1
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Higasi PMR, Velasco JA, Pellegrini VOA, de Araújo EA, França BA, Keller MB, Labate CA, Blossom BM, Segato F, Polikarpov I. Light-stimulated T. thermophilus two-domain LPMO9H: Low-resolution SAXS model and synergy with cellulases. Carbohydr Polym 2021; 260:117814. [PMID: 33712158 DOI: 10.1016/j.carbpol.2021.117814] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/06/2021] [Accepted: 02/10/2021] [Indexed: 12/19/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs), monocopper enzymes that oxidatively cleave recalcitrant polysaccharides, have important biotechnological applications. Thermothelomyces thermophilus is a rich source of biomass-active enzymes, including many members from auxiliary activities family 9 LPMOs. Here, we report biochemical and structural characterization of recombinant TtLPMO9H which oxidizes cellulose at the C1 and C4 positions and shows enhanced activity in light-driven catalysis assays. TtLPMO9H also shows activity against xyloglucan. The addition of TtLPMO9H to endoglucanases from four different glucoside hydrolase families (GH5, GH12, GH45 and GH7) revealed that the product formation was remarkably increased when TtLPMO9H was combined with GH7 endoglucanase. Finally, we determind the first low resolution small-angle X-ray scattering model of the two-domain TtLPMO9H in solution that shows relative positions of its two functional domains and a conformation of the linker peptide, which can be relevant for the catalytic oxidation of cellulose and xyloglucan.
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Affiliation(s)
- Paula M R Higasi
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense 400, São Carlos, São Paulo, Brazil
| | - Josman A Velasco
- Lorena School of Engineering, University of São Paulo, Estrada Municipal do Campinho s/n, Lorena, São Paulo, Brazil
| | - Vanessa O A Pellegrini
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense 400, São Carlos, São Paulo, Brazil
| | - Evandro A de Araújo
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense 400, São Carlos, São Paulo, Brazil
| | - Bruno Alves França
- Lorena School of Engineering, University of São Paulo, Estrada Municipal do Campinho s/n, Lorena, São Paulo, Brazil
| | - Malene B Keller
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Carlos A Labate
- Luiz de Queiroz College of Agriculture, University of São Paulo, Av. Pádua Dias 11, Piracicaba, São Paulo, Brazil
| | - Benedikt M Blossom
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Fernando Segato
- Lorena School of Engineering, University of São Paulo, Estrada Municipal do Campinho s/n, Lorena, São Paulo, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense 400, São Carlos, São Paulo, Brazil.
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2
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Pena CE, Costa MGS, Batista PR. Glycosylation effects on the structure and dynamics of a full-length Cel7A cellulase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140248. [PMID: 31279935 DOI: 10.1016/j.bbapap.2019.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 11/17/2022]
Abstract
Fungi cellulases are used to degrade cellulose-containing biomass for bioethanol production. Industrial cellulases such as Cel7A from Trichoderma reesei (TrCel7A) are critical in this process. Thus, the understanding of structure and dynamics is crucial for engineering variants with improved cellulolytic activity. This cellulase consists of two domains connected by a flexible and highly glycosylated linker. However, the linker flexibility has hindered the determination of Cel7A complete structure. Herein, based on atomic and sparse data, we applied integrative modelling to build a model of the complete enzyme structure. Next, through simulations, we studied the glycosylation effects on the structure and dynamics of a solubilized TrCel7A. Essential dynamics analysis showed that O-glycosylation in the linker led to the stabilization of protein overall dynamics. O-linked glycans seem to restrict protein dihedral angles distribution in this region, selecting more elongated conformations. Besides the reduced flexibility, functional interdomain motions occurred in a more concerted way in the glycosylated system. In contrast, in the absence of glycosylation, we observed vast conformational plasticity with the functional domains frequently collapsing. We report here evidence that targeting Cel7A linker flexibility by point mutations including modification of glycosylation sites could be a promising design strategy to improve cellulase activity.
