101
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Alqus R, Eichhorn SJ, Bryce RA. Molecular Dynamics of Cellulose Amphiphilicity at the Graphene–Water Interface. Biomacromolecules 2015; 16:1771-83. [DOI: 10.1021/acs.biomac.5b00307] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rasha Alqus
- Manchester
Pharmacy School, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Stephen J. Eichhorn
- Centre
for Graphene Science, College of Engineering, Maths and Physical Sciences, University of Exeter, Physics Building, Stocker Road, Exeter, Devon, EX4 4QL, United Kingdom
| | - Richard A. Bryce
- Manchester
Pharmacy School, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom
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102
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Oehme DP, Downton MT, Doblin MS, Wagner J, Gidley MJ, Bacic A. Unique aspects of the structure and dynamics of elementary Iβ cellulose microfibrils revealed by computational simulations. PLANT PHYSIOLOGY 2015; 168:3-17. [PMID: 25786828 PMCID: PMC4424011 DOI: 10.1104/pp.114.254664] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/06/2015] [Indexed: 05/18/2023]
Abstract
The question of how many chains an elementary cellulose microfibril contains is critical to understanding the molecular mechanism(s) of cellulose biosynthesis and regulation. Given the hexagonal nature of the cellulose synthase rosette, it is assumed that the number of chains must be a multiple of six. We present molecular dynamics simulations on three different models of Iβ cellulose microfibrils, 18, 24, and 36 chains, to investigate their structure and dynamics in a hydrated environment. The 36-chain model stays in a conformational space that is very similar to the initial crystalline phase, while the 18- and 24-chain models sample a conformational space different from the crystalline structure yet similar to conformations observed in recent high-temperature molecular dynamics simulations. Major differences in the conformations sampled between the different models result from changes to the tilt of chains in different layers, specifically a second stage of tilt, increased rotation about the O2-C2 dihedral, and a greater sampling of non-TG exocyclic conformations, particularly the GG conformation in center layers and GT conformation in solvent-exposed exocyclic groups. With a reinterpretation of nuclear magnetic resonance data, specifically for contributions made to the C6 peak, data from the simulations suggest that the 18- and 24-chain structures are more viable models for an elementary cellulose microfibril, which also correlates with recent scattering and diffraction experimental data. These data inform biochemical and molecular studies that must explain how a six-particle cellulose synthase complex rosette synthesizes microfibrils likely comprised of either 18 or 24 chains.
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Affiliation(s)
- Daniel P Oehme
- IBM Research Collaboratory for Life Sciences-Melbourne, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); IBM Research-Australia, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany (M.S.D., A.B.) and Bio21 Molecular Science and Biotechnology Institute (A.B.), University of Melbourne, Parkville, Victoria 3010, Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls and Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia 4072, Australia (M.J.G.)
| | - Matthew T Downton
- IBM Research Collaboratory for Life Sciences-Melbourne, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); IBM Research-Australia, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany (M.S.D., A.B.) and Bio21 Molecular Science and Biotechnology Institute (A.B.), University of Melbourne, Parkville, Victoria 3010, Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls and Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia 4072, Australia (M.J.G.)
| | - Monika S Doblin
- IBM Research Collaboratory for Life Sciences-Melbourne, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); IBM Research-Australia, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany (M.S.D., A.B.) and Bio21 Molecular Science and Biotechnology Institute (A.B.), University of Melbourne, Parkville, Victoria 3010, Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls and Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia 4072, Australia (M.J.G.)
| | - John Wagner
- IBM Research Collaboratory for Life Sciences-Melbourne, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); IBM Research-Australia, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany (M.S.D., A.B.) and Bio21 Molecular Science and Biotechnology Institute (A.B.), University of Melbourne, Parkville, Victoria 3010, Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls and Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia 4072, Australia (M.J.G.)
| | - Michael J Gidley
- IBM Research Collaboratory for Life Sciences-Melbourne, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); IBM Research-Australia, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany (M.S.D., A.B.) and Bio21 Molecular Science and Biotechnology Institute (A.B.), University of Melbourne, Parkville, Victoria 3010, Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls and Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia 4072, Australia (M.J.G.)
| | - Antony Bacic
- IBM Research Collaboratory for Life Sciences-Melbourne, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); IBM Research-Australia, Carlton, Victoria 3010, Australia (D.P.O., M.T.D., J.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany (M.S.D., A.B.) and Bio21 Molecular Science and Biotechnology Institute (A.B.), University of Melbourne, Parkville, Victoria 3010, Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls and Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia 4072, Australia (M.J.G.)
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103
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Vermaas JV, Crowley MF, Beckham GT, Payne CM. Effects of lytic polysaccharide monooxygenase oxidation on cellulose structure and binding of oxidized cellulose oligomers to cellulases. J Phys Chem B 2015; 119:6129-43. [PMID: 25785779 DOI: 10.1021/acs.jpcb.5b00778] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In nature, polysaccharide glycosidic bonds are cleaved by hydrolytic enzymes for a vast array of biological functions. Recently, a new class of enzymes that utilize an oxidative mechanism to cleave glycosidic linkages was discovered; these enzymes are called lytic polysaccharide monooxygenases (LPMO). These oxidative enzymes are synergistic with cocktails of hydrolytic enzymes and are thought to act primarily on crystalline regions, in turn providing new sites of productive attachment and detachment for processive hydrolytic enzymes. In the case of cellulose, the homopolymer of β-1,4-d-glucose, enzymatic oxidation occurs at either the reducing end or the nonreducing end of glucose, depending on enzymatic specificity, and results in the generation of oxidized chemical substituents at polymer chain ends. LPMO oxidation of cellulose is thought to produce either a lactone at the reducing end of glucose that can spontaneously or enzymatically convert to aldonic acid or 4-keto-aldose at the nonreducing end that may further oxidize to a geminal diol. Here, we use molecular simulation to examine the effect of oxidation on the structure of crystalline cellulose. The simulations highlight variations in behaviors depending on the chemical identity of the oxidized species and its location within the cellulose fibril, as different oxidized species introduce steric effects that disrupt local crystallinity and in some cases reduce the work needed for polymer decrystallization. Reducing-end oxidations are easiest to decrystallize when located at the end of the fibril, whereas nonreducing end oxidations readily decrystallize from internal cleavage sites despite their lower solvent accessibility. The differential in decrystallization free energy suggests a molecular mechanism consistent with experimentally observed LPMO/cellobiohydrolase synergy. Additionally, the soluble oxidized cellobiose products released by hydrolytic cellulases may bind to the active sites of cellulases with different affinities relative to cellobiose itself, which potentially affects hydrolytic turnover through product inhibition. To examine the effect of oxidation on cello-oligomer binding, we use thermodynamic integration to compute the relative change in binding free energy between the hydrolyzed and oxidized products in the active site of Family 7 and Family 6 processive glycoside hydrolases, Trichoderma reesei Cel7A and Cel6A, which are key industrial cellulases and commonly used model systems for fungal cellulases. Our results suggest that the equilibrium between the two reducing end oxidized products, favoring the linear aldonic acid, may increase product inhibition, which would in turn reduce processive substrate turnover. In the case of LMPO action at the nonreducing end, oxidation appears to lower affinity with the nonreducing end specific cellulase, reducing product inhibition and potentially promoting processive cellulose turnover. Overall, this suggests that oxidation of recalcitrant polysaccharides by LPMOs accelerates degradation not only by increasing the concentration of chain termini but also by reducing decrystallization work, and that product inhibition may be somewhat reduced as a result.
