; 20:15473-81. [DOI: 10.1002/chem.201403998] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Indexed: 11/10/2022]
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Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
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Pol-Fachin L, Verli H. Structural glycobiology of the major allergen of Artemisia vulgaris pollen, Art v 1: O-glycosylation influence on the protein dynamics and allergenicity. Glycobiology 2012; 22:817-25. [DOI: 10.1093/glycob/cws056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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X-ray crystal structures and conformational analysis of cyclic acetals derived from tartaric acid and rigid spacer units. Struct Chem 2012. [DOI: 10.1007/s11224-011-9934-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Goddard-Borger ED, Carapito R, Jeltsch JM, Phalip V, Stick RV, Varrot A. α-l-Arabinofuranosylated pyrrolidines as arabinanase inhibitors. Chem Commun (Camb) 2011; 47:9684-6. [DOI: 10.1039/c1cc13675e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Taha HA, Roy PN, Lowary TL. Theoretical Investigations on the Conformation of the β-d-Arabinofuranoside Ring. J Chem Theory Comput 2010; 7:420-32. [DOI: 10.1021/ct100450s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hashem A. Taha
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2 and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Pierre-Nicholas Roy
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2 and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Todd L. Lowary
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2 and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
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Rhoad JS, Cagg BA, Carver PW. Scanning the Potential Energy Surface of Furanosyl Oxocarbenium Ions: Models for Reactive Intermediates in Glycosylation Reactions. J Phys Chem A 2010; 114:5180-6. [DOI: 10.1021/jp9100448] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jonathan S. Rhoad
- Department of Chemistry, Missouri Western State University, 4525 Downs Drive, St. Joseph, Missouri 64507
| | - Brett A. Cagg
- Department of Chemistry, Missouri Western State University, 4525 Downs Drive, St. Joseph, Missouri 64507
| | - Patrick W. Carver
- Department of Chemistry, Missouri Western State University, 4525 Downs Drive, St. Joseph, Missouri 64507
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Taha HA, Castillo N, Sears DN, Wasylishen RE, Lowary TL, Roy PN. Conformational Analysis of Arabinofuranosides: Prediction of 3JH,H Using MD Simulations with DFT-Derived Spin−Spin Coupling Profiles. J Chem Theory Comput 2009; 6:212-22. [DOI: 10.1021/ct900477x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Hashem A. Taha
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Norberto Castillo
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Devin N. Sears
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Roderick E. Wasylishen
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Todd L. Lowary
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Pierre-Nicholas Roy
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
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Carapito R, Imberty A, Jeltsch JM, Byrns SC, Tam PH, Lowary TL, Varrot A, Phalip V. Molecular basis of arabinobio-hydrolase activity in phytopathogenic fungi: crystal structure and catalytic mechanism of Fusarium graminearum GH93 exo-alpha-L-arabinanase. J Biol Chem 2009; 284:12285-96. [PMID: 19269961 PMCID: PMC2673297 DOI: 10.1074/jbc.m900439200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 02/19/2009] [Indexed: 11/06/2022] Open
Abstract
The phytopathogenic fungus Fusarium graminearum secretes a very diverse pool of glycoside hydrolases (GHs) aimed at degrading plant cell walls. alpha-l-Arabinanases are essential GHs participating in the complete hydrolysis of hemicellulose, a natural resource for various industrial processes, such as bioethanol or pharmaceuticals production. Arb93A, the exo-1,5-alpha-l-arabinanase of F. graminearum encoded by the gene fg03054.1, belongs to the GH93 family, for which no structural data exists. The enzyme is highly active (1065 units/mg) and displays a strict substrate specificity for linear alpha-1,5-l-arabinan. Biochemical assays and NMR experiments demonstrated that the enzyme releases alpha-1,5-l-arabinobiose from the nonreducing end of the polysaccharide. We determined the crystal structure of the native enzyme and its complex with alpha-1,5-l-arabinobiose, a degradation product of alpha-Me-1,5-l-arabinotetraose, at 1.85 and 2.05A resolution, respectively. Arb93A is a monomeric enzyme, which presents the six-bladed beta-propeller fold characteristic of sialidases of clan GHE. The configuration of the bound arabinobiose is consistent with the retaining mechanism proposed for the GH93 family. Catalytic residues were proposed from the structural analysis, and site-directed mutagenesis was used to validate their role. They are significantly different from those observed for GHE sialidases.