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Affiliation(s)
- Carlos Eduardo Pena
- Fundação Oswaldo Cruz, Programa de Computação Científica, Rio de Janeiro 21040-900, Brazil; Instituto Oswaldo Cruz, Programa de Pós-graduação em Biologia Computacional e Sistemas, Rio de Janeiro 21040-900, Brazil
| | - Mauricio G S Costa
- Fundação Oswaldo Cruz, Programa de Computação Científica, Rio de Janeiro 21040-900, Brazil; Instituto Oswaldo Cruz, Programa de Pós-graduação em Biologia Computacional e Sistemas, Rio de Janeiro 21040-900, Brazil; École Normale Supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, Cachan 94235, France
| | - Paulo Ricardo Batista
- Fundação Oswaldo Cruz, Programa de Computação Científica, Rio de Janeiro 21040-900, Brazil; Instituto Oswaldo Cruz, Programa de Pós-graduação em Biologia Computacional e Sistemas, Rio de Janeiro 21040-900, Brazil.
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3
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Nomura T, Iwase H, Saka N, Takahashi N, Mikami B, Mizutani K. High-resolution crystal structures of the glycoside hydrolase family 45 endoglucanase EG27II from the snail Ampullaria crossean. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:426-436. [PMID: 30988259 DOI: 10.1107/s2059798319003000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/27/2019] [Indexed: 11/10/2022]
Abstract
Although endogenous animal cellulases have great potential for industrial applications such as bioethanol production, few investigations have focused on these enzymes. In this study, the glycoside hydrolase family 45 (GH45) subfamily B endoglucanase EG27II from the snail Ampullaria crossean was expressed using a Pichia pastoris expression system and the crystal structure of the apo form was determined at 1.00 Å resolution; this is the highest resolution structure of an animal endoglucanase. The results showed that EG27II has a double-ψ six-stranded β-barrel and that the structure of EG27II more closely resembles those of subfamily C enzymes than those of subfamily A enzymes. The structure of EG27II complexed with cellobiose was also determined under cryoconditions and at room temperature at three pH values, pH 4.0, 5.5 and 8.0, and no structural changes were found to be associated with the change in pH. The structural comparison and catalytic activity measurements showed that Asp137 and Asn112 function as the catalytic acid and base, respectively, and that Asp27 is also an important residue for catalysis. These high-resolution structures of EG27II provide a large amount of information for structure-based enzyme modification and cell-surface engineering, which will advance biofuel production using animal-derived cellulases.
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Affiliation(s)
- Taisuke Nomura
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hisamu Iwase
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Naoki Saka
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Nobuyuki Takahashi
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Bunzo Mikami
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kimihiko Mizutani
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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4
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Tan P, Liang Y, Xu Q, Mamontov E, Li J, Xing X, Hong L. Gradual Crossover from Subdiffusion to Normal Diffusion: A Many-Body Effect in Protein Surface Water. PHYSICAL REVIEW LETTERS 2018; 120:248101. [PMID: 29956983 DOI: 10.1103/physrevlett.120.248101] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/12/2018] [Indexed: 06/08/2023]
Abstract
Dynamics of hydration water is essential for the function of biomacromolecules. Previous studies have demonstrated that water molecules exhibit subdiffusion on the surface of biomacromolecules; yet the microscopic mechanism remains vague. Here, by performing neutron scattering, molecular dynamics simulations, and analytic modeling on hydrated perdeuterated protein powders, we found water molecules jump randomly between trapping sites on protein surfaces, whose waiting times obey a broad distribution, resulting in subdiffusion. Moreover, the subdiffusive exponent gradually increases with observation time towards normal diffusion due to a many-body volume-exclusion effect.
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Affiliation(s)
- Pan Tan
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yihao Liang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Eugene Mamontov
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jinglai Li
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiangjun Xing
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, China
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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5
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Silveira RL, Skaf MS. Concerted motions and large-scale structural fluctuations of Trichoderma reesei Cel7A cellobiohydrolase. Phys Chem Chem Phys 2018; 20:7498-7507. [PMID: 29488531 DOI: 10.1039/c8cp00101d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Cellobiohydrolases (CBHs) are key enzymes for the saccharification of cellulose and play major roles in industrial settings for biofuel production. The catalytic core domain of these enzymes exhibits a long and narrow binding tunnel capable of binding glucan chains from crystalline cellulose and processively hydrolyze them. The binding cleft is topped by a set of loops, which are believed to play key roles in substrate binding and cleavage processivity. Here, we present an analysis of the loop motions of the Trichoderma reesei Cel7A catalytic core domain (TrCel7A) using conventional and accelerated molecular dynamics simulations. We observe that the loops exhibit highly coupled fluctuations and cannot move independently of each other. In the absence of a substrate, the characteristic large amplitude dynamics of TrCel7A consists of breathing motions, where the loops undergo open-and-close fluctuations. Upon substrate binding, the open-close fluctuations of the loops are quenched and one of the loops moves parallel to the binding site, possibly to allow processive motion along the glucan chain. Using microsecond accelerated molecular dynamics, we observe large-scale fluctuations of the loops (up to 37 Å) and the entire exposure of the TrCel7A binding site in the absence of the substrate, resembling an endoglucanase. These results suggest that the initial CBH-substrate contact and substrate recognition by the enzyme are similar to that of endoglucanases and, once bound to the substrate, the loops remain closed for proper enzymatic activity.