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Affiliation(s)
- Josh V Vermaas
- †Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,‡National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Michael F Crowley
- §Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Gregg T Beckham
- ‡National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Christina M Payne
- ∥Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States.,⊥Center for Computational Science, University of Kentucky, Lexington, Kentucky 40506, United States
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104
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Dupree R, Simmons TJ, Mortimer JC, Patel D, Iuga D, Brown SP, Dupree P. Probing the molecular architecture of Arabidopsis thaliana secondary cell walls using two- and three-dimensional (13)C solid state nuclear magnetic resonance spectroscopy. Biochemistry 2015; 54:2335-45. [PMID: 25739924 DOI: 10.1021/bi501552k] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The plant secondary cell wall is a thickened polysaccharide and phenolic structure, providing mechanical strength to cells, particularly in woody tissues. It is the main feedstock for the developing bioenergy and green chemistry industries. Despite the role that molecular architecture (the arrangement of biopolymers relative to each other, and their conformations) plays in dictating biomass properties, such as recalcitrance to breakdown, it is poorly understood. Here, unprocessed dry (13)C-labeled stems from the model plant Arabidopsis thaliana were analyzed by a variety of (13)C solid state magic angle spinning nuclear magnetic resonance methods, such as one-dimensional cross-polarization and direct polarization, two-dimensional refocused INADEQUATE, RFDR, PDSD, and three-dimensional DARR, demonstrating their viability for the study of native polymer arrangements in intact secondary cell walls. All carbon sites of the two main glucose environments in cellulose (previously assigned to microfibril surface and interior residues) are clearly resolved, as are carbon sites of the other major components of the secondary cell wall: xylan and lignin. The xylan carbon 4 chemical shift is markedly different from that reported previously for solution or primary cell wall xylan, indicating significant changes in the helical conformation in these dried stems. Furthermore, the shift span indicates that xylan adopts a wide range of conformations in this material, with very little in the 31 conformation typical of xylan in solution. Additionally, spatial connections of noncarbohydrate species were observed with both cellulose peaks conventionally assigned as "surface" and as "interior" cellulose environments, raising questions about the origin of these two cellulose signals.
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Affiliation(s)
- Ray Dupree
- †Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
| | - Thomas J Simmons
- ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K
| | - Jennifer C Mortimer
- ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K
| | - Dharmesh Patel
- †Department of Physics, University of Warwick, Coventry CV4 7AL, U.K.,‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K
| | - Dinu Iuga
- †Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
| | - Steven P Brown
- †Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
| | - Paul Dupree
- ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K
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105
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Tolonen LK, Bergenstråhle-Wohlert M, Sixta H, Wohlert J. Solubility of Cellulose in Supercritical Water Studied by Molecular Dynamics Simulations. J Phys Chem B 2015; 119:4739-48. [DOI: 10.1021/acs.jpcb.5b01121] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lasse K. Tolonen
- Department
of Forest Products Technology, Aalto University, P.O. Box 16300, FI-00076 Espoo, Finland
| | - Malin Bergenstråhle-Wohlert
- Wallenberg
Wood Science Center, KTH Royal Institute of Technology, Teknikringen 56-58, SE-10040 Stockholm, Sweden
| | - Herbert Sixta
- Department
of Forest Products Technology, Aalto University, P.O. Box 16300, FI-00076 Espoo, Finland
| | - Jakob Wohlert
- Wallenberg
Wood Science Center, KTH Royal Institute of Technology, Teknikringen 56-58, SE-10040 Stockholm, Sweden
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106
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Abstract
In this work, the physicochemical property and its Effect of hydrous amorphous cellulose has been studied using molecular dynamics. Both intramolecular and intermolecular hydrogen bonds in cellulose molecules decrease with increasing water content, directly leading to the decline of cellulose cohesive energy density, solubility parameters, and mechanical parameters. High water content in amorphous cellulose gives bigger interchain distance of cellulose molecules, indicating that the intermolecular interaction of cellulose molecules is weakened greatly by water.
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107
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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108
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Wu J, Delcheva I, Ngothai Y, Krasowska M, Beattie DA. Bubble-surface interactions with graphite in the presence of adsorbed carboxymethylcellulose. SOFT MATTER 2015; 11:587-99. [PMID: 25515526 DOI: 10.1039/c4sm02380c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The adsorption of carboxymethylcellulose (CMC), and the subsequent effect on bubble-surface interactions, has been studied for a graphite surface. CMC adsorbs on highly oriented pyrolytic graphite (HOPG) in specific patterns: when adsorbed from a solution of low concentration it forms stretched, isolated and sparsely distributed chains, while upon adsorption from a solution of higher concentration, it forms an interconnected network of multilayer features. The amount and topography of the adsorbed CMC affect the electrical properties as well as the wettability of the polymer-modified HOPG surface. Adsorption of CMC onto the HOPG surface causes the zeta potential to be more negative and the modified surface becomes more hydrophilic. This increase in both the absolute value of zeta potential and the surface hydrophilicity originates from the carboxymethyl groups of the CMC polymer. The effect of the adsorbed polymer layer on wetting film drainage and bubble-surface/particle attachment was determined using high speed video microscopy to monitor single bubble-surface collision, and single bubble Hallimond tube flotation experiments. The time of wetting film drainage and the time of three-phase contact line spreading gets significantly longer for polymer-modified HOPG surfaces, indicating that the film rupture and three-phase contact line expansion were inhibited by the presence of polymer. The effect of longer drainage times and slower dewetting correlated with reduced flotation recovery. The molecular kinetic (MK) model was used to quantify the effect of the polymer on dewetting dynamics, and showed an increase in the jump frequency for the polymer adsorbed at the higher concentration.
