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Molecular aspects of plant cell wall architecture

Grant number: 14/10448-1
Support Opportunities:Scholarships in Brazil - Post-Doctoral
Effective date (Start): August 01, 2014
Effective date (End): July 31, 2019
Field of knowledge:Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
Principal Investigator:Munir Salomao Skaf
Grantee:Rodrigo Leandro Silveira
Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
Associated research grant:13/08293-7 - CCES - Center for Computational Engineering and Sciences, AP.CEPID
Associated scholarship(s):16/22956-7 - Hybrid QM/MM simulations of feruloyl esterases: cleavage mechanism of lignin-carbohydrate complexes in plant cell walls, BE.EP.PD


The bagasse of sugar cane is an abundant biomass from Brazilian agroindustry, which holds a promising venue for the production of second-generation ethanol. One of the major challenges in the development of a sustainable means of obtaining biofuels and other valuable chemicals from sugar cane bagasse and other biomass feedstocks is the recalcitrance of the lignocellulosic cell walls to the action of degrading enzymes, which currently demands expensive biochemical and thermochemical pretreatments. Therefore, understanding the microscopic nature of plant cell wall architecture, the molecular aspects associated with its structural strength, as well as the interactions between cell walls and carbohydrate degrading enzymes is of the utmost importance in this field.Plant cell walls are comprised of cellulosic microfibrils embedded in a matrix of non-cellulosic polysaccharides such as lignin and hemicellulose. The highly hydrated ligno-hemicellulose matrix coats cellulose microfibrils and is presumably responsible for much of the strong cohesion forces between microfibrils. It is known, for instance, that by genetically manipulating lignin and hemicellulose expression and composition in plants one may modify, and eventually control, cell wall strength. Different plan species present distinct hemicellulose composition and content, and this is the main reason behind the observed differences in biomass feedstocks texture and hardness. Nevertheless, very little is known about this problem at a molecular level.The team involved in this project will to apply the Kovalenko-Hirata 3D-RISM Integral Equation approaches to investigate solvation properties around hemicellulose-coated cellulose microfribrils and specially the potential of mean force (PMF) between two long parallel microfibrils in the presence of the polysaccharide matrix embedded in an aqueous environment. We would like to answer questions such as how different hemicellulose types and composition affect the PMF between microfibrils; what is the attending role of the surrounding solvent, if any. To achieve that goal, we should prepare crystalline cellulose microfibrils (which we already have) using fully atomistic models and coat them with different types and composition of hemicellulose, starting at the composition adequate for sugar cane. Lignin could be added as well. It is desirable that the polysaccharide matrix is treated as fully flexible solvent molecules. In addition to cell walls, we also propose using multiscale computer simulations approaches at various levels of refinement, ranging from hybrid QM/MM to coarse-graining MD simulations, in order to investigate the dynamics of carbohydrate modifying enzymes and its interactions with model cell walls of varying complexity. (AU)