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Affiliation(s)
- Rodrigo L Silveira
- Institute of Chemistry, University of Campinas, Cx. P. 6154, Campinas, 13084-862, SP, Brazil.
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6
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Goodell B, Zhu Y, Kim S, Kafle K, Eastwood D, Daniel G, Jellison J, Yoshida M, Groom L, Pingali SV, O’Neill H. Modification of the nanostructure of lignocellulose cell walls via a non-enzymatic lignocellulose deconstruction system in brown rot wood-decay fungi. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:179. [PMID: 28702084 PMCID: PMC5504834 DOI: 10.1186/s13068-017-0865-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/30/2017] [Indexed: 06/01/2023]
Abstract
Wood decayed by brown rot fungi and wood treated with the chelator-mediated Fenton (CMF) reaction, either alone or together with a cellulose enzyme cocktail, was analyzed by small angle neutron scattering (SANS), sum frequency generation (SFG) spectroscopy, Fourier transform infrared (FTIR) analysis, X-ray diffraction (XRD), atomic force microscopy (AFM), and transmission electron microscopy (TEM). Results showed that the CMF mechanism mimicked brown rot fungal attack for both holocellulose and lignin components of the wood. Crystalline cellulose and lignin were both depolymerized by the CMF reaction. Porosity of the softwood cell wall did not increase during CMF treatment, enzymes secreted by the fungi did not penetrate the decayed wood. The enzymes in the cellulose cocktail also did not appear to alter the effects of the CMF-treated wood relative to enhancing cell wall deconstruction. This suggests a rethinking of current brown rot decay models and supports a model where monomeric sugars and oligosaccharides diffuse from the softwood cell walls during non-enzymatic action. In this regard, the CMF mechanism should not be thought of as a "pretreatment" used to permit enzymatic penetration into softwood cell walls, but instead it enhances polysaccharide components diffusing to fungal enzymes located in wood cell lumen environments during decay. SANS and other data are consistent with a model for repolymerization and aggregation of at least some portion of the lignin within the cell wall, and this is supported by AFM and TEM data. The data suggest that new approaches for conversion of wood substrates to platform chemicals in biorefineries could be achieved using the CMF mechanism with >75% solubilization of lignocellulose, but that a more selective suite of enzymes and other downstream treatments may be required to work when using CMF deconstruction technology. Strategies to enhance polysaccharide release from lignocellulose substrates for enhanced enzymatic action and fermentation of the released fraction would also aid in the efficient recovery of the more uniform modified lignin fraction that the CMF reaction generates to enhance biorefinery profitability.