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Affiliation(s)
- Jueying Wu
- Ian Wark Research Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
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109
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Computerized Models of Carbohydrates. POLYSACCHARIDES 2015. [DOI: 10.1007/978-3-319-16298-0_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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110
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Miyamoto H, Schnupf U, Brady JW. Water structuring over the hydrophobic surface of cellulose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:11017-11023. [PMID: 25365241 DOI: 10.1021/jf501763r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Many important biological solutes possess not only polar and hydrogen-bonding functionalities but also weakly hydrating, or hydrophobic, surfaces. While the aggregation of these hydrophobic surfaces has been shown to play an important role in the aggregation of individual chains of cellulose, it is not known whether the water structuring imposed by these hydrophobic surfaces more closely resembles that associated with small hydrophobic solutes like methane and fats or more closely resembles that associated with extended hydrophobic surfaces like mica or waxy planes. By using molecular dynamics simulations to characterize the water molecule orientations over different regions of the 100 surface of cellulose in contact with water, it was found that the hydrophobic strips of the cellulose crystal are sufficiently narrow that they hydrate like a fatty acid chain, rather than like a more extended surface, suggesting that their aggregation would be dominated by entropy rather than enthalpy.
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Affiliation(s)
- Hitomi Miyamoto
- Department of Food Science, Cornell University , Ithaca, New York 14853, United States
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111
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Petridis L, O’Neill HM, Johnsen M, Fan B, Schulz R, Mamontov E, Maranas J, Langan P, Smith JC. Hydration Control of the Mechanical and Dynamical Properties of Cellulose. Biomacromolecules 2014; 15:4152-9. [DOI: 10.1021/bm5011849] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | | | | | - Bingxin Fan
- Department
of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Roland Schulz
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | | | - Janna Maranas
- Department
of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Paul Langan
- Department
of Chemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Jeremy C. Smith
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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112
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Debranching of soluble wheat arabinoxylan dramatically enhances recalcitrant binding to cellulose. Biotechnol Lett 2014; 37:633-41. [DOI: 10.1007/s10529-014-1705-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
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113
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114
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Mostofian B, Cheng X, Smith JC. Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride. J Phys Chem B 2014; 118:11037-49. [PMID: 25180945 DOI: 10.1021/jp502889c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Ionic liquids have become a popular solvent for cellulose pretreatment in biorefineries due to their efficiency in dissolution and their reusability. Understanding the interactions between cations, anions, and cellulose is key to the development of better solvents and the improvement of pretreatment conditions. While previous studies described the interactions between ionic liquids and cellulose fibers, shedding light on the initial stages of the cellulose dissolution process, we study the end state of that process by exploring the structure and dynamics of a single cellulose decamer solvated in 1-butyl-3-methyl-imidazolium chloride (BmimCl) and in water using replica-exchange molecular dynamics. In both solvents, global structural features of the cellulose chain are similar. However, analyses of local structural properties show that cellulose explores greater conformational variability in the ionic liquid than in water. For instance, in BmimCl the cellulose intramolecular hydrogen bond O3H'···O5 is disrupted more often resulting in greater flexibility of the solute. Our results indicate that the cellulose chain is more dynamic in BmimCl than in water, which may play a role in the favorable dissolution of cellulose in the ionic liquid. Calculation of the configurational entropy of the cellulose decamer confirms its higher conformational flexibility in BmimCl than in water at elevated temperatures.
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Affiliation(s)
- Barmak Mostofian
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
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115
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Karuna N, Zhang L, Walton JH, Couturier M, Oztop MH, Master ER, McCarthy MJ, Jeoh T. The impact of alkali pretreatment and post-pretreatment conditioning on the surface properties of rice straw affecting cellulose accessibility to cellulases. BIORESOURCE TECHNOLOGY 2014; 167:232-40. [PMID: 24983695 DOI: 10.1016/j.biortech.2014.05.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/29/2014] [Accepted: 05/31/2014] [Indexed: 05/18/2023]
Abstract
Rice straw was pretreated with sodium hydroxide and subsequently conditioned to reduce the pH to 5-6 by either: (1) extensive water washing or (2) acidification with hydrochloric acid then water washing. Alkali pretreatment improved the enzymatic digestibility of rice straw by increasing the cellulose accessibility to cellulases. However, acidification after pretreatment reversed the gains in cellulose accessibility to cellulases and enzymatic digestibility due to precipitation of solubilized compounds. Surface composition analyses by ToF-SIMS confirmed a reduction in surface lignin by pretreatment and water washing, and suggested that acidification precipitated a chemically modified form of lignin on the surfaces of rice straw. The spin-spin relaxation times (T2) of the samples indicated increased porosity in alkali pretreated rice straw. The acidified pretreated rice straw had reduced amounts of water in the longer T2 proton pools associated with water in the pores of the biomass likely due to back-filling by the precipitated components.
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Affiliation(s)
- Nardrapee Karuna
- Department of Biological and Agricultural Engineering, University of California at Davis, One Shields Ave., Davis, CA 95616, USA
| | - Lu Zhang
- Department of Food Science and Technology, University of California at Davis, One Shields Ave., Davis, CA 95616, USA
| | - Jeffrey H Walton
- University of California at Davis Nuclear Magnetic Resonance Facility, One Shields Ave., Davis, CA 95616, USA
| | - Marie Couturier
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Mecit H Oztop
- Department of Food Engineering, Middle East Technical University, 06800, Ankara, Turkey
| | - Emma R Master
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Michael J McCarthy
- Department of Biological and Agricultural Engineering, University of California at Davis, One Shields Ave., Davis, CA 95616, USA; Department of Food Science and Technology, University of California at Davis, One Shields Ave., Davis, CA 95616, USA
| | - Tina Jeoh
- Department of Biological and Agricultural Engineering, University of California at Davis, One Shields Ave., Davis, CA 95616, USA.