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Affiliation(s)
- Raphaël Carapito
- UMR 7175, Ecole Supérieure de Biotechnologie de Strasbourg, Université de Strasbourg-CNRS, Boulevard Sébastien Brandt, BP 10413, 67412 Illkirch-Graffenstaden, France
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Sánchez-Medina I, Frank M, von der Lieth CW, Kamerling JP. Conformational analysis of the neutral exopolysaccharide produced by Lactobacillus delbrueckii ssp. bulgaricus LBB.B26. Org Biomol Chem 2008; 7:280-7. [PMID: 19109672 DOI: 10.1039/b810468a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational properties of the neutral exopolysaccharide produced by Lactobacillus delbrueckii ssp. bulgaricus LBB.B26 have been studied by NMR measurements and molecular modelling. The exopolysaccharide, with an average molecular mass of 1.3 x 10(6) Da, was previously determined to consist of pentasaccharide repeating units with the following structure: -->3)-beta-D-Galp-(1-->4)-beta-D-Glcp-(1-->3)-beta-d-Galf-(1-->3)-[alpha-D-Glcp-(1-->6)-]alpha-D-Galp-(1-->. Adiabatic maps were generated for each of the disaccharide fragments in the repeating unit. In addition, free energy maps calculated from MD simulations were obtained for each of the glycosidic linkages in an extended repeating unit and the influence of the Galf residue on the conformational properties of the repeating unit was investigated. The values of the global energy minima provided by the free energy maps were used to build a polymer chain. The polysaccharide was shown to have a random coil structure, without stable extended helical motifs.
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Affiliation(s)
- Inmaculada Sánchez-Medina
- Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands
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Singh BK, Yadav AK, Kumar B, Gaikwad A, Sinha SK, Chaturvedi V, Tripathi RP. Preparation and reactions of sugar azides with alkynes: synthesis of sugar triazoles as antitubercular agents. Carbohydr Res 2008; 343:1153-62. [DOI: 10.1016/j.carres.2008.02.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 02/13/2008] [Accepted: 02/14/2008] [Indexed: 11/30/2022]
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Ding X, Kong F. Glycosylation with 1,2-Anhydromannofuranose Benzyl Ether as the Glycosyl Donor: A Comparison Between Sugar Pyranose and Furanose Acceptors for their Primary Hydroxy Activity. J Carbohydr Chem 2008. [DOI: 10.1080/07328309908544035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Xianglan Ding
- a Research Center for Eco-Environmental Science, Academia Sinica , P.O.Box 2871, Beijing 100085, China
- b Research Center for Eco-Environmental Science, Academia Sinica , P.O.Box 2871, Beijing 100085, China
| | - Fanzuo Kong
- a Research Center for Eco-Environmental Science, Academia Sinica , P.O.Box 2871, Beijing 100085, China
- b Research Center for Eco-Environmental Science, Academia Sinica , P.O.Box 2871, Beijing 100085, China
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Dowd MK, French AD, Reilly PJ. MM3 Modeling of Ribose and 2-Deoxyribose Ring Puckering. J Carbohydr Chem 2008. [DOI: 10.1080/07328300008544137] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Michael K. Dowd
- a U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- b U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- c Department of Chemical Engineering , Iowa State University , Ames, IA 50011, USA
| | - Alfred D. French
- a U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- b U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- c Department of Chemical Engineering , Iowa State University , Ames, IA 50011, USA
| | - Peter J. Reilly