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Affiliation(s)
- Barry Goodell
- Department of Microbiology, Morrill Science Center IV, University of Massachusetts, Amherst, MA 01003-9298 USA
| | - Yuan Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Seong Kim
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, PA USA
| | - Kabindra Kafle
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, PA USA
| | - Daniel Eastwood
- Department of Biosciences, Swansea University, Singleton Park Campus, Swansea, UK
| | - Geoffrey Daniel
- Department of Forest Products/Wood Science, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Jody Jellison
- Center for Agriculture, Food and the Environment, University of Massachusetts, 316 Stockbridge Hall, Amherst, USA
| | - Makoto Yoshida
- Department of Environmental and Natural Resource Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Leslie Groom
- USDA Forest Service, Southern Research Station, Pineville, Louisiana 71360 USA
| | - Sai Venkatesh Pingali
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Hugh O’Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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7
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Crystal structures of wild‐type
Trichoderma reesei
Cel7A catalytic domain in open and closed states. FEBS Lett 2016; 590:4429-4438. [DOI: 10.1002/1873-3468.12464] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/03/2016] [Accepted: 10/10/2016] [Indexed: 11/07/2022]
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8
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Deleting the Ig-Like Domain of Alicyclobacillus acidocaldarius Endoglucanase Cel9A Causes a Simultaneous Increase in the Activity and Stability. Mol Biotechnol 2016; 58:12-21. [PMID: 26537871 DOI: 10.1007/s12033-015-9900-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Endoglucanase Cel9A from Alicyclobacillus acidocaldarius (AaCel9A) is a monomeric enzyme with 537 residues. This enzyme has an Ig-like domain in the N-terminus of the catalytic domain. In this study, the role of the Ig-like domain on the activity, stability, and structural rigidity of AaCel9A and the effect of calcium on enzyme activity and stability were examined by comparing a truncated enzyme with deletion of the Ig-like domain (AaCel9AΔN) to the wild-type enzyme. Our results showed that the deletion of the Ig-like domain increased the catalytic efficiency of the truncated enzyme up to threefold without any significant changes in the K m of the enzyme. Furthermore, pH and temperature optimum for activity were shifted from 6.5 to 7.5 and from 65 to 60 °C, respectively, by deletion of the Ig-like domain. The thermal stability and fluorescence quenching results indicated that the stability and rigidity of the truncated enzyme have been more than that of the wild-type enzyme. Calcium similarly increased the catalytic efficiency of the enzymes (up to 40 %) and remarkably raised the stability of the AaCel9A compared to the AaCel9AΔN. This shows that Ig-like domain has a role in the increase of the enzyme stability by calcium in the wild-type enzyme.
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9
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Biophysical and biochemical studies of a major endoglucanase secreted by Xanthomonas campestris pv. campestris. Enzyme Microb Technol 2016; 91:1-7. [PMID: 27444323 DOI: 10.1016/j.enzmictec.2016.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 05/14/2016] [Accepted: 05/20/2016] [Indexed: 12/23/2022]
Abstract
Endoglucanases are the main cellulolytic enzymes secreted by the bacterium Xanthomonas campestris pv. campestris (Xcc). The major endoglucanase exported by this bacterium into an external milieu is an enzyme XccCel5A, which belongs to GH5 family subfamily 1 and is encoded by the gene engXCA. We purified XccCel5A using ammonium sulfate precipitation followed by size exclusion chromatography and identified it by zymogram analysis. Circular dichroism and fluorescence spectroscopy studies showed that XccCel5A is stable in a wide pH range and up to about 55°C and denatures at the higher temperatures. The optimal conditions for enzyme activity were identified as T=45°C and pH=7.0. Under the optimum conditions the catalytic efficiency (kcat/KM) of the enzyme was determined as 5.16×10(4)s(-1)M(-1) using carboxymethylcellulose (CMC) as a substrate. Our SAXS studies revealed extended tadpole-shape molecular assembly, typical for cellulases, and allowed to determine an overall shape of the enzyme and a relative position of the catalytic and cellulose binding domains.
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10
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Souza TV, Araujo JN, da Silva VM, Liberato MV, Pimentel AC, Alvarez TM, Squina FM, Garcia W. Chemical stability of a cold-active cellulase with high tolerance toward surfactants and chaotropic agent. ACTA ACUST UNITED AC 2015; 9:1-8. [PMID: 28352586 PMCID: PMC5360981 DOI: 10.1016/j.btre.2015.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 11/28/2022]
Abstract
CelE1 is a cold-active endo-acting glucanase with high activity at a broad temperature range and under alkaline conditions. Here, we examined the effects of pH on the secondary and tertiary structures, net charge, and activity of CelE1. Although variation in pH showed a small effect in the enzyme structure, the activity was highly influenced at acidic conditions, while reached the optimum activity at pH 8. Furthermore, to estimate whether CelE1 could be used as detergent additives, CelE1 activity was evaluated in the presence of surfactants. Ionic and nonionic surfactants were not able to reduce CelE1 activity significantly. Therefore, CelE1 was found to be promising candidate for use as detergent additives. Finally, we reported a thermodynamic analysis based on the structural stability and the chemical unfolding/refolding process of CelE1. The results indicated that the chemical unfolding proceeds as a reversible two-state process. These data can be useful for biotechnological applications.