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116
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Uto T, Mawatari S, Yui T. Theoretical Study of the Structural Stability of Molecular Chain Sheet Models of Cellulose Crystal Allomorphs. J Phys Chem B 2014; 118:9313-21. [DOI: 10.1021/jp503535d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Takuya Uto
- Department
of Applied Chemistry,
Faculty of Engineering, University of Miyazaki, Nishi 1-1 Gakuen-kibanadai, Miyazaki 889-2191, Japan
| | - Sho Mawatari
- Department
of Applied Chemistry,
Faculty of Engineering, University of Miyazaki, Nishi 1-1 Gakuen-kibanadai, Miyazaki 889-2191, Japan
| | - Toshifumi Yui
- Department
of Applied Chemistry,
Faculty of Engineering, University of Miyazaki, Nishi 1-1 Gakuen-kibanadai, Miyazaki 889-2191, Japan
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117
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Tolmachev DA, Lukasheva NV. Study of the process of mineralization of nanofibrils of native bacterial cellulose in solutions of mineral ions: Modeling via the method of molecular dynamics. POLYMER SCIENCE SERIES A 2014. [DOI: 10.1134/s0965545x14040166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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118
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Hoja J, Maurer RJ, Sax AF. Adsorption of Glucose, Cellobiose, and Cellotetraose onto Cellulose Model Surfaces. J Phys Chem B 2014; 118:9017-27. [DOI: 10.1021/jp5025685] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Johannes Hoja
- Department
of Chemistry, University of Graz, 8010 Graz, Austria
| | - Reinhard J. Maurer
- Department
Chemie, Technische Universität München, 85748 Garching, Germany
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119
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White PB, Wang T, Park YB, Cosgrove DJ, Hong M. Water-polysaccharide interactions in the primary cell wall of Arabidopsis thaliana from polarization transfer solid-state NMR. J Am Chem Soc 2014; 136:10399-409. [PMID: 24984197 DOI: 10.1021/ja504108h] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polysaccharide-rich plant cell walls are hydrated under functional conditions, but the molecular interactions between water and polysaccharides in the wall have not been investigated. In this work, we employ polarization transfer solid-state NMR techniques to study the hydration of primary-wall polysaccharides of the model plant, Arabidopsis thaliana. By transferring water (1)H polarization to polysaccharides through distance- and mobility-dependent (1)H-(1)H dipolar couplings and detecting it through polysaccharide (13)C signals, we obtain information about water proximity to cellulose, hemicellulose, and pectins as well as water mobility. Both intact and partially extracted cell wall samples are studied. Our results show that water-pectin polarization transfer is much faster than water-cellulose polarization transfer in all samples, but the extent of extraction has a profound impact on the water-polysaccharide spin diffusion. Removal of calcium ions and the consequent extraction of homogalacturonan (HG) significantly slowed down spin diffusion, while further extraction of matrix polysaccharides restored the spin diffusion rate. These trends are observed in cell walls with similar water content, thus they reflect inherent differences in the mobility and spatial distribution of water. Combined with quantitative analysis of the polysaccharide contents, our results indicate that calcium ions and HG gelation increase the amount of bound water, which facilitates spin diffusion, while calcium removal disrupts the gel and gives rise to highly dynamic water, which slows down spin diffusion. The recovery of spin diffusion rates after more extensive extraction is attributed to increased water-exposed surface areas of the polysaccharides. Water-pectin spin diffusion precedes water-cellulose spin diffusion, lending support to the single-network model of plant primary walls in which a substantial fraction of the cellulose surface is surrounded by pectins.
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Affiliation(s)
- Paul B White
- Department of Chemistry and Ames Laboratory, Iowa State University , Ames, Iowa 50011, United States
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120
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Khandelwal M, Windle A. Origin of chiral interactions in cellulose supra-molecular microfibrils. Carbohydr Polym 2014; 106:128-31. [DOI: 10.1016/j.carbpol.2014.01.050] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 01/14/2014] [Accepted: 01/18/2014] [Indexed: 11/13/2022]
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121
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Hadden JA, French AD, Woods RJ. Effect of microfibril twisting on theoretical powder diffraction patterns of cellulose Iβ. CELLULOSE (LONDON, ENGLAND) 2014; 21:879-884. [PMID: 24729665 PMCID: PMC3979627 DOI: 10.1007/s10570-013-0051-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Previous studies of calculated diffraction patterns for cellulose crystallites suggest that distortions that arise once models have been subjected to MD simulation are the result of both microfibril twisting and changes in unit cell dimensions induced by the empirical force field; to date, it has not been possible to separate the individual contributions of these effects. To provide a better understanding of how twisting manifests in diffraction data, the present study demonstrates a method for generating twisted and linear cellulose structures that can be compared without the bias of dimensional changes, allowing assessment of the impact of twisting alone. Analysis of unit cell dimensions, microfibril volume, hydrogen bond patterns, glycosidic torsion angles, and hydroxymethyl group orientations confirmed that the twisted and linear structures collected with this method were internally consistent, and theoretical powder diffraction patterns for the two were shown to be effectively indistinguishable. These results indicate that differences between calculated patterns for the crystal coordinates and twisted structures from MD simulation can result entirely from changes in unit cell dimensions, and not from microfibril twisting alone. Although powder diffraction patterns for models in the 81-chain size regime were shown to be unaffected by twisting, suggesting that a modest degree of twist is not inconsistent with experimental data, it may be that other diffraction techniques are capable of detecting this structural difference. Until such time as definitive experimental evidence comes to light, the results of this study suggest that both twisted and linear microfibrils may represent an appropriate model for cellulose Iβ.
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Affiliation(s)
- Jodi A. Hadden
- Complex Carbohydrate Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602
| | - Alfred D. French
- Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124
| | - Robert J. Woods
- Complex Carbohydrate Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
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122
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Hayes JA, Eccles KS, Coles SJ, Lawrence SE, Moynihan HA. Supramolecular stacking motifs in the solid state of amide and triazole derivatives of cellobiose. Carbohydr Res 2014; 388:67-72. [PMID: 24631669 DOI: 10.1016/j.carres.2014.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 01/29/2014] [Accepted: 02/07/2014] [Indexed: 10/25/2022]
Abstract
1-Acetamido-1-deoxy-(4-O-β-d-glucopyranosyl-β-d-glucopyranose) (5) and 1-deoxy-1-(4-phenyl-1,2,3-triazolyl)-(4-O-β-d-glucopyranosyl-β-d-glucopyranose) (7) were synthesised from 1-azido-1-deoxy-(4-O-β-d-glucopyranosyl-β-d-glucopyranose) (2) and crystallised as dihydrates. Crystal structural analysis of 5·2H2O displayed an acetamide C(4) chain and stacked cellobiose residues. The structure of 7·2H2O featured π-π stacking and stacking of the cellobiose residues.