- a U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- b U. S. Department of Agriculture , Southern Regional Research Center , P. O. Box 19687, New Orleans, LA 70179, USA
- c Department of Chemical Engineering , Iowa State University , Ames, IA 50011, USA
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Seo M, Castillo N, Ganzynkowicz R, Daniels CR, Woods RJ, Lowary TL, Roy PN. Approach for the Simulation and Modeling of Flexible Rings: Application to the α-D-Arabinofuranoside Ring, a Key Constituent of Polysaccharides from Mycobacterium tuberculosis.. J Chem Theory Comput 2008; 4:184-191. [PMID: 25339852 PMCID: PMC4203666 DOI: 10.1021/ct700284r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A number of lower organisms (bacteria, fungi, and parasites) produce glycoconjugates that contain furanose rings. Of particular interest to our group are cell wall polysaccharides from mycobacteria, including the human pathogen, Mycobacterium tuberculosis, which contain a large number of arabinofuranose resides. As part of a larger project on the conformational analysis of these molecules, we report here molecular dynamics simulations on methyl α-D-arabinofuranoside (1) using the AMBER force field and the GLYCAM carbohydrate parameter set. We initially studied the ability of this method to predict rotamer populations about the hydroxymethyl group (C4-C5) bond. Importantly, we show that simulation times of up to 200 ns are required in order to obtain convergence of the rotamer populations for this ring system. We also propose a new charge derivation approach that accounts for the flexibility of the furanoside ring by taking an average of the charges from a large number of conformers across the psuedorotational itinerary. The approach yields rotamer populations that are in good agreement with available NMR data and, in addition, provides insight into the nature of the puckering angle and amplitude in 1.
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Miyanaga A, Koseki T, Miwa Y, Mese Y, Nakamura S, Kuno A, Hirabayashi J, Matsuzawa H, Wakagi T, Shoun H, Fushinobu S. The family 42 carbohydrate-binding module of family 54 alpha-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose. Biochem J 2006; 399:503-11. [PMID: 16846393 PMCID: PMC1615903 DOI: 10.1042/bj20060567] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Alpha-L-arabinofuranosidase catalyses the hydrolysis of the alpha-1,2-, alpha-1,3-, and alpha-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan. AkAbf54 (the glycoside hydrolase family 54 alpha-L-arabinofuranosidase from Aspergillus kawachii) consists of two domains, a catalytic and an arabinose-binding domain. The latter has been named AkCBM42 [family 42 CBM (carbohydrate-binding module) of AkAbf54] because homologous domains are classified into CBM family 42. In the complex between AkAbf54 and arabinofuranosyl-alpha-1,2-xylobiose, the arabinose moiety occupies the binding pocket of AkCBM42, whereas the xylobiose moiety is exposed to the solvent. AkCBM42 was found to facilitate the hydrolysis of insoluble arabinoxylan, because mutants at the arabinose binding site exhibited markedly decreased activity. The results of binding assays and affinity gel electrophoresis showed that AkCBM42 interacts with arabinose-substituted, but not with unsubstituted, hemicelluloses. Isothermal titration calorimetry and frontal affinity chromatography analyses showed that the association constant of AkCBM42 with the arabinose moiety is approximately 10(3) M(-1). These results indicate that AkCBM42 binds the non-reducing-end arabinofuranosidic moiety of hemicellulose. To our knowledge, this is the first example of a CBM that can specifically recognize the side-chain monosaccharides of branched hemicelluloses.
