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Bharadwaj VS, Crowley MF, Peña MJ, Urbanowicz B, O'Neill M. Mechanism and Reaction Energy Landscape for Apiose Cross-Linking by Boric Acid in Rhamnogalacturonan II. J Phys Chem B 2020; 124:10117-10125. [PMID: 33112619 DOI: 10.1021/acs.jpcb.0c06920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhamnogalacturonan II (RG-II)-the most complex polysaccharide known in nature-exists as a borate cross-linked dimer in the plant primary cell wall. Boric acid facilitates the formation of this cross-link on the apiosyl residues of RG-II's side chain A. Here, we detail the reaction mechanism for the cross-linking process with ab initio calculations coupled with transition state theory. We determine the formation of the first ester linkage to be the rate-limiting step of the mechanism. Our findings demonstrate that the regio- and stereospecific nature of subsequent steps in the reaction itinerary presents four distinct energetically plausible reaction pathways. This has significant implications for the overall structure of the cross-linked RG-II dimer assembly. Our transition state and reaction path analyses reveal key geometric insights that corroborate previous experimental hypotheses on borate ester formation reactions.
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Affiliation(s)
- Vivek S Bharadwaj
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Michael F Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Maria J Peña
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Breeanna Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Malcolm O'Neill
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
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2
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Mayfield AB, Metternich JB, Trotta AH, Jacobsen EN. Stereospecific Furanosylations Catalyzed by Bis-thiourea Hydrogen-Bond Donors. J Am Chem Soc 2020; 142:4061-4069. [PMID: 32013410 DOI: 10.1021/jacs.0c00335] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We report a new method for stereoselective O-furanosylation reactions promoted by a precisely tailored bis-thiourea hydrogen-bond-donor catalyst. Furanosyl donors outfitted with an anomeric dialkylphosphate leaving group undergo substitution with high anomeric selectivity, providing access to the challenging 1,2-cis substitution pattern with a range of alcohol acceptors. A variety of stereochemically distinct, benzyl-protected glycosyl donors were engaged successfully as substrates. Mechanistic studies support a stereospecific mechanism in which rate-determining substitution occurs from a catalyst-donor resting-state complex.
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Affiliation(s)
- Andrew B Mayfield
- Department of Chemistry & Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Jan B Metternich
- Department of Chemistry & Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Adam H Trotta
- Department of Chemistry & Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Eric N Jacobsen
- Department of Chemistry & Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
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Encalada AMI, Pérez CD, Flores SK, Rossetti L, Fissore EN, Rojas AM. Antioxidant pectin enriched fractions obtained from discarded carrots (Daucus carota L.) by ultrasound-enzyme assisted extraction. Food Chem 2019; 289:453-460. [PMID: 30955636 DOI: 10.1016/j.foodchem.2019.03.078] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 03/12/2019] [Accepted: 03/17/2019] [Indexed: 10/27/2022]
Abstract
Carrot residues were upgraded as pectin-enriched fractions (PEFs) useful for functional food formulation due to co-extracted antioxidants (α- and β-carotenes, lutein, α-tocopherol), and gelling effect. High power ultrasound (US)-enzyme assisted extraction was applied for efficiency and sustainability. Carrot powder (CP) in citrate-buffer (pH 5.20) was submitted to US-pretreatment (12.27 W/cm2: 20 kHz, 80% amplitude, 20 min) and a subsequent digestion (5 h-40 °C) without or with hemicellulase or cellulase. US-hemicellulase led to the highest PEF yield (27.1%), and extracted almost the whole pectin content of CP. US-pretreatment increased the extraction yield of all PEFs, but the existence of an additional positive effect of the following step depended on the enzyme used. PEFs contained 40-47% of UA with low DM (24-49.9%), and co-extracted antioxidants. US decreased the antioxidant contents, DM, and molecular weight, but allowed obtaining calcium crosslinked true gels, also with higher elastic modulus than non-US-extracted PEFs, being promising as food additives.