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Scientific publications (14)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
AUSTIN, HARRY P.; ALLEN, MARK D.; DONOHOE, BRYON S.; RORRER, NICHOLAS A.; KEARNS, FIONA L.; SILVEIRA, RODRIGO L.; POLLARD, BENJAMIN C.; DOMINICK, GRAHAM; DUMAN, RAMONA; EL OMARI, KAMEL; et al. Characterization and engineering of a plastic-degrading aromatic polyesterase. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v. 115, n. 19, p. E4350-E4357, . (13/08293-7, 14/10448-1, 16/22956-7)
SILVEIRA, RODRIGO L.; SKAF, MUNIR S.. Molecular dynamics of the Bacillus subtilis expansin EXLX1: interaction with substrates and structural basis of the lack of activity of mutants. Physical Chemistry Chemical Physics, v. 18, n. 5, p. 3510-3521, . (13/08293-7, 14/10448-1)
PEREIRA, CAROLINE S.; SILVEIRA, RODRIGO L.; SKAF, MUNIR S.. QM/MM Simulations of Enzymatic Hydrolysis of Cellulose: Probing the Viability of an Endocyclic Mechanism for an Inverting Cellulase. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 61, n. 4, p. 11-pg., . (13/08293-7, 14/10448-1, 15/25031-1)
SILVEIRA, RODRIGO L.; STOYANOV, STANISLAV R.; GUSAROV, SERGEY; SKAF, MUNIR S.; KOVALENKO, ANDRIY. Supramolecular Interactions in Secondary Plant Cell Walls: Effect of Lignin Chemical Composition Revealed with the Molecular Theory of Solvation. Journal of Physical Chemistry Letters, v. 6, n. 1, p. 206-211, . (13/08293-7, 14/10448-1)
BUSSE-WICHER, MARTA; LI, AN; SILVEIRA, RODRIGO L.; PEREIRA, CAROLINE S.; TRYFONA, THEODORA; GOMES, THIAGO C. F.; SKAF, MUNIR S.; DUPREE, PAUL. Evolution of Xylan Substitution Patterns in Gymnosperms and Angiosperms: Implications for Xylan Interaction with Cellulose. Plant Physiology, v. 171, n. 4, p. 2418-2431, . (13/08293-7, 14/10448-1, 15/25031-1)
SILVEIRA, RODRIGO L.; STOYANOV, STANISLAV R.; KOVALENKO, ANDRIY; SKAF, MUNIR S.. Cellulose Aggregation under Hydrothermal Pretreatment Conditions. Biomacromolecules, v. 17, n. 8, p. 2582-2590, . (13/08293-7, 14/10448-1)
SILVEIRA, RODRIGO L.; SKAF, MUNIR S.. Concerted motions and large-scale structural fluctuations of Trichoderma reesei Cel7A cellobiohydrolase. Physical Chemistry Chemical Physics, v. 20, n. 11, p. 7498-7507, . (13/08293-7, 14/10448-1)
PEREIRA, CAROLINE S.; SILVEIRA, RODRIGO L.; DUPREE, PAUL; SKAF, MUNIR S.. Effects of Xylan Side-Chain Substitutions on Xylan-Cellulose Interactions and Implications for Thermal Pretreatment of Cellulosic Biomass. Biomacromolecules, v. 18, n. 4, p. 1311-1321, . (13/08293-7, 14/10448-1, 15/25031-1)
SILVEIRA, RODRIGO L.; SKAF, MUNIR S.. Molecular Dynamics Simulations of Family 7 Cellobiohydrolase Mutants Aimed at Reducing Product Inhibition. Journal of Physical Chemistry B, v. 119, n. 29, p. 9295-9303, . (13/08293-7, 14/10448-1)
LIBERATO, MARCELO V.; SILVEIRA, RODRIGO L.; PRATES, ERICA T.; DE ARAUJO, EVANDRO A.; PELLEGRINI, VANESSA O. A.; CAMILO, CESAR M.; KADOWAKI, MARCO A.; NETO, MARIO DE O.; POPOV, ALEXANDER; SKAF, MUNIR S.; et al. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. SCIENTIFIC REPORTS, v. 6, . (13/08293-7, 09/52840-7, 10/18773-8, 13/15582-5, 08/56255-9, 14/10448-1)
MALLINSON, SAM J. B.; MACHOVINA, MELODIE M.; SILVEIRA, RODRIGO L.; GARCIA-BORRAS, MARC; GALLUP, NATHAN; JOHNSON, CHRISTOPHER W.; ALLEN, MARK D.; SKAF, MUNIR S.; CROWLEY, MICHAEL F.; NEIDLE, ELLEN L.; et al. A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion. NATURE COMMUNICATIONS, v. 9, . (13/08293-7, 14/10448-1, 16/22956-7)
TRENTIN, LUCAS N.; PEREIRA, CAROLINE S.; SILVEIRA, RODRIGO L.; HILL, STEFAN; SORIEUL, MATHIAS; SKAF, MUNIR S.. Nanoscale Wetting of Crystalline Cellulose. Biomacromolecules, v. 22, n. 10, p. 4251-4261, . (19/17373-0, 13/08293-7, 14/10448-1, 15/25031-1)
SILVEIRA, RODRIGO L.; KNOTT, BRANDON C.; PEREIRA, CAROLINE S.; CROWLEY, MICHAEL F.; SKAF, MUNIR S.; BECKHAM, GREGG T.. Transition Path Sampling Study of the Feruloyl Esterase Mechanism. Journal of Physical Chemistry B, v. 125, n. 8, p. 2018-2030, . (15/25031-1, 17/01151-3, 16/22956-7, 13/08293-7, 14/10448-1)
GALE, ELLA; WIRAWAN, REMIGIUS H.; SILVEIRA, RODRIGO L.; PEREIRA, CAROLINE S.; JOHNS, MARCUS A.; SKAF, MUNIR S.; SCOTT, JANET L.. Directed Discovery of Greener Cosolvents: New Cosolvents for Use in Ionic Liquid Based Organic Electrolyte Solutions for Cellulose Dissolution. ACS SUSTAINABLE CHEMISTRY & ENGINEERING, v. 4, n. 11, p. 6200-6207, . (13/08293-7, 14/10448-1, 15/25031-1)

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