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Affiliation(s)
- Akimasa Miyanaga
- *Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takuya Koseki
- †National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima 739-0046, Japan
| | - Yozo Miwa
- ‡Department of Biosphere Science, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima 739-8528, Japan
| | - Yuichiro Mese
- ‡Department of Biosphere Science, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima 739-8528, Japan
| | - Sachiko Nakamura
- §Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology, AIST Central-2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8566, Japan
| | - Atsushi Kuno
- §Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology, AIST Central-2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8566, Japan
| | - Jun Hirabayashi
- §Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology, AIST Central-2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8566, Japan
| | - Hiroshi Matsuzawa
- ∥Department of Clinical Pharmacy, Aomori University, 2-3-1 Kohbata, Aomori 030-0943, Japan
| | - Takayoshi Wakagi
- *Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hirofumi Shoun
- *Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shinya Fushinobu
- *Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- To whom correspondence should be addressed (email )
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Ralet MC, André-Leroux G, Quéméner B, Thibault JF. Sugar beet (Beta vulgaris) pectins are covalently cross-linked through diferulic bridges in the cell wall. PHYTOCHEMISTRY 2005; 66:2800-14. [PMID: 16297942 DOI: 10.1016/j.phytochem.2005.09.039] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 09/28/2005] [Accepted: 09/30/2005] [Indexed: 05/05/2023]
Abstract
Arabinan and galactan side chains of sugar beet pectins are esterified by ferulic acid residues that can undergo in vivo oxidative reactions to form dehydrodiferulates. After acid and enzymatic degradation of sugar beet cell walls and fractionation of the solubilized products by hydrophobic interaction chromatography, three dehydrodiferulate-rich fractions were isolated. The structural identification of the different compounds present in these fractions was performed by electrospray-ion trap-mass spectrometry (before and after (18)O labeling) and high-performance anion-exchange chromatography. Several compounds contained solely Ara (terminal or alpha-1-->5-linked-dimer) and dehydrodiferulate. The location of the dehydrodiferulate was assigned in some cases to the O-2 and in others to the O-5 of non-reducing Ara residues. One compound contained Gal (beta-1-->4-linked-dimer), Ara (alpha-1-->5-linked-dimer) and dehydrodiferulate. The location of the dehydrodiferulate was unambiguously assigned to the O-2 of the non-reducing Ara residue and O-6 of the non-reducing Gal residue. These results provide direct evidence that pectic arabinans and galactans are covalently cross-linked (intra- or inter-molecularly) through dehydrodiferulates in sugar beet cell walls. Molecular modeling was used to compute and structurally characterize the low energy conformations of the isolated compounds. Interestingly, the conformations of the dehydrodiferulate-bridged arabinan and galactan fragments selected from an energetic criterion, evidenced very nice agreement with the experimental occurrence of the dehydrodiferulated pectins. The present work combines for the first time intensive mass spectrometry data and molecular modeling to give structural relevance of a molecular cohesion between rhamnogalacturonan fragments.
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Affiliation(s)
- Marie-Christine Ralet
- Unité Biopolymères Interactions Assemblages, Institut National de la Recherche Agronomique, rue de la tsaven Géraudière B.P. 71627, 44316 Nantes Cedex 03, France.
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Houseknecht JB, Lowary TL, Hadad CM. Gas- and Solution-Phase Energetics of the Methyl α- and β-d-Aldopentofuranosides. J Phys Chem A 2003. [DOI: 10.1021/jp027716w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Todd L. Lowary
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
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Rockenbauer A, Gaudel-Siri A, Siri D, Berchadsky Y, Le Moigne F, Olive G, Tordo P. Large Phosphorus Hyperfine Coupling as a Sensitive Tool for Studying Molecular Dynamics: ESR and Molecular Mechanics Studies of Ring Interconversion in the cis-2,5-Diphosphoryl-2,5-dimethyl-pyrrolidinoxyl Radical. J Phys Chem A 2003. [DOI: 10.1021/jp0213351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Antal Rockenbauer