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Affiliation(s)
- John A Hayes
- Department of Chemistry / Analytical and Biological Chemistry Research Facility / Synthesis and Solid State Pharmaceutical Centre, University College Cork, College Road, Cork, Ireland
| | - Kevin S Eccles
- Department of Chemistry / Analytical and Biological Chemistry Research Facility / Synthesis and Solid State Pharmaceutical Centre, University College Cork, College Road, Cork, Ireland
| | - Simon J Coles
- UK National Crystallographic Service, Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Simon E Lawrence
- Department of Chemistry / Analytical and Biological Chemistry Research Facility / Synthesis and Solid State Pharmaceutical Centre, University College Cork, College Road, Cork, Ireland
| | - Humphrey A Moynihan
- Department of Chemistry / Analytical and Biological Chemistry Research Facility / Synthesis and Solid State Pharmaceutical Centre, University College Cork, College Road, Cork, Ireland.
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123
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Srinivas G, Cheng X, Smith JC. Coarse-Grain Model for Natural Cellulose Fibrils in Explicit Water. J Phys Chem B 2014; 118:3026-34. [DOI: 10.1021/jp407953p] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Goundla Srinivas
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O.
Box 2008, Oak Ridge, Tennessee 37831-6164, United States
- Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, 2907 East Lee Street, Greensboro, North Carolina 27401, United States
| | - Xiaolin Cheng
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O.
Box 2008, Oak Ridge, Tennessee 37831-6164, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Science, Knoxville, Tennessee 37996-0840, United States
| | - Jeremy C. Smith
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O.
Box 2008, Oak Ridge, Tennessee 37831-6164, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Science, Knoxville, Tennessee 37996-0840, United States
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124
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Inouye H, Zhang Y, Yang L, Venugopalan N, Fischetti RF, Gleber SC, Vogt S, Fowle W, Makowski B, Tucker M, Ciesielski P, Donohoe B, Matthews J, Himmel ME, Makowski L. Multiscale deconstruction of molecular architecture in corn stover. Sci Rep 2014; 4:3756. [PMID: 24441444 PMCID: PMC3895879 DOI: 10.1038/srep03756] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 12/09/2013] [Indexed: 11/23/2022] Open
Abstract
Lignocellulosic composite in corn stover is a candidate biofuel feedstock of substantial abundance and sustainability. Its utilization is hampered by resistance of constituent cellulose fibrils to deconstruction. Here we use multi-scale studies of pretreated corn stover to elucidate the molecular mechanism of deconstruction and investigate the basis of recalcitrance. Dilute acid pretreatment has modest impact on fibrillar bundles at 0.1 micron length scales while leading to significant disorientation of individual fibrils. It disintegrates many fibrils into monomeric cellulose chains or small side-by-side aggregates. Residual crystalline fibrils lose amorphous surface material, change twist and where still cross-linked, coil around one another. Yields from enzymatic digestion are largely due to hydrolysis of individual cellulose chains and fragments generated during pretreatments. Fibrils that remain intact after pretreatment display substantial resistance to enzymatic digestion. Optimization of yield will require strategies that maximize generation of fragments and minimize preservation of intact cellulosic fibrils.
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Affiliation(s)
- Hideyo Inouye
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA 02115
| | - Yan Zhang
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA 02115
| | - Lin Yang
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973
| | - Nagarajan Venugopalan
- GM/CA CAT, XSD, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Robert F. Fischetti
- GM/CA CAT, XSD, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - S. Charlotte Gleber
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Stefan Vogt
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - W. Fowle
- Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Bryan Makowski
- Department of Physics, Rensselaer Polytechnic Institute, Troy, NY, 12180
| | - Melvin Tucker
- Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401
| | - Peter Ciesielski
- Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401
| | - Bryon Donohoe
- Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401
| | - James Matthews
- Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401
| | - Michael E. Himmel
- Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401
| | - Lee Makowski
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA 02115
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115
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125
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Selig MJ, Thygesen LG, Felby C. Correlating the ability of lignocellulosic polymers to constrain water with the potential to inhibit cellulose saccharification. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:159. [PMID: 25426165 PMCID: PMC4243321 DOI: 10.1186/s13068-014-0159-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/08/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Studies in bioconversions have continuously sought the development of processing strategies to overcome the "close physical association" between plant cell wall polymers thought to significantly contribute to biomass recalcitrance [Adv Space Res 18:251-265, 1996],[ Science 315:804-807, 2007]. To a lesser extent, studies have sought to understand biophysical factors responsible for the resistance of lignocelluloses to enzymatic degradation. Provided here are data supporting our hypothesis that the inhibitory potential of different cell wall polymers towards enzymatic cellulose hydrolysis is related to how much these polymers constrain the water surrounding them. We believe the entropy-reducing constraint imparted to polymer associated water plays a negative role by increasing the probability of detrimental interactions such as junction zone formation and the non-productive binding of enzymes. RESULTS Selected commercial lignocellulose-derived polymers, including hemicelluloses, pectins, and lignin, showed varied potential to inhibit 24-h cellulose conversion by a mix of purified cellobiohydrolase I and β-glucosidase. At low dry matter loadings (0.5% w/w), insoluble hemicelluloses were most inhibitory (reducing conversion relative to cellulose-only controls by about 80%) followed by soluble xyloglucan and wheat arabinoxylan (reductions of about 70% and 55%, respectively), while the lignin and pectins tested were the least inhibitory (approximately 20% reduction). Low field nuclear magnetic resonance (LF-NMR) relaxometry used to observe water-related proton relaxation in saturated polymer suspensions (10% dry solids, w/w) showed spin-spin, T2, relaxation time curves generally approached zero faster for the most inhibitory polymer preparations. The manner of this decline varied between polymers, indicating different biophysical aspects may differentially contribute to overall water constraint in each case. To better compare the LF-NMR data to inhibitory potential, T2 values from monocomponent exponential fits of relaxation curves were used as a measure of overall water constraint. These values generally correlated faster relaxation times (greater water constraint) with greater inhibition of the model cellulase system by the polymers. CONCLUSIONS The presented correlation of cellulase inhibition and proton relaxation data provides support for our water constraint-biomass recalcitrance hypothesis. Deeper investigation into polymer-cellulose-cellulase interactions should help elucidate the types of interactions that may be propagating this correlation. If these observations can be verified to be more than correlative, the hypothesis and data presented suggest that a focus on water-polymer interactions and ways to alter them may help resolve key biological lignocellulose processing bottlenecks.