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Affiliation(s)
- Alondra M Idrovo Encalada
- Departamento de Industrias, ITAPROQ (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Ciudad Universitaria, C1428BGA Buenos Aires, Argentina
| | - Carolina D Pérez
- Instituto de Tecnología de Alimentos (ITA), Instituto Nacional de Tecnología Agropecuaria (INTA), CC-77, B1708WAB Morón, Province of Buenos Aires, Argentina
| | - Silvia K Flores
- Departamento de Industrias, ITAPROQ (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Ciudad Universitaria, C1428BGA Buenos Aires, Argentina
| | - Luciana Rossetti
- Instituto de Tecnología de Alimentos (ITA), Instituto Nacional de Tecnología Agropecuaria (INTA), CC-77, B1708WAB Morón, Province of Buenos Aires, Argentina
| | - Eliana N Fissore
- Departamento de Industrias, ITAPROQ (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Ciudad Universitaria, C1428BGA Buenos Aires, Argentina
| | - Ana M Rojas
- Departamento de Industrias, ITAPROQ (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Ciudad Universitaria, C1428BGA Buenos Aires, Argentina.
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Rheological and chemical properties of pectin enriched fractions from different sources extracted with citric acid. Carbohydr Polym 2017; 156:443-451. [DOI: 10.1016/j.carbpol.2016.09.042] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 08/28/2016] [Accepted: 09/14/2016] [Indexed: 02/02/2023]
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Pičmanová M, Møller BL. Apiose: one of nature's witty games. Glycobiology 2016; 26:430-42. [DOI: 10.1093/glycob/cww012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/24/2016] [Indexed: 11/13/2022] Open
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Mäkelä MR, Donofrio N, de Vries RP. Plant biomass degradation by fungi. Fungal Genet Biol 2014; 72:2-9. [PMID: 25192611 DOI: 10.1016/j.fgb.2014.08.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/19/2014] [Accepted: 08/25/2014] [Indexed: 12/27/2022]
Abstract
Plant biomass degradation by fungi has implications for several fields of science. The enzyme systems employed by fungi for this are broadly used in various industrial sectors such as food & feed, pulp & paper, detergents, textile, wine, and more recently biofuels and biochemicals. In addition, the topic is highly relevant in the field of plant pathogenic fungi as they degrade plant biomass to either gain access to the plant or as carbon source, resulting in significant crop losses. Finally, fungi are the main degraders of plant biomass in nature and as such have an essential role in the global carbon cycle and ecology in general. In this review we provide a global view on the development of this research topic in saprobic ascomycetes and basidiomycetes and in plant pathogenic fungi and link this to the other papers of this special issue on plant biomass degradation by fungi.
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Affiliation(s)
- Miia R Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Nicole Donofrio
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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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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Basanta MF, Ponce NMA, Rojas AM, Stortz CA. Effect of extraction time and temperature on the characteristics of loosely bound pectins from Japanese plum. Carbohydr Polym 2012; 89:230-5. [PMID: 24750628 DOI: 10.1016/j.carbpol.2012.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/28/2012] [Accepted: 03/01/2012] [Indexed: 11/26/2022]
Abstract
The cell wall composition of Japanese plums (Prunus salicina) at six developmental stages was previously evaluated (Ponce et al., J. Agric. Food Chem. 2010, 58, 2562-2570). This fruit is an interesting source of pectins, polysaccharides of valuable functionality for pharmaceutical and food formulations. In the present work it was investigated how the different conditions for the aqueous extraction of pectins from Japanese plums affect the yield as well as their chemical and rheological characteristics. It has been determined that extraction with water at room temperature for periods longer than 2h did not produce additional increment of yield (12%) but decreased the average molecular weights of the extracted pectins. Pectins with a degree of methylation ≈40% with high viscosity in water and with adequate molecular weights (≈72,000) were obtained. Conversely, utilization of boiling water for extraction increased considerably the yields (33-38%) but the extracted pectins showed significant lower viscosity in water in spite of their higher molecular weights. The poorer thickening ability was associated to the lower proportion of arabinose residues present in the hairy regions of the pectin macromolecules extracted by hot water, which led the polymers to interact more transiently in a 2% w/v water solution.