- Chemical Research Center, Institute of Chemistry H-1075 Budapest, Pusztaszeri 59, Hungary, Laboratoire de Chimie Théorique et Modélisation Moléculaire, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case D42, 13397 Marseille, Cédex 20, France, and Laboratoire Structure et Réactivité des Espèces Paramagnétiques, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case 521, 13397 Marseille, Cédex 20, France
| | - Anouk Gaudel-Siri
- Chemical Research Center, Institute of Chemistry H-1075 Budapest, Pusztaszeri 59, Hungary, Laboratoire de Chimie Théorique et Modélisation Moléculaire, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case D42, 13397 Marseille, Cédex 20, France, and Laboratoire Structure et Réactivité des Espèces Paramagnétiques, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case 521, 13397 Marseille, Cédex 20, France
| | - Didier Siri
- Chemical Research Center, Institute of Chemistry H-1075 Budapest, Pusztaszeri 59, Hungary, Laboratoire de Chimie Théorique et Modélisation Moléculaire, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case D42, 13397 Marseille, Cédex 20, France, and Laboratoire Structure et Réactivité des Espèces Paramagnétiques, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case 521, 13397 Marseille, Cédex 20, France
| | - Yves Berchadsky
- Chemical Research Center, Institute of Chemistry H-1075 Budapest, Pusztaszeri 59, Hungary, Laboratoire de Chimie Théorique et Modélisation Moléculaire, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case D42, 13397 Marseille, Cédex 20, France, and Laboratoire Structure et Réactivité des Espèces Paramagnétiques, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case 521, 13397 Marseille, Cédex 20, France
| | - François Le Moigne
- Chemical Research Center, Institute of Chemistry H-1075 Budapest, Pusztaszeri 59, Hungary, Laboratoire de Chimie Théorique et Modélisation Moléculaire, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case D42, 13397 Marseille, Cédex 20, France, and Laboratoire Structure et Réactivité des Espèces Paramagnétiques, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case 521, 13397 Marseille, Cédex 20, France
| | - Gilles Olive
- Chemical Research Center, Institute of Chemistry H-1075 Budapest, Pusztaszeri 59, Hungary, Laboratoire de Chimie Théorique et Modélisation Moléculaire, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case D42, 13397 Marseille, Cédex 20, France, and Laboratoire Structure et Réactivité des Espèces Paramagnétiques, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case 521, 13397 Marseille, Cédex 20, France
| | - Paul Tordo
- Chemical Research Center, Institute of Chemistry H-1075 Budapest, Pusztaszeri 59, Hungary, Laboratoire de Chimie Théorique et Modélisation Moléculaire, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case D42, 13397 Marseille, Cédex 20, France, and Laboratoire Structure et Réactivité des Espèces Paramagnétiques, UMR 6517, CNRS-Universités d'Aix-Marseille I et III, Case 521, 13397 Marseille, Cédex 20, France
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Rockey WM, Dowd MK, Reilly PJ, French AD. Modeling of deoxy- and dideoxyaldohexopyranosyl ring puckering with MM3(92). Carbohydr Res 2001; 335:261-73. [PMID: 11595220 DOI: 10.1016/s0008-6215(01)00240-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Extensive variations of the ring structures of three deoxyaldohexopyranoses, L-fucose, D-quinovose, and L-rhamnose, and four dideoxyaldohexopyranoses, D-digitoxose, abequose, paratose, and tyvelose, were studied by energy minimization with the molecular mechanics algorithm MM3(92). Chair conformers, 4C(1) in D-quinovose and the equivalent 1C(4) in L-fucose and L-rhamnose, overwhelmingly dominate in the three deoxyhexoses; in the D-dideoxyhexoses, 4C(1) is again dominant, but with increased amounts of 1C(4) forms in the alpha anomers of the three 3,6-dideoxyhexoses, abequose, paratose, and tyvelose and in both alpha and beta anomers of the 2,6-dideoxyhexose D-digitoxose. In general, modeled proton-proton coupling constants agreed well with experimental values. Computed anomeric ratios strongly favor the beta configuration except for D-digitoxose, which is almost equally divided between alpha and beta configurations, and L-rhamnose, where the beta configuration is somewhat favored. MM3(92) appears to overstate the prevalence of the equatorial beta anomer in all three deoxyhexoses, as earlier found with fully oxygenated aldohexopyranoses.