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Affiliation(s)
- Michael J Selig
- IGN, Faculty of Science, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg, Denmark
| | - Lisbeth G Thygesen
- IGN, Faculty of Science, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg, Denmark
| | - Claus Felby
- IGN, Faculty of Science, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg, Denmark
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126
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Atalla R, Crowley M, Himmel M, Atalla R. Irreversible transformations of native celluloses, upon exposure to elevated temperatures. Carbohydr Polym 2014; 100:2-8. [DOI: 10.1016/j.carbpol.2013.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 06/04/2013] [Accepted: 06/07/2013] [Indexed: 11/27/2022]
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127
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Hosoya T, Sakaki S. Levoglucosan formation from crystalline cellulose: importance of a hydrogen bonding network in the reaction. CHEMSUSCHEM 2013; 6:2356-2368. [PMID: 24243863 DOI: 10.1002/cssc.201300338] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/22/2013] [Indexed: 06/02/2023]
Abstract
Levoglucosan (1,6-anhydro-β-D-glucopyranose) formation by the thermal degradation of native cellulose was investigated by MP4(SDQ)//DFT(B3LYP) and DFT(M06-2X)//DFT(B3LYP) level computations. The computational results of dimer models lead to the conclusion that the degradation occurs by a concerted mechanism similar to the degradation of methyl β-D-glucoside reported in our previous study. One-chain models of glucose hexamer, in which the interchain hydrogen bonds of real cellulose crystals are absent, do not exhibit the correct reaction behavior of levoglucosan formation; for instance, the activation enthalpy (Ea =≈38 kcal mol(-1) ) is considerably underestimated compared to the experimental value (48-60 kcal mol(-1) ). This problem is solved with the use of two-chain models that contain interchain hydrogen bonds. The theoretical study of this model clearly shows that the degradation of the internal glucosyl residue leads to the formation of a levoglucosan precursor at the chain end and levoglucosan is selectively formed from this levoglucosan end. The calculated Ea (56-62 kcal mol(-1) ) agrees well with the experimental value. The computational results of three-chain models indicate that this degradation occurs selectively on the crystalline surface. All these computational results provide a comprehensive understanding of several experimental facts, the mechanisms of which have not yet been elucidated.
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Affiliation(s)
- Takashi Hosoya
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna (Austria).
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128
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Characterization of crystalline cellulose in biomass: Basic principles, applications, and limitations of XRD, NMR, IR, Raman, and SFG. KOREAN J CHEM ENG 2013. [DOI: 10.1007/s11814-013-0162-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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129
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Lindner B, Petridis L, Schulz R, Smith JC. Solvent-Driven Preferential Association of Lignin with Regions of Crystalline Cellulose in Molecular Dynamics Simulation. Biomacromolecules 2013; 14:3390-8. [DOI: 10.1021/bm400442n] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin Lindner
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Building 6011, Oak Ridge, Tennessee 37830-6309, United States
- Genome
Science and Technology, University of Tennessee—Knoxville, F337 Walters Life Sciences, 1414
Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Loukas Petridis
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Building 6011, Oak Ridge, Tennessee 37830-6309, United States
| | - Roland Schulz
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Building 6011, Oak Ridge, Tennessee 37830-6309, United States
- Genome
Science and Technology, University of Tennessee—Knoxville, F337 Walters Life Sciences, 1414
Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Building 6011, Oak Ridge, Tennessee 37830-6309, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters
Life Sciences, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
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130
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Ciesielski PN, Matthews JF, Tucker MP, Beckham GT, Crowley MF, Himmel ME, Donohoe BS. 3D electron tomography of pretreated biomass informs atomic modeling of cellulose microfibrils. ACS NANO 2013; 7:8011-9. [PMID: 23988022 DOI: 10.1021/nn4031542] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Fundamental insights into the macromolecular architecture of plant cell walls will elucidate new structure-property relationships and facilitate optimization of catalytic processes that produce fuels and chemicals from biomass. Here we introduce computational methodology to extract nanoscale geometry of cellulose microfibrils within thermochemically treated biomass directly from electron tomographic data sets. We quantitatively compare the cell wall nanostructure in corn stover following two leading pretreatment strategies: dilute acid with iron sulfate co-catalyst and ammonia fiber expansion (AFEX). Computational analysis of the tomographic data is used to extract mathematical descriptions for longitudinal axes of cellulose microfibrils from which we calculate their nanoscale curvature. These nanostructural measurements are used to inform the construction of atomistic models that exhibit features of cellulose within real, process-relevant biomass. By computational evaluation of these atomic models, we propose relationships between the crystal structure of cellulose Iβ and the nanoscale geometry of cellulose microfibrils.
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Affiliation(s)
- Peter N Ciesielski
- Biosciences Center, National Renewable Energy Laboratory , 15013 Denver West Parkway, Golden, Colorado 80401, United States
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131
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Devarajan A, Markutsya S, Lamm MH, Cheng X, Smith JC, Baluyut JY, Kholod Y, Gordon MS, Windus TL. Ab Initio Study of Molecular Interactions in Cellulose Iα. J Phys Chem B 2013; 117:10430-43. [DOI: 10.1021/jp406266u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | | | | | - Xiaolin Cheng
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6309, United States
| | - Jeremy C. Smith
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6309, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters
Life Sciences, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
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132
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Hydration and saccharification of cellulose Iβ, II and IIII at increasing dry solids loadings. Biotechnol Lett 2013; 35:1599-607. [DOI: 10.1007/s10529-013-1258-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/24/2013] [Indexed: 12/01/2022]
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133
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Oliveira RP, Driemeier C. CRAFS: a model to analyze two-dimensional X-ray diffraction patterns of plant cellulose. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889813014805] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Cellulose from higher plants is a vast renewable resource organized as crystals. Analysis of these crystals by X-ray diffraction poses very specific challenges, including ubiquitous crystallite texture and substantial overlapping of diffraction peaks. In this article, a tailor-made model named Cellulose Rietveld Analysis for Fine Structure (CRAFS) is developed to analyze two-dimensional X-ray diffraction patterns from raw and processed plant cellulose. One-dimensional powder diffractograms are analyzable as a particular case. The CRAFS model considers cellulose Iβ crystal structure, fibrillar crystal shape, paracrystalline peak broadening, pseudo-Voigt peak profiles, harmonic crystallite orientation distribution function and diffraction in fiber geometry. Formulated on the basis of the Rietveld method, CRAFS is presently written in the MATLAB computing language. A set of meaningful coefficients are output from each analyzed pattern. To exemplify model applicability, representative samples are analyzed, bringing some general insights and evidencing the model's potential for systematic parameterization of the fine structure of raw and processed plant celluloses.