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Affiliation(s)
- María F Basanta
- Departamento de Química Orgánica-CIHIDECAR, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Nora M A Ponce
- Departamento de Química Orgánica-CIHIDECAR, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Ana M Rojas
- Departamento de Industrias, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Carlos A Stortz
- Departamento de Química Orgánica-CIHIDECAR, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
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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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Lagaert S, Beliën T, Volckaert G. Plant cell walls: Protecting the barrier from degradation by microbial enzymes. Semin Cell Dev Biol 2009; 20:1064-73. [DOI: 10.1016/j.semcdb.2009.05.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 05/25/2009] [Indexed: 10/20/2022]
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Stortz CA, Johnson GP, French AD, Csonka GI. Comparison of different force fields for the study of disaccharides. Carbohydr Res 2009; 344:2217-28. [PMID: 19758584 DOI: 10.1016/j.carres.2009.08.019] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 08/13/2009] [Accepted: 08/18/2009] [Indexed: 11/30/2022]
Abstract
Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying beta-cellobiose, alpha-maltose, and alpha-galabiose [alpha-D-Galp-(1-->4)-alpha-D-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl, and glycosidic linkage orientations were minimized by the different methods, some at two dielectric constants. By comparing these results and the available crystal structure data and/or higher level density functional theory results, it was concluded that the newer parameterizations for force fields (GROMOS, GLYCAM06, OPLS-2005 and CSFF) give results that are reasonably similar to each other, whereas the older parameterizations for Amber, CHARMM or OPLS were more divergent. However, MM3, an older force field, gave energy and geometry values comparable to those of the newer parameterizations, but with less sensitivity to dielectric constant values. These systems worked better than MM2 variants, which were still acceptable. PM3CARB-1 also gave adequate results in terms of linkage and exocyclic torsion angles. GROMOS, GLYCAM06, and MM3 appear to be the best choices, closely followed by MM4, CSFF, and OPLS-2005. With GLYCAM06 and to a lesser extent, CSFF, and OPLS-2005, a number of the conformers that were stable with MM3 changed to other forms.
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Affiliation(s)
- Carlos A Stortz
- Departamento de Química Orgánica-CIHIDECAR, FCEyN-Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina.
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Caffall KH, Mohnen D. The structure, function, and biosynthesis of plant cell wall pectic polysaccharides. Carbohydr Res 2009; 344:1879-900. [PMID: 19616198 DOI: 10.1016/j.carres.2009.05.021] [Citation(s) in RCA: 931] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 05/04/2009] [Accepted: 05/06/2009] [Indexed: 11/15/2022]
Abstract
Plant cell walls consist of carbohydrate, protein, and aromatic compounds and are essential to the proper growth and development of plants. The carbohydrate components make up approximately 90% of the primary wall, and are critical to wall function. There is a diversity of polysaccharides that make up the wall and that are classified as one of three types: cellulose, hemicellulose, or pectin. The pectins, which are most abundant in the plant primary cell walls and the middle lamellae, are a class of molecules defined by the presence of galacturonic acid. The pectic polysaccharides include the galacturonans (homogalacturonan, substituted galacturonans, and RG-II) and rhamnogalacturonan-I. Galacturonans have a backbone that consists of alpha-1,4-linked galacturonic acid. The identification of glycosyltransferases involved in pectin synthesis is essential to the study of cell wall function in plant growth and development and for maximizing the value and use of plant polysaccharides in industry and human health. A detailed synopsis of the existing literature on pectin structure, function, and biosynthesis is presented.
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Affiliation(s)
- Kerry Hosmer Caffall
- University of Georgia, Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, Athens, 30602, United States
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Michaud P, Da Costa A, Courtois B, Courtois J. Polysaccharide Lyases: Recent Developments as Biotechnological Tools. Crit Rev Biotechnol 2008; 23:233-66. [PMID: 15224891 DOI: 10.1080/07388550390447043] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Polysaccharide lyases, which are polysaccharide cleavage enzymes, act mainly on anionic polysaccharides. Produced by prokaryote and eukaryote organisms, these enzymes degrade (1,4) glycosidic bond by a beta elimination mechanism and have unsaturated oligosaccharides as major products. New polysaccharides are cleaved only by their specific polysaccharide lyases. From anionic polysaccharides controlled degradations, various biotechnological applications were investigated. This review catalogues the degradation of bacterial, plant and animal polysaccharides (neutral and anionic) by this family of carbohydrate acting enzymes.
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Affiliation(s)
- P Michaud
- Laboratoire des Glucides--LPMV, IUT/Génie Biologique, Université de Picardie Jules Verne, Avenue des Facultés, Le Bailly, 80025 Amiens Cedex, France.