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Affiliation(s)
- W M Rockey
- Department of Chemical Engineering, Iowa State University, Ames, IA 50011, USA
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24
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Houseknecht JB, McCarren PR, Lowary TL, Hadad CM. Conformational studies of methyl 3-O-methyl-alpha-D-arabinofuranoside: an approach for studying the conformation of furanose rings. J Am Chem Soc 2001; 123:8811-24. [PMID: 11535088 DOI: 10.1021/ja003768s] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A computational method for probing furanose conformation has been developed using a methylated monosaccharide derivative 1. First, a large library of conformers was generated by a systematic pseudo Monte Carlo search followed by optimization with the AMBER molecular mechanics force field. A subset of these conformers was then subjected to ab initio and density functional theory calculations in both the gas and aqueous phases. These calculations indicate that entropic contributions to the Gibbs free energy are important determinants of the Boltzmann distribution for the conformational preferences of 1 in the gas phase. The results obtained at each level of theory are discussed and compared with the experimentally determined conformer distribution from NMR studies in aqueous solution. In addition, the ability of each level of theory to reproduce the experimentally measured 1H-1H coupling constants in 1 is discussed. Empirical Karplus equations and density functional theory methods were used to determine average 3J(H1,H2), 3J(H2,H3), and 3J(H3,H4) for each level of theory. On the basis of this comparison, consideration of solvation with the MN-GSM model provided good agreement with the experimental data.
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Affiliation(s)
- J B Houseknecht
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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25
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McCarren PR, Gordon MT, Lowary TL, Hadad CM. Computational Studies of the Arabinofuranose Ring: Conformational Preferences of Fully Relaxed Methyl α-d-arabinofuranoside. J Phys Chem A 2001. [DOI: 10.1021/jp004611p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Patrick R. McCarren
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Matthew T. Gordon
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Todd L. Lowary
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Christopher M. Hadad
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
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26
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Probing furanose ring conformation by gas-phase computational methods: energy profile and structural parameters in methyl beta-D-arabinofuranoside as a function of ring conformation. J Org Chem 2000; 65:4954-63. [PMID: 10956478 DOI: 10.1021/jo000426w] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The potential energy surface of methyl beta-D-arabinofuranoside (3) has been studied by ab initio molecular orbital (HF/6-31G) and density functional theory (B3LYP/6-31G) calculations via minimization of the 10 possible envelope conformers. The partial potential energy surface identified that the global minimum and lowest energy northern conformer was E(2). In the HF calculations, (2)E was the most stable southern conformer, while the density functional theory methods identified (4)E as the local minimum in this hemisphere. Additional calculations at higher levels of theory showed that the B3LYP-derived energies of many of the envelope conformers of 3 are dependent upon the basis set used. It has also been demonstrated that B3LYP/6-31+G//B3LYP/6-31G single point energies are essentially the same as those obtained from full geometry optimizations at the B3LYP/6-31+G level. The northern and southern minima of the B3LYP/6-31+G surface are, respectively, the E(2) and (2)E conformers. The B3LYP/6-31G geometries were used to study the relationship between ring conformation and various structural parameters including bond angles, dihedral angles, bond lengths, and interatomic distances.
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27
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D'Souza FW, Ayers JD, McCarren PR, Lowary TL. Arabinofuranosyl Oligosaccharides from Mycobacteria: Synthesis and Effect of Glycosylation on Ring Conformation and Hydroxymethyl Group Rotamer Populations. J Am Chem Soc 2000. [DOI: 10.1021/ja993543l] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Francis W. D'Souza
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Joseph D. Ayers
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Patrick R. McCarren
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Todd L. Lowary
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
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28
