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Golden, CO, United States

Nimlos M.R.,National Bioenergy Center | Beckham G.T.,National Bioenergy Center | Beckham G.T.,Colorado School of Mines | Matthews J.F.,Biosciences Center | And 3 more authors.
Journal of Biological Chemistry | Year: 2012

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 Cel7ACBMto 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 1CBMs interact with and recognize specific cellulose surfaces and provide insights into the initial events of cellulase adsorption and diffusion on cellulose. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.

Momeni M.H.,Swedish University of Agricultural Sciences | Payne C.M.,Biosciences Center | Payne C.M.,University of Kentucky | Hansson H.,Swedish University of Agricultural Sciences | And 7 more authors.
Journal of Biological Chemistry | Year: 2013

Background: Family 7 cellulases exhibit significant hydrolytic potential in cellulose degradation. Results: Wereport the Heterobasidion irregulare GH7 structure and compare it with other GH7 cellobiohydrolases with simulation. Conclusion: H. irregulare Cel7A exhibits intermediate dynamical and structural properties between Phanerochaete chrysosporium Cel7D and Hypocrea jecorina Cel7A. Significance: These results highlight regions of family 7 cellobiohydrolases important for carbohydrate processivity and association- dissociation rates on cellulose. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.

Chmely S.C.,National Renewable Energy Laboratory | Kim S.,National Renewable Energy Laboratory | Ciesielski P.N.,Biosciences Center | Jimenez-Oses G.,University of California at Los Angeles | And 3 more authors.
ACS Catalysis | Year: 2013

We employ density functional theory (DFT) calculations and kinetics measurements to understand the mechanism of a xantphos-containing molecular ruthenium catalyst acting on an alkyl aryl ether linkage similar to that found in lignin to produce acetophenone and phenol. The most favorable reaction pathway suggested from DFT is compared to kinetics measurements, and good agreement is found between the predicted and the measured activation barriers. The DFT calculations reveal several interesting features, including an unusual 5-membered transition state structure for oxidative insertion in contrast to the typically proposed 3-membered transition state, a preference for an O-bound over a C-bound Ru-enolate, and a significant kinetic preference for the order of product release from the catalyst. The experimental measurements confirm that the reaction proceeds via a free ketone intermediate, but also suggest that the conversion of the intermediate ketone to acetophenone and phenol does not necessarily require ketone dissociation from the catalyst. Overall, this work elucidates the kinetically and thermodynamically preferred reaction pathways for tandem alcohol dehydrogenation and reductive ether bond cleavage by the ruthenium-xantphos catalyst. © 2013 American Chemical Society.

Neto C.,University of Lisbon | Fonseca J.P.,Biosciences Center | Costa J.C.,University of Lisbon | Bioret F.,University of Western Brittany
Acta Botanica Gallica | Year: 2015

Omphalodes kuzinskyanae Willk. is an endangered annual plant of the family Boraginaceae, endemic to a narrow coastal area in the Lisbon region (Portugal). Omphalodes littoralis Lehm. occurs in northwest Spain (subsp. gallaecica) and northwest France (subsp. littoralis). Three approaches were used to assess the ecological requirements of O. kuzinskyanae: (1) physical and chemical characterization of their habitat soil; (2) phytosociological analysis; (3) comparison of several life history parameters under different light conditions. Germination experiments were conducted to evaluate seed dormancy. The results show that O. kuzinskyanae occurs in thin sandy soil with a substantial amount of organic matter and clay, mostly over limestone pavements. Phytosociological analysis shows that O. kuzinskyanae occurs both in sciophytic and heliophytic communities. Life history comparisons demonstrated that this plant has a strong preference for sciophytic conditions: under strong shade, plants have a higher survival rate, attain a greater height and width, and produce approximately nine times more seeds than in sunny conditions. In contrast with O. kuzinskyanae, published data on O. littoralis indicate that this species occurs in heliophytic conditions. This group of Omphalodes is possibly limited both in geographical distribution and habitat by its vulnerability to hydric stress. Scenarios are discussed that can explain the extensive gap separating the present ranges of the two species and their ecological differences. We propose two new syntaxa: Linario arenariae-Omphalodetum littoralis, Geranio purpurei-Galietum minutuli omphalodetosum kuzinskyanae. © 2015 © 2015 Société botanique de France.

Jinkerson R.E.,Colorado School of Mines | Subramanian V.,Colorado School of Mines | Subramanian V.,Biosciences Center | Posewitz M.C.,Colorado School of Mines
Biofuels | Year: 2011

Biofuels derived from algal energy carriers, including lipids, starch and hydrogen, offer a promising, renewable alternative to fossil fuels. Unfortunately, native algal metabolisms are not optimized for the accumulation of these renewable bioenergy carriers. Systems biology, which includes genomics, transcriptomics, proteomics, metabolomics and lipidomics, can inform and provide key insights to advance algal strain development for biotechnological applications. Recent advances in analytical technologies have enabled these sophisticated, high-throughput, holistic 'omics' techniques to generate highly accurate and quantitative datasets that can be leveraged to improve biofuel phenotypes in phototrophic microorganisms. The study of algal genomes and transcriptomes allows for the identification of genes, metabolic pathways and regulatory networks. Investigations of algal proteomes reveal protein levels, locations and post-translational modifications, while study of the metabolome reveals metabolite fluxes and intermediates. All of these systems-biology tools are integral for investigating algal metabolism from the whole-cell perspective. This review focuses on how systems biology has been applied to studying metabolic networks in algae and cyanobacteria, and how these technologies can be used to improve bioenergy-carrier accumulation. © 2011 Future Science Ltd.

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