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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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Guadalupe Z, Ayestarán B. Polysaccharide profile and content during the vinification and aging of Tempranillo red wines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:10720-10728. [PMID: 18001031 DOI: 10.1021/jf0716782] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Passing from must to wine produced a loss of low-molecular-weight grape structural glucosyl polysaccharides, and an important gain in yeast mannoproteins (MP) and grape-derived arabinogalactan proteins (AGP), and rhamnogalacturonans-II (RG-II). AGP were more easily extracted than RG-II, and small quantities of RG-II monomers and galacturonans were detected. Postmaceration produced a reduction in all grape polysaccharide families, particularly acute in AGP. The reduction of polysaccharides during malolactic fermentation only affected grape AGP, and MP were continuously liberated during the entire vinification process. Wine oak and bottle aging was associated with a relative stability of the polysaccharide families. AGP were thus the majority polysaccharides in young wines but, contrary to what may be thought, structural glucosyl oligosaccharides dominated in musts and MP in aged wines. Precipitation of polysaccharides was noticeable during vinification, and it mainly affected high-molecular-weight AGP and MP. Hydrolytic phenomena affected the balance of wine polysaccharides during late maceration-fermentation.
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Affiliation(s)
- Zenaida Guadalupe
- Department of Agriculture and Food Science, University of La Rioja, Spain.
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Production, purification and characterization of an endopolygalacturonase from Mucor rouxii NRRL 1894. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Gerbst AG, Grachev AA, Shashkov AS, Nifantiev NE. Computation techniques in the conformational analysis of carbohydrates. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2007. [DOI: 10.1134/s1068162007010037] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Stortz CA. MM3 potential energy surfaces of trisaccharide models of lambda-, mu-, and nu-carrageenans. Carbohydr Res 2006; 341:2531-42. [PMID: 16952344 DOI: 10.1016/j.carres.2006.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Revised: 08/11/2006] [Accepted: 08/16/2006] [Indexed: 11/22/2022]
Abstract
The adiabatic potential energy surfaces (PES) of six trisaccharides, sulfated derivatives of alpha-D-Gal p-(1-->3)-beta-D-Gal p-(1-->4)-alpha-D-Gal p and beta-D-Gal p-(1-->4)-alpha-D-Gal p-(1-->3)-beta-D-Gal p representing models of lambda-, mu-, and nu-carrageenans were obtained using the MM3 force-field at epsilon = 3. Each PES was described by a single contour map for which the energy is plotted against the two psi glycosidic angles, given the small variations of the phi glycosidic torsional angle in the low-energy regions of disaccharide maps. Most surfaces appear as expected from the maps of the disaccharidic repeating units of carrageenans, with less important factors altering the additive effect of both linkages. Only small interactions between the first and third monosaccharidic moieties of the trisaccharides are observed. The flexibility of the alpha-linkages appears nearly identical to that in their disaccharide counterparts, with only one exception, where it appears reduced by the presence of the third monosaccharide. On the other hand, the flexibility of the beta-linkage appears to be equal or sometimes even higher than that observed for the corresponding disaccharide.
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Affiliation(s)
- Carlos A Stortz
- Departamento de Química Orgánica-CIHIDECAR, Facultad de Ciencias Exactas y Naturales, UBA, Ciudad Universitaria, 1428 Buenos Aires, Argentina.
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Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K. Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate. Biochem Biophys Res Commun 2006; 347:1021-9. [PMID: 16870154 DOI: 10.1016/j.bbrc.2006.07.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 07/05/2006] [Indexed: 11/30/2022]
Abstract
Bacillus subtilis strain 168 YteR has been identified as a novel enzyme "unsaturated rhamnogalacturonyl hydrolase" classified in glycoside hydrolase family 105. This enzyme acts specifically on unsaturated rhamnogalacturonan (RG) produced from plant cell wall RG type-I treated with RG lyases, releasing unsaturated galacturonic acid (DeltaGalA) from the substrate. The most likely candidate catalytic residue is Asp-143. Here, we show the structure of D143N in complex with unsaturated RG disaccharide (substrate) determined at 1.9A resolution by X-ray crystallography. This structural feature directly contributes to the postulation of the enzyme reaction mechanism. YteR triggers the hydration of vinyl ether group in DeltaGalA, but not of glycoside bond, by using Asp-143 as a general acid and base catalyst. Asp-143 donates proton to the double bond of DeltaGalA as an acid catalyst and also deprotonates a water molecule as a base catalyst. Deprotonated water molecule attacks the C5 atom of DeltaGalA.
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Affiliation(s)
- Takafumi Itoh
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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The pectic polysaccharide rhamnogalacturonan II is present as a dimer in pectic populations of bilberries and black currants in muro and in juice. Carbohydr Polym 2006. [DOI: 10.1016/j.carbpol.2006.02.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
The assembly of cell wall components, cellulose and xyloglucan (XG), was investigated at the atomistic scale using molecular dynamics simulations. A molecular model of a cellulose crystal corresponding to the allomorph Ibeta and exhibiting a flexible complex external morphology was employed to mimic the cellulose microfibril. The xyloglucan molecules considered were the three typical basic repeat units, differing only in the size of one of the lateral chain. All the investigated XG fragments adsorb nonspecifically onto cellulose fiber; multiple arrangements are equally probable, and every cellulose surface was capable of binding the short XG molecules. The following structural effects emerged: XG molecules that do not have any long side chains tended to adapt themselves nicely to the topology of the microfibril, forming a flat, outstretched conformation with all the sugar residues interacting with the surface. In contrast, the XG molecules, which have long side chains, were not able to adopt a flat conformation that would enable the interaction of all the XG residues with the surface. In addition to revealing the fundamental atomistic details of the XG adsorption on cellulose, the present calculations give a comprehensive understanding of the way the XG molecules can unsorb from cellulose to create a network that forms the cell wall. Our revisited view of the adsorption features of XG on cellulose microfibrils is consistent with experimental data, and a model of the network is proposed.
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Affiliation(s)
- Jaroslav Hanus
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), ICMG FR 2607, BP 53, 38041, Grenoble Cedex 9, France
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Takashima S, Abe T, Yoshida S, Kawahigashi H, Saito T, Tsuji S, Tsujimoto M. Analysis of Sialyltransferase-Like Proteins from Oryza sativa. ACTA ACUST UNITED AC 2006; 139:279-87. [PMID: 16452316 DOI: 10.1093/jb/mvj029] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Sialic acids are widely distributed among living creatures, from bacteria to mammals, but it has been commonly accepted that they do not exist in plants. However, with the progress of genome analyses, putative gene homologs of animal sialyltransferases have been detected in the genome of some plants. In this study, we cloned three genes from Oryza sativa (Japanese rice) that encode sialyltransferase-like proteins, designated OsSTLP1, 2, and 3, and analyzed the enzymatic activity of the proteins. OsSTLP1, 2, and 3 consist of 393, 396, and 384 amino acids, respectively, and each contains sequences similar to the sialyl motifs that are highly conserved among animal sialyltransferases. The recombinant soluble forms of OsSTLPs produced by COS-7 cells were analyzed for sialyltransferase-like activity. OsSTLP1 exhibited such activity toward the oligosaccharide Galbeta1,4GlcNAc and such glycoproteins as asialofetuin, alpha1-acid glycoprotein, and asialo-alpha1-acid glycoprotein; OsSTLP3 exhibited similar activity toward asialofetuin; and OsSTLP2 exhibited no sialyltransferase-like activity. The sialic acid transferred by OsSTLP1 or 3 was linked to galactose of Galbeta1,4GlcNAc through alpha2,6-linkage. This is the first report of plant proteins having sialyltransferase-like activity.
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Affiliation(s)
- Shou Takashima
- Cellular Biochemistry Laboratory and Plant Functions Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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24
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Mazeau K, Rinaudo M. The prediction of the characteristics of some polysaccharides from molecular modeling. Comparison with effective behavior. Food Hydrocoll 2004. [DOI: 10.1016/j.foodhyd.2004.04.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Berteau O, Stenutz R. Web resources for the carbohydrate chemist. Carbohydr Res 2004; 339:929-36. [PMID: 15010300 DOI: 10.1016/j.carres.2003.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2003] [Accepted: 11/14/2003] [Indexed: 10/26/2022]
Abstract
Bioinformatics has played a pivotal role in advancing genetics and protein sciences. The large amount of information generated by genomics, and now proteomics, has been a driving force. By comparison, glycobiology still generates small amounts of data. The need to organize our knowledge about carbohydrates is however growing constantly and has given rise to an increasing number of public databases and freely available tools. This review gives an overview of the carbohydrate-oriented resources currently available on the Internet. Many of the resources are seldom referred to in the literature and difficult to find, in part because of the constant flux of the net itself, but also because many efforts have been lead by a single individual. As the World Wide Web has matured the number of 'permanent' resources, maintained by organizations rather than individuals, has increased. In this paper, we present some of the more useful and accessible public tools and databases. There are also a few commercial initiatives but these have not been reviewed.
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Affiliation(s)
- Olivier Berteau
- Department of Chemistry, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
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26
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Stortz CA, Cerezo AS. MM3 potential energy surfaces of trisaccharides. II. Carrageenan models containing 3,6-anhydro-D-galactose. Biopolymers 2003; 70:227-39. [PMID: 14517911 DOI: 10.1002/bip.10468] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The adiabatic potential energy surfaces (PES) of six trisaccharides-namely 3,6-An-alpha-D-Galp-(1-->3)-beta-D-Galp-(1-->4)-3,6-An-alpha-D-Galp, beta-D-Galp-(1-->4)-3,6-An-alpha-D-Galp-(1-->3)-beta-D-Galp, and their derivatives sulfated on positions 2 and 4 of the beta-galactose unit-were obtained using the MM3 force field. Each PES was described by a single contour map for which the energy is plotted against the two psi glycosidic angles, given the small variations of the phi glycosidic torsional angle in the low-energy regions of disaccharide maps. In five of the six examples, the surfaces are those expected from the maps of the disaccharidic repeating units of carrageenans, with less important factors altering the additive effect of both linkages. However, when a sulfate group is present on C2 of a beta-galactose reducing end, a new low-energy minimum in a different region is produced, originated in a hydrogen bond between the first and third monosaccharidic moieties of the trisaccharide. The flexibility of the beta-linkages is nearly identical to that in their disaccharide counterparts, while that of the alpha-linkages is slightly reduced, independent of their presence closer or further away from the reducing end. A fair agreement is observed between the x-ray fiber diffraction analysis for a kappa-carrageenan double helix and the surfaces obtained for the trisaccharide analogs of that polymer.
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Affiliation(s)
- Carlos A Stortz
- Departamento de Quimica Orgánica-CIHIDECAR, Fac. Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina.
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27
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Vanhaverbeke C, Heyraud A, Mazeau K. Conformational analysis of the exopolysaccharide from Burkholderia caribensis strain MWAP71: impact on the interaction with soils. Biopolymers 2003; 69:480-97. [PMID: 12879494 DOI: 10.1002/bip.10432] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The strain MWAP71 of Burkholderia caribensis produces a branched charged exopolysaccharide (EPS) that is responsible for soil aggregation. Understanding the conformational properties of the isolated polysaccharide is a prerequisite for proper investigation of the interactions between the polysaccharide and the soil at the atomic level. The aim of this study is first to have an overall view of the flexibility of the backbone and then to ascertain the role played by side groups in the conformational properties of the main chain. Conformational analysis of each oligomeric segment of the polysaccharide has been performed by means of adiabatic mapping of the backbone glycosidic torsion angles using the MM3(92) force field. Substitution by an acetyl group or by a Kdo unit has only a slight effect on the potential energy surfaces of the fragment model compounds. Calculated partition functions, however, indicate that the overall flexibility is slightly larger for the substituted oligomers than for the unsubstituted ones. Prediction of selected average interproton distances from the AB and BC potential energy surfaces allows comparison between modeling results and NMR measurements performed on the ABC fragment. Agreement between the experimental and the predicted data suggests that the established surfaces correctly reflect the observed conformational behavior of such fragments and validate the modeling protocol. The above results have been extended to regular and disordered long polymer chains, differing in Kdo content. It is found that Kdo affects the helical conformations of the polysaccharide. The number of stable helices is considerably larger with Kdo than without Kdo. On the contrary, Kdo has only a moderate effect on unperturbed disordered conformations of the polysaccharide. Predicted persistence length of 70 A suggests that the polymer is semirigid with moderate extension. A further validation of the modeling results is obtained by the good concordance between this predicted value and the experimental one of 95 A, measured from light scattering and viscosity experiments. The results lead to an understanding of the interactions of this polysaccharide with soils.
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Affiliation(s)
- Cécile Vanhaverbeke
- Centre de Recherches sur les Macromolécules Végétales, CNRS and Université Joseph Fourier, B.P.53, F-38041 Grenoble, France
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28
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Stortz CA, Cerezo AS. MM3 potential energy surfaces of the 2-linked glucosyl trisaccharides alpha-kojitriose and beta-sophorotriose. Carbohydr Res 2003; 338:1679-89. [PMID: 12873423 DOI: 10.1016/s0008-6215(03)00265-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The adiabatic potential energy surfaces (PES) of two trisaccharides with 2-linkages (alpha-kojitriose and beta-sophorotriose) were obtained using the MM3 force field, and are represented by a single 3D contour map for which the energy is plotted against the two psi glycosidic angles. In spite of the proximity of the positions where the two monosaccharidic units are linked to the central monosaccharide, an almost independent behavior of both linkages was found for the alpha-linked trisaccharide alpha-kojitriose, i.e., the surfaces are those expected from the maps of the disaccharide containing the same linkage. A slight shift of the position of the global minimum is found to occur, due to a hydrogen bond between the third and first monosaccharide units, which also leads to an increase in flexibility. On the other hand, for the beta-linked trisaccharide beta-sophorotriose, the surface is sharply different from that expected by observation of the disaccharide map. Some of the expected minima cannot appear unless a serious deformation of the phi and/or psi angles is produced. Furthermore, the global minimum corresponds to a combination of different conformations for each of the linkages, whereas another minimum with only slightly higher energy has both glycosidic linkages in a conformation less favored for the disaccharide, though close to that predicted in crystal diffraction studies.
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Affiliation(s)
- Carlos A Stortz
- Departamento de Química Orgánica-CIHIDECAR, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina.
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29
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Rodríguez-Carvajal MA, Hervé du Penhoat C, Mazeau K, Doco T, Pérez S. The three-dimensional structure of the mega-oligosaccharide rhamnogalacturonan II monomer: a combined molecular modeling and NMR investigation. Carbohydr Res 2003; 338:651-71. [PMID: 12644378 DOI: 10.1016/s0008-6215(03)00003-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, we describe the first optimized molecular models of the mega-oligosaccharide rhamnogalaturonan II, that is found in the primary cell walls of all higher plants. The 750 MHz 1H NMR data previously reported and new heteronuclear correlation spectra (sensitivity-enhanced HSQC and HSQC-TOCSY) were first reassigned in light of the modifications in the primary structure. In turn, the experimental NMR data revealed the presence of an additional sugar, alpha-Araf (E-chain), and also the disaccharidic repeating unit of RG-I, another component of the pectic matrix. Due to a fuller picture of the primary structure of RG-II, a much more complete assignment of the NOE data has been achieved. A systematic computational study based on these NOEs lead us to a realistic three-dimensional description of the RG-II, in excellent agreement with the molecular dimensions obtained from various experimental methods.
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Affiliation(s)
- Miguel A Rodríguez-Carvajal
- Centre de Recherches sur les Macromolécules Végétales, CNRS (associated with University Joseph Fourier), BP 53, 38041 Cedex 9, Grenoble, France
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30
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Stortz CA, Cerezo AS. Depicting the MM3 potential energy surfaces of trisaccharides by single contour maps: application to beta-cellotriose and alpha-maltotriose. Carbohydr Res 2003; 338:95-107. [PMID: 12504386 DOI: 10.1016/s0008-6215(02)00360-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The adiabatic potential energy surfaces (PES) of two trisaccharides (beta-cellotriose and alpha-maltotriose) were obtained using the MM3 force field. Each PES can be described by a single 3D contour map for which the energy is plotted against the two psi glycosidic angles. Given the usually small variations of the phi glycosidic torsional angle in the low-energy regions of disaccharide maps (at least with MM3), it is valid to leave both phi glycosidic angles to relax in the process of building the conformational map of trisaccharides. The surfaces are those expected from the map of disaccharides containing the same linkages and monosaccharide units (i.e., beta-cellobiose and alpha-maltose), with second-order factors altering the 'symmetry' of both linkages. A large low-energy region appears for beta-cellotriose, comprising four minima in close proximity, with barriers between them below 0.6 kcal/mol. On the other hand, for alpha-maltotriose a main global minimum is observed, with several surrounding local minima. The surfaces obtained agree with single-crystal X-ray data on these trisaccharides and derivatives. A reduction of the linkage flexibilities is observed when passing from the disaccharides to the trisaccharides. Furthermore, the linkage closer to the reducing end appears to be less flexible than the linkage closer to the non-reducing end.
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Affiliation(s)
- Carlos A Stortz
- Departamento de Qui;mica Orgánica-CIHIDECAR, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina.
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31
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Riou V, Vernhet A, Doco T, Moutounet M. Aggregation of grape seed tannins in model wine—effect of wine polysaccharides. Food Hydrocoll 2002. [DOI: 10.1016/s0268-005x(01)00034-0] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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de Vries RP, Visser J. Aspergillus enzymes involved in degradation of plant cell wall polysaccharides. Microbiol Mol Biol Rev 2001; 65:497-522, table of contents. [PMID: 11729262 PMCID: PMC99039 DOI: 10.1128/mmbr.65.4.497-522.2001] [Citation(s) in RCA: 542] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Degradation of plant cell wall polysaccharides is of major importance in the food and feed, beverage, textile, and paper and pulp industries, as well as in several other industrial production processes. Enzymatic degradation of these polymers has received attention for many years and is becoming a more and more attractive alternative to chemical and mechanical processes. Over the past 15 years, much progress has been made in elucidating the structural characteristics of these polysaccharides and in characterizing the enzymes involved in their degradation and the genes of biotechnologically relevant microorganisms encoding these enzymes. The members of the fungal genus Aspergillus are commonly used for the production of polysaccharide-degrading enzymes. This genus produces a wide spectrum of cell wall-degrading enzymes, allowing not only complete degradation of the polysaccharides but also tailored modifications by using specific enzymes purified from these fungi. This review summarizes our current knowledge of the cell wall polysaccharide-degrading enzymes from aspergilli and the genes by which they are encoded.
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Affiliation(s)
- R P de Vries
- Molecular Genetics of Industrial Microorganisms, Wageningen University, 6703 HA Wageningen, The Netherlands.
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33
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Monteiro C, Hervé du Penhoat C. Translational Diffusion of Dilute Aqueous Solutions of Sugars as Probed by NMR and Hydrodynamic Theory. J Phys Chem A 2001. [DOI: 10.1021/jp0113836] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Céline Monteiro
- Centre de Recherches sur les Macromolécules Végétales, CNRS (associated with University Joseph Fourier), BP 53, 38041 Grenoble Cedex 9, France
| | - Catherine Hervé du Penhoat
- Centre de Recherches sur les Macromolécules Végétales, CNRS (associated with University Joseph Fourier), BP 53, 38041 Grenoble Cedex 9, France
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34
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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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35
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Ridley BL, O'Neill MA, Mohnen D. Pectins: structure, biosynthesis, and oligogalacturonide-related signaling. PHYTOCHEMISTRY 2001; 57:929-67. [PMID: 11423142 DOI: 10.1016/s0031-9422(01)00113-3] [Citation(s) in RCA: 1133] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Pectin is a family of complex polysaccharides present in all plant primary cell walls. The complicated structure of the pectic polysaccharides, and the retention by plants of the large number of genes required to synthesize pectin, suggests that pectins have multiple functions in plant growth and development. In this review we summarize the current level of understanding of pectin primary and tertiary structure, and describe new methods that may be useful to study localized pectin structure in the plant cell wall. We also discuss progress in our understanding of how pectin is biosynthesized and review the biological activities and possible modes of action of pectic oligosaccharides referred to as oligogalacturonides. We present our view of critical questions regarding pectin structure, biosynthesis, and function that need to be addressed in the coming decade. As the plant community works towards understanding the functions of the tens of thousands of genes expressed by plants, a large number of those genes are likely to be involved in the synthesis, turnover, biological activity, and restructuring of pectin. A combination of genetic, molecular, biochemical and chemical approaches will be necessary to fully understand the function and biosynthesis of pectin.
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Affiliation(s)
- B L Ridley
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, 220 Riverbend Road, Athens, GA 30602-4712, USA
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36
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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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37
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Remodelling Pectin Structure In Potato. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0168-7972(00)80129-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
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38
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Abstract
The 'adiabatic' (phi, psi) potential-energy surface of the disaccharide alpha-D-galactopyranosyl-(1-->3)-beta-D-galactopyranose was obtained by several established methods, using the MM3 molecular mechanics force field. The constrained minimizations throughout the whole grid were carried out using sharply different dielectric constants. The attainment of the 'true' adiabatic map is very difficult due to the 'multiple minimum problem', originating in the large number of exocyclic pendant groups present in a disaccharide. However, these results suggest that at low dielectric constants, the usual approach starting with conformers carrying cooperative hydrogen bonds results in a good approximation to the true adiabatic map, while at high dielectric constants this approach fails due to the damping of electrostatic and hydrogen-bonding interactions.
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Affiliation(s)
- C A Stortz
- Departamento de Química Orgánica-CIHIDECAR, Facultad de Ciencias Exactas y Naturales, UBA, Ciudad Universitaria, Argentina.
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