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Gordon MT, Lowary TL, Hadad CM. A Computational Study of Methyl α-D-Arabinofuranoside: Effect of Ring Conformation on Structural Parameters and Energy Profile. J Am Chem Soc 1999. [DOI: 10.1021/ja9915091] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Matthew T. Gordon
- Contribution from the Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Todd L. Lowary
- Contribution from the Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Christopher M. Hadad
- Contribution from the Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
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29
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Gohlke H, Immel S, Lichtenthaler FW. Conformations and lipophilicity profiles of some cyclic β-(1→3)- and β-(1→6)-linked oligogalactofuranosides. Carbohydr Res 1999. [DOI: 10.1016/s0008-6215(99)00174-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Evdokimov AG, Kalb (Gilbo AJ, Koetzle TF, Klooster WT, Martin JML. Structures of Furanosides: Density Functional Calculations and High-Resolution X-ray and Neutron Diffraction Crystal Structures. J Phys Chem A 1999. [DOI: 10.1021/jp9837840] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Artem G. Evdokimov
- Departments of Structural Biology and Organic Chemistry, Weizmann Institute of Science, P. O. Box 26, IL-76100 Rehovot, Israel, and Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973
| | - A. Joseph Kalb (Gilbo
- Departments of Structural Biology and Organic Chemistry, Weizmann Institute of Science, P. O. Box 26, IL-76100 Rehovot, Israel, and Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973
| | - Thomas F. Koetzle
- Departments of Structural Biology and Organic Chemistry, Weizmann Institute of Science, P. O. Box 26, IL-76100 Rehovot, Israel, and Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973
| | - Wim T. Klooster
- Departments of Structural Biology and Organic Chemistry, Weizmann Institute of Science, P. O. Box 26, IL-76100 Rehovot, Israel, and Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973
| | - Jan M. L. Martin
- Departments of Structural Biology and Organic Chemistry, Weizmann Institute of Science, P. O. Box 26, IL-76100 Rehovot, Israel, and Department of Chemistry, Brookhaven National Laboratory, Upton, New York 11973
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31
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Mazeau K, Pérez S. The preferred conformations of the four oligomeric fragments of Rhamnogalacturonan II. Carbohydr Res 1998; 311:203-17. [PMID: 9825523 DOI: 10.1016/s0008-6215(98)00190-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rhamnogalacturonan II (RG-II) is a structurally complex pectic mega-oligosaccharide that is released enzymatically from the primary cell wall of higher plants. RG-II contains 28 monosaccharide units (MW approximately equal to 6 KDa) which belong to 12 different families of glycosyl residues, including very unusual ones such as Kdo, Dha, aceric acid, and apiose. Eighteen different disaccharide segments can be identified, and so far the primary structure has not yet been determined. These monomeric units are arranged into four structurally well-defined oligosaccharide side chains, linked to a pectic backbone made up of 1,4-linked alpha-D-galactosyluronic acid residues. The specific attachment sites of these four side-chains on the pectic backbone remains to be elucidated. The present work presents a three-dimensional database of all the monosaccharide and disaccharide components of RG-II. The conformational behavior of D-Apif and L-AceAf monosaccharide has been assessed through computations performed with the molecular mechanics program MM3 using the flexible residue approach. For each furanosyl residue, energies of various envelope and twist conformers were systematically calculated as a function of the puckering parameters Q and phi. Energy minima are observed in both the Northern and Southern zones of the conformational wheel of each monosaccharide. As for the constituting segments, the conformational behaviour of 18 different disaccharides was evaluated using the flexible residue procedure of the MM3 molecular mechanics procedure. For each disaccharide, the adiabatic energy surface, along with the locations of the local energy minima and drawings of the conformations of each local minimum located in the energy maps have been established. The geometries of the minima and the potential energy surfaces of the different fragments were included in the database of the POLYS, a program for building oligo and polysaccharides. All these results were used for the generation, prior to a complete optimization, of the complete structure of each fragment of RG-II. It is shown that both A and B fragments are very flexible about the two sidechain glycosidic linkages which are closest to the backbone. The remaining part of the sidechain is rigid for the heavily branched A fragment, it is flexible for the more linear B fragment. The lowest energy conformer of each fragment results in good exposure of the hydroxyl groups of the apiosyl residues. Some possible implications of these features in boron complexation are presented.