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134
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Markutsya S, Devarajan A, Baluyut JY, Windus TL, Gordon MS, Lamm MH. Evaluation of coarse-grained mapping schemes for polysaccharide chains in cellulose. J Chem Phys 2013; 138:214108. [DOI: 10.1063/1.4808025] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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135
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Molecular dynamics study of carbohydrate binding module mutants of fungal cellobiohydrolases. Carbohydr Res 2013; 374:96-102. [DOI: 10.1016/j.carres.2013.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/31/2013] [Accepted: 04/03/2013] [Indexed: 11/19/2022]
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136
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Zhao Z, Shklyaev OE, Nili A, Mohamed MNA, Kubicki JD, Crespi VH, Zhong L. Cellulose Microfibril Twist, Mechanics, and Implication for Cellulose Biosynthesis. J Phys Chem A 2013; 117:2580-9. [DOI: 10.1021/jp3089929] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhen Zhao
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
| | - Oleg E. Shklyaev
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Departments
of Physics, Chemistry, and Materials Science and Engineering, The Pennsylvania State University, State College, Pennsylvania
16801, United States
| | - Abdolmajid Nili
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Departments
of Physics, Chemistry, and Materials Science and Engineering, The Pennsylvania State University, State College, Pennsylvania
16801, United States
| | - Mohamed Naseer Ali Mohamed
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Department of Geosciences, Pennsylvania State University, State College, Pennsylvania 16801,
United States
| | - James D. Kubicki
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Department of Geosciences, Pennsylvania State University, State College, Pennsylvania 16801,
United States
| | - Vincent H. Crespi
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Departments
of Physics, Chemistry, and Materials Science and Engineering, The Pennsylvania State University, State College, Pennsylvania
16801, United States
| | - Linghao Zhong
- Center for Lignocellulose
Structure and Formation, Pennsylvania State University, State College, Pennsylvania 16801, United States
- Department
of Chemistry, Pennsylvania State University, Mont Alto, Pennsylvania 17237, United States
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137
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Bechtold T, Manian AP, Öztürk HB, Paul U, Široká B, Široký J, Soliman H, Vo LT, Vu-Manh H. Ion-interactions as driving force in polysaccharide assembly. Carbohydr Polym 2013; 93:316-23. [DOI: 10.1016/j.carbpol.2012.01.064] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 01/17/2012] [Accepted: 01/19/2012] [Indexed: 11/29/2022]
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138
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Gu J, Catchmark JM, Kaiser EQ, Archibald DD. Quantification of cellulose nanowhiskers sulfate esterification levels. Carbohydr Polym 2013; 92:1809-16. [DOI: 10.1016/j.carbpol.2012.10.078] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 10/24/2012] [Accepted: 10/30/2012] [Indexed: 10/27/2022]
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139
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A model for estimating the medium properties of Avicel to ethanol conversion. Bioprocess Biosyst Eng 2013; 36:1311-8. [DOI: 10.1007/s00449-012-0879-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 12/20/2012] [Indexed: 10/27/2022]
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140
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Thomas LH, Forsyth VT, Šturcová A, Kennedy CJ, May RP, Altaner CM, Apperley DC, Wess TJ, Jarvis MC. Structure of cellulose microfibrils in primary cell walls from collenchyma. PLANT PHYSIOLOGY 2013; 161:465-76. [PMID: 23175754 PMCID: PMC3532275 DOI: 10.1104/pp.112.206359] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/13/2012] [Indexed: 05/17/2023]
Abstract
In the primary walls of growing plant cells, the glucose polymer cellulose is assembled into long microfibrils a few nanometers in diameter. The rigidity and orientation of these microfibrils control cell expansion; therefore, cellulose synthesis is a key factor in the growth and morphogenesis of plants. Celery (Apium graveolens) collenchyma is a useful model system for the study of primary wall microfibril structure because its microfibrils are oriented with unusual uniformity, facilitating spectroscopic and diffraction experiments. Using a combination of x-ray and neutron scattering methods with vibrational and nuclear magnetic resonance spectroscopy, we show that celery collenchyma microfibrils were 2.9 to 3.0 nm in mean diameter, with a most probable structure containing 24 chains in cross section, arranged in eight hydrogen-bonded sheets of three chains, with extensive disorder in lateral packing, conformation, and hydrogen bonding. A similar 18-chain structure, and 24-chain structures of different shape, fitted the data less well. Conformational disorder was largely restricted to the surface chains, but disorder in chain packing was not. That is, in position and orientation, the surface chains conformed to the disordered lattice constituting the core of each microfibril. There was evidence that adjacent microfibrils were noncovalently aggregated together over part of their length, suggesting that the need to disrupt these aggregates might be a constraining factor in growth and in the hydrolysis of cellulose for biofuel production.
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141
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Tolmachev DA, Lukasheva NV. Interactions binding mineral and organic phases in nanocomposites based on bacterial cellulose and calcium phosphates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:13473-13484. [PMID: 22880938 DOI: 10.1021/la302418x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The interactions responsible for the adhesion of calcium phosphate (CP) nanocrystals and bacterial cellulose (BC) nanofibrils in the composite material obtained by mixing aqueous suspensions of presynthesized CP and BC and the dependence of these interactions on the CP morphology and chemical structure have been elucidated by molecular mechanics calculations of the CP-BC interfacial structures. The interactions between the superficial CP and BC crystal layers have been simulated. Two crystalline CP structures (i.e., hydroxyapatite (HAP) and whitlockite) with two morphologies (plate-shaped and rod-shaped) were considered. Electrostatics has been found to be the major contributor to the adhesion of the CP crystallites and BC nanofibers, and the formation of interfacial hydrogen bonds makes a minor contribution to the interaction energy. It has also been found that, in general, the energy gain resulting from whitlockite-BC binding is greater than that for HAP-BC binding, and the binding of the rod-shaped crystallites of whitlockite with BC is the most profitable. The energy loss and entropy gain upon replacement of the BC-water and CP-water contacts by the BC-CP contacts have been estimated.