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Affiliation(s)
- Thaís V Souza
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Juscemácia N Araujo
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Viviam M da Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Marcelo V Liberato
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Agnes C Pimentel
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Thabata M Alvarez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
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11
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O'Neill H, Shah R, Evans BR, He J, Pingali SV, Chundawat SPS, Jones AD, Langan P, Davison BH, Urban V. Production of bacterial cellulose with controlled deuterium-hydrogen substitution for neutron scattering studies. Methods Enzymol 2015; 565:123-46. [PMID: 26577730 DOI: 10.1016/bs.mie.2015.08.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Isotopic enrichment of biomacromolecules is a widely used technique that enables the investigation of the structural and dynamic properties to provide information not accessible with natural abundance isotopic composition. This study reports an approach for deuterium incorporation into bacterial cellulose. A media formulation for growth of Acetobacter xylinus subsp. sucrofermentans and Gluconacetobacter hansenii was formulated that supports cellulose production in deuterium (D) oxide. The level of D incorporation can be varied by altering the ratio of deuterated and protiated glycerol used during cell growth in the D2O-based growth medium. Spectroscopic analysis and mass spectrometry show that the level of deuterium incorporation is high (>90%) for the perdeuterated form of bacterial cellulose. The small-angle neutron scattering profiles of the cellulose with different amounts of D incorporation are all similar indicating that there are no structural changes in the cellulose due to substitution of deuterium for hydrogen. In addition, by varying the amount of deuterated glycerol in the media it was possible to vary the scattering length density of the deuterated cellulose. The ability to control deuterium content of cellulose extends the range of experiments using techniques such as neutron scattering to reveal information about the structure and dynamics of cellulose, and its interactions with other biomacromolecules as well as synthetic polymers used for development of composite materials.
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Affiliation(s)
- Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
| | - Riddhi Shah
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
| | - Barbara R Evans
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Junhong He
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Sai Venkatesh Pingali
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA; Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Paul Langan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Brian H Davison
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Volker Urban
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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12
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de Oliveira LC, da Silva VM, Colussi F, Cabral AD, de Oliveira Neto M, Squina FM, Garcia W. Conformational changes in a hyperthermostable glycoside hydrolase: enzymatic activity is a consequence of the loop dynamics and protonation balance. PLoS One 2015; 10:e0118225. [PMID: 25723179 PMCID: PMC4344334 DOI: 10.1371/journal.pone.0118225] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 01/10/2015] [Indexed: 11/20/2022] Open
Abstract
Endo-β-1, 4-mannanase from Thermotoga petrophila (TpMan) is a modular hyperthermostable enzyme involved in the degradation of mannan-containing polysaccharides. The degradation of these polysaccharides represents a key step for several industrial applications. Here, as part of a continuing investigation of TpMan, the region corresponding to the GH5 domain (TpManGH5) was characterized as a function of pH and temperature. The results indicated that the enzymatic activity of the TpManGH5 is pH-dependent, with its optimum activity occurring at pH 6. At pH 8, the studies demonstrated that TpManGH5 is a molecule with a nearly spherical tightly packed core displaying negligible flexibility in solution, and with size and shape very similar to crystal structure. However, TpManGH5 experiences an increase in radius of gyration in acidic conditions suggesting expansion of the molecule. Furthermore, at acidic pH values, TpManGH5 showed a less globular shape, probably due to a loop region slightly more expanded and flexible in solution (residues Y88 to A105). In addition, molecular dynamics simulations indicated that conformational changes caused by pH variation did not change the core of the TpManGH5, which means that only the above mentioned loop region presents high degree of fluctuations. The results also suggested that conformational changes of the loop region may facilitate polysaccharide and enzyme interaction. Finally, at pH 6 the results indicated that TpManGH5 is slightly more flexible at 65°C when compared to the same enzyme at 20°C. The biophysical characterization presented here is well correlated with the enzymatic activity and provide new insight into the structural basis for the temperature and pH-dependent activity of the TpManGH5. Also, the data suggest a loop region that provides a starting point for a rational design of biotechnological desired features.
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Affiliation(s)
- Leandro C de Oliveira
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, UNESP-Univ Estadual Paulista, São José do Rio Preto, SP, Brazil
| | - Viviam M da Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Francieli Colussi
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Aline D Cabral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Mario de Oliveira Neto
- Departamento de Física e Biofísica, Instituto de Biociências, UNESP-Univ Estadual Paulista, Botucatu, SP, Brazil
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
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13
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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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14
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Vermaas JV, Petridis L, Qi X, Schulz R, Lindner B, Smith JC. Mechanism of lignin inhibition of enzymatic biomass deconstruction. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:217. [PMID: 26697106 PMCID: PMC4687093 DOI: 10.1186/s13068-015-0379-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/09/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route to biofuel production. However, the inhibition of enzymatic activity in pretreated biomass by lignin severely limits the efficiency of this process. RESULTS By performing atomic-detail molecular dynamics simulation of a biomass model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed lignin inhibition mechanisms. We find that lignin binds preferentially both to the elements of cellulose to which the cellulases also preferentially bind (the hydrophobic faces) and also to the specific residues on the cellulose-binding module of the cellulase that are critical for cellulose binding of TrCel7A (Y466, Y492, and Y493). CONCLUSIONS Lignin thus binds exactly where for industrial purposes it is least desired, providing a simple explanation of why hydrolysis yields increase with lignin removal.
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Affiliation(s)
- Josh V. Vermaas
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
- />Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 61801 Urbana, IL USA
| | - Loukas Petridis
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
| | - Xianghong Qi
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
- />Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, 37996 Knoxville, TN USA
| | - Roland Schulz
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
- />Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, 37996 Knoxville, TN USA
| | - Benjamin Lindner
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
| | - Jeremy. C. Smith
- />UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN USA
- />Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, 37996 Knoxville, TN USA
- />University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, P.O.Box 2008, Oak Ridge, TN 37831-6309 USA
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15
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Greene ER, Himmel ME, Beckham GT, Tan Z. Glycosylation of Cellulases: Engineering Better Enzymes for Biofuels. Adv Carbohydr Chem Biochem 2015; 72:63-112. [PMID: 26613815 DOI: 10.1016/bs.accb.2015.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cellulose in plant cell walls is the largest reservoir of renewable carbon on Earth. The saccharification of cellulose from plant biomass into soluble sugars can be achieved using fungal and bacterial cellulolytic enzymes, cellulases, and further converted into fuels and chemicals. Most fungal cellulases are both N- and O-glycosylated in their native form, yet the consequences of glycosylation on activity and structure are not fully understood. Studying protein glycosylation is challenging as glycans are extremely heterogeneous, stereochemically complex, and glycosylation is not under direct genetic control. Despite these limitations, many studies have begun to unveil the role of cellulase glycosylation, especially in the industrially relevant cellobiohydrolase from Trichoderma reesei, Cel7A. Glycosylation confers many beneficial properties to cellulases including enhanced activity, thermal and proteolytic stability, and structural stabilization. However, glycosylation must be controlled carefully as such positive effects can be dampened or reversed. Encouragingly, methods for the manipulation of glycan structures have been recently reported that employ genetic tuning of glycan-active enzymes expressed from homogeneous and heterologous fungal hosts. Taken together, these studies have enabled new strategies for the exploitation of protein glycosylation for the production of enhanced cellulases for biofuel production.
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16
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Bodenheimer AM, Cuneo MJ, Swartz PD, He J, O’Neill HM, Myles DAA, Evans BR, Meilleur F. Crystallization and preliminary X-ray diffraction analysis of Hypocrea jecorina Cel7A in two new crystal forms. Acta Crystallogr F Struct Biol Commun 2014; 70:773-6. [PMID: 24915091 PMCID: PMC4051535 DOI: 10.1107/s2053230x14008851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 04/17/2014] [Indexed: 11/10/2022] Open
Abstract
Cel7A (previously known as cellobiohydrolase I) from Hypocrea jecorina was crystallized in two crystalline forms, neither of which have been previously reported. Both forms co-crystallize under the same crystallization conditions. The first crystal form belonged to space group C2, with unit-cell parameters a=152.5, b=44.9, c=57.6 Å, β=101.2°, and diffracted X-rays to 1.5 Å resolution. The second crystal form belonged to space group P6₃22, with unit-cell parameters a=b≃155, c≃138 Å, and diffracted X-rays to 2.5 Å resolution. The crystals were obtained using full-length Cel7A, which consists of a large 434-residue N-terminal catalytic domain capable of cleaving cellulose, a 27-residue flexible linker and a small 36-residue C-terminal carbohydrate-binding module (CBM). However, a preliminary analysis of the electron-density maps suggests that the linker and CBM are disordered in both crystal forms. Complete refinement and structure analysis are currently in progress.
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Affiliation(s)
- Annette M. Bodenheimer
- Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Matthew J. Cuneo
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul D. Swartz
- Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Junhong He
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Hugh M. O’Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dean A. A. Myles
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Barbara R. Evans
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Flora Meilleur
- Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh, North Carolina, USA
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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17
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Sammond DW, Yarbrough JM, Mansfield E, Bomble YJ, Hobdey SE, Decker SR, Taylor LE, Resch MG, Bozell JJ, Himmel ME, Vinzant TB, Crowley MF. Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity. J Biol Chem 2014; 289:20960-9. [PMID: 24876380 DOI: 10.1074/jbc.m114.573642] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The inhibitory action of lignin on cellulase cocktails is a major challenge to the biological saccharification of plant cell wall polysaccharides. Although the mechanism remains unclear, hydrophobic interactions between enzymes and lignin are hypothesized to drive adsorption. Here we evaluate the role of hydrophobic interactions in enzyme-lignin binding. The hydrophobicity of the enzyme surface was quantified using an estimation of the clustering of nonpolar atoms, identifying potential interaction sites. The adsorption of enzymes to lignin surfaces, measured using the quartz crystal microbalance, correlates to the hydrophobic cluster scores. Further, these results suggest a minimum hydrophobic cluster size for a protein to preferentially adsorb to lignin. The impact of electrostatic contribution was ruled out by comparing the isoelectric point (pI) values to the adsorption of proteins to lignin surfaces. These results demonstrate the ability to predict enzyme-lignin adsorption and could potentially be used to design improved cellulase cocktails, thus lowering the overall cost of biofuel production.
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Affiliation(s)
| | | | - Elisabeth Mansfield
- the Applied Chemicals and Materials Division, National Institute for Standards and Technology, Boulder, Colorado 80305, and
| | | | | | | | | | - Michael G Resch
- From the Biosciences Center and National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Joseph J Bozell
- the Center for Renewable Carbon, Center for the Catalytic Conversion of Biomass (C3Bio), University of Tennessee, Knoxville, Tennessee 37917
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18
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Gusakov AV. Comment on “Revealing Nature’s Cellulase Diversity: The Digestion Mechanism of
Caldicellulosiruptor bescii
CelA”. Science 2014; 344:578. [DOI: 10.1126/science.1251248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Alexander V. Gusakov
- Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119991, Russia
- A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russia
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19
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Deciphering the effect of the different N-glycosylation sites on the secretion, activity, and stability of cellobiohydrolase I from Trichoderma reesei. Appl Environ Microbiol 2014; 80:3962-71. [PMID: 24747898 DOI: 10.1128/aem.00261-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
N-linked glycosylation modulates and diversifies the structures and functions of the eukaryotic proteome through both intrinsic and extrinsic effects on proteins. We investigated the significance of the three N-linked glycans on the catalytic domain of cellobiohydrolase I (CBH1) from the filamentous fungus Trichoderma reesei in its secretion and activity. While the removal of one or two N-glycosylation sites hardly affected the extracellular secretion of CBH1, eliminating all of the glycosylation sites did induce expression of the unfolded protein response (UPR) target genes, and secretion of this CBH1 variant was severely compromised in a calnexin gene deletion strain. Further characterization of the purified CBH1 variants showed that, compared to Asn270, the thermal reactivity of CBH1 was significantly decreased by removal of either Asn45 or Asn384 glycosylation site during the catalyzed hydrolysis of soluble substrate. Combinatorial loss of these two N-linked glycans further exacerbated the temperature-dependent inactivation. In contrast, this thermal labile property was less severe when hydrolyzing insoluble cellulose. Analysis of the structural integrity of CBH1 variants revealed that removal of N-glycosylation at Asn384 had a more pronounced effect on the integrity of regular secondary structure compared to the loss of Asn45 or Asn270. These data implicate differential roles of N-glycosylation modifications in contributing to the stability of specific functional regions of CBH1 and highlight the potential of improving the thermostability of CBH1 by tuning proper interactions between glycans and functional residues.
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20
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Granum DM, Schutt TC, Maupin CM. Computational Evaluation of the Dynamic Fluctuations of Peripheral Loops Enclosing the Catalytic Tunnel of a Family 7 Cellobiohydrolase. J Phys Chem B 2014; 118:5340-9. [DOI: 10.1021/jp5011555] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David M. Granum
- Chemical
and Biological Engineering
Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Timothy C. Schutt
- Chemical
and Biological Engineering
Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - C. Mark Maupin