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Affiliation(s)
- K Mazeau
- Centre de Recherches sur les Macromolécules Végétales, CNRS, Grenoble, France
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Grůza J, Koča J, Pérez S, Imberty A. Comparison of force-fields parametrizations as applied to conformational analysis of ribofuranosides. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(97)00149-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Fernández-Bolaños J, Zafra E, García S, Fernández-Bolaños J, Fuentes J. 4-Thiopyranoside and 4-thiofuranoside derivatives of d-galactosamine. Carbohydr Res 1997. [DOI: 10.1016/s0008-6215(97)00218-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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34
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Pitson SM, Voragen AG, Vincken JP, Beldman G. Action patterns and mapping of the substrate-binding regions of endo-(1-->5)-alpha-L-arabinanases from Aspergillus niger and Aspergillus aculeatus. Carbohydr Res 1997; 303:207-18. [PMID: 9352635 DOI: 10.1016/s0008-6215(97)00159-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The substrate binding sites of endo-(1-->5)-alpha-L-arabinanases (EC 3.2.1.99) from Aspergillus niger and Aspergillus aculeatus were investigated using reduced and regular (1-->5)-alpha-L-arabino-oligosaccharides and high performance anion exchange chromatographic analysis. Calculation of bond cleavage frequencies and kcat/K(m) parameters for these substrates enabled the determination of the number of arabinofuranosyl binding subsites and the estimation of the binding affinities of each subsite. The A. aculeatus endo-arabinanase has six subsites arranged symmetrically around the catalytic site, while the A. niger endo-arabinanase has five subsites; two from the catalytic site towards the non-reducing end of the bound substrate and three toward the reducing end. The two subsites directly adjacent to the catalytic sites in both the A. niger and A. aculeatus endo-arabinanase have near-zero net free energy of binding. These results are unlike most glycopyranosyl endo-hydrolases studied which have net negative (unfavourable) energies of interaction at these two subsites, and may be related to the greater conformational flexibility of arabinofuranosyl residues than glycopyranosyl residues. The complete subsite maps are also rationalized with regard to the observed action patterns of these enzymes on linear (1-->5)-alpha-L-arabinan.
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Affiliation(s)
- S M Pitson
- Department of Food Science, Wageningen Agricultural University, The Netherlands
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35
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French AD, Dowd MK, Reilly PJ. MM3 modeling of fructose ring shapes and hydrogen bonding. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0166-1280(96)04546-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Beldman G, Schols H, Pitson S, Searle-van Leeuwen M, Voragen A. Arabinans and arabinan degrading enzymes. ADVANCES IN MACROMOLECULAR CARBOHYDRATE RESEARCH 1997. [DOI: 10.1016/s1874-5261(97)80003-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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37
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Pérez S, Kouwijzer M, Mazeau K, Engelsen SB. Modeling polysaccharides: present status and challenges. JOURNAL OF MOLECULAR GRAPHICS 1996; 14:307-21, 361-2. [PMID: 9195482 DOI: 10.1016/s0263-7855(97)00011-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The most recent tools that have been developed for modeling the three-dimensional features of polysaccharides and carbohydrate polymers are presented. The presentation starts with a description of the conformations of the monosaccharides, and of the flexible rings such as in the case of five-membered rings, and a thorough description of the conformational space that is available for a disaccharide unit, either in vacuo or in an aqueous phase. The extension to the modeling of the parent polysaccharides is addressed, based on the assumption that owing to the size and relative rigidity of the intervening monosaccharides units, the rotations at a particular linkage can be, under some conditions, considered as independent of nearest neighbor interactions. Appropriate modeling techniques are described that can provide insights into the dimensions of the chain in a solution which is best described as a random coil accompanied by the occurrence of local "helical" regions. With the help of such descriptors such as helical parameters, the ordered state of polysaccharide strands can be readily characterized. The generation of double or triple helices can be then attempted in order to explore the occurrence of such multi-stranded arrangements that may be energetically stable. The final step in the determination of the structure of polysaccharides in the ordered state, is the investigation of the interactions of different helices. This may lead to either the best arrangement(s) between two polymeric chains, or to the prediction of the dimensions, and the symmetry of a three-dimensional lattice. Some of the tools which have been developed should allow automatic scarches for meaningful correlations between structures and functions, through exploratory data analysis. Structure-function or structure-property correlation could be then used to model changes arising from structural alterations. This would open the field of polysaccharide engineering.
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Affiliation(s)
- S Pérez
- Centre de Recherches sur les Macromolécules Végétales, CNRS, Grenoble, France
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39
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Cros S, Imberty A, Bouchemal N, Du Penhoat CH, Perez S. Modeling of arabinofuranose and arabinan, II. Nmr and Conformational analysis of arabinobiose and arabinan. Biopolymers 1994. [DOI: 10.1002/bip.360341014] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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