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Affiliation(s)
- D A Tolmachev
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bol'shoi pr. 31, St. Petersburg, 199004 Russia
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142
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Liu H, Cheng G, Kent M, Stavila V, Simmons BA, Sale KL, Singh S. Simulations Reveal Conformational Changes of Methylhydroxyl Groups during Dissolution of Cellulose Iβ in Ionic Liquid 1-Ethyl-3-methylimidazolium Acetate. J Phys Chem B 2012; 116:8131-8. [DOI: 10.1021/jp301673h] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hanbin Liu
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California
- Sandia National Laboratories, Livermore, California
| | - Gang Cheng
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California
- Sandia National Laboratories, Livermore, California
| | - Michael Kent
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California
- Sandia National Laboratories, Albuquerque, New Mexico
| | | | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California
- Sandia National Laboratories, Livermore, California
| | - Kenneth L Sale
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California
- Sandia National Laboratories, Livermore, California
| | - Seema Singh
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California
- Sandia National Laboratories, Livermore, California
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143
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Chang R, Gross AS, Chu JW. Degree of Polymerization of Glucan Chains Shapes the Structure Fluctuations and Melting Thermodynamics of a Cellulose Microfibril. J Phys Chem B 2012; 116:8074-83. [DOI: 10.1021/jp302974x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Adam S. Gross
- Department of Chemical and Biomolecular
Engineering and Energy Biosciences Institute, University of California, Berkeley, 94720, United States
| | - Jhih-Wei Chu
- Department of Chemical and Biomolecular
Engineering and Energy Biosciences Institute, University of California, Berkeley, 94720, United States
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144
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Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases. Structure 2012; 20:1051-61. [PMID: 22578542 DOI: 10.1016/j.str.2012.04.002] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 03/20/2012] [Accepted: 04/04/2012] [Indexed: 01/22/2023]
Abstract
The use of cellulases remains a major cost in the production of renewable fuels and chemicals from lignocellulosic biomass. Fungi secrete copper-dependent polysaccharide monooxygenases (PMOs) that oxidatively cleave crystalline cellulose and improve the effectiveness of cellulases. However, the means by which PMOs recognize and cleave their substrates in the plant cell wall remain unclear. Here, we present structures of Neurospora crassa PMO-2 and PMO-3 at 1.10 and 1.37 Å resolution, respectively. In the structures, dioxygen species are found in the active sites, consistent with the proposed cleavage mechanism. Structural and sequence comparisons between PMOs also reveal that the enzyme substrate-binding surfaces contain highly varied aromatic amino acid and glycosylation positions. The structures reported here provide evidence for a wide range of PMO substrate recognition patterns in the plant cell wall, including binding modes that traverse multiple glucan chains.
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145
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Široká B, Manian AP, Noisternig MF, Henniges U, Kostic M, Potthast A, Griesser UJ, Bechtold T. Wash-dry cycle induced changes in low-ordered parts of regenerated cellulosic fibers. J Appl Polym Sci 2012. [DOI: 10.1002/app.36894] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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146
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Nimlos MR, Beckham GT, Matthews JF, Bu L, Himmel ME, Crowley MF. Binding preferences, surface attachment, diffusivity, and orientation of a family 1 carbohydrate-binding module on cellulose. J Biol Chem 2012; 287:20603-12. [PMID: 22496371 PMCID: PMC3370244 DOI: 10.1074/jbc.m112.358184] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cellulase enzymes often contain carbohydrate-binding modules (CBMs) for binding to cellulose. The mechanisms by which CBMs recognize specific surfaces of cellulose and aid in deconstruction are essential to understand cellulase action. The Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase, Cel7A, is known to selectively bind to hydrophobic surfaces of native cellulose. It is most commonly suggested that three aromatic residues identify the planar binding face of this CBM, but several recent studies have challenged this hypothesis. Here, we use molecular simulation to study the CBM binding orientation and affinity on hydrophilic and hydrophobic cellulose surfaces. Roughly 43 μs of molecular dynamics simulations were conducted, which enables statistically significant observations. We quantify the fractions of the CBMs that detach from crystal surfaces or diffuse to other surfaces, the diffusivity along the hydrophobic surface, and the overall orientation of the CBM on both hydrophobic and hydrophilic faces. The simulations demonstrate that there is a thermodynamic driving force for the Cel7A CBM to bind preferentially to the hydrophobic surface of cellulose relative to hydrophilic surfaces. In addition, the simulations demonstrate that the CBM can diffuse from hydrophilic surfaces to the hydrophobic surface, whereas the reverse transition is not observed. Lastly, our simulations suggest that the flat faces of Family 1 CBMs are the preferred binding surfaces. These results enhance our understanding of how Family 1 CBMs interact with and recognize specific cellulose surfaces and provide insights into the initial events of cellulase adsorption and diffusion on cellulose.
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Affiliation(s)
- Mark R Nimlos
- National Bioenergy Center, National Renewable Energy Center, Golden, Colorado 80401, USA.
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147
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Gomes TCF, Skaf MS. Cellulose-Builder: A toolkit for building crystalline structures of cellulose. J Comput Chem 2012; 33:1338-46. [DOI: 10.1002/jcc.22959] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/05/2012] [Accepted: 02/07/2012] [Indexed: 12/31/2022]
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148
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Bazooyar F, Momany FA, Bolton K. Validating empirical force fields for molecular-level simulation of cellulose dissolution. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.01.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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149
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Matthews JF, Beckham GT, Bergenstråhle-Wohlert M, Brady JW, Himmel ME, Crowley MF. Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields. J Chem Theory Comput 2012; 8:735-48. [DOI: 10.1021/ct2007692] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Gregg T. Beckham
- Department of Chemical Engineering, Colorado School of Mines, Golden, Colorado, United
States
| | - Malin Bergenstråhle-Wohlert
- Department of Food
Science, Cornell University, Ithaca, New
York, United States
- Wallenberg
Wood Science Center, Royal Institute of Technology, Stockholm, Sweden
| | - John W. Brady
- Department of Food
Science, Cornell University, Ithaca, New
York, United States
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150
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Santhanam N, Badri DV, Decker SR, Manter DK, Reardon KF, Vivanco JM. Lignocellulose Decomposition by Microbial Secretions. SIGNALING AND COMMUNICATION IN PLANTS 2012. [DOI: 10.1007/978-3-642-23047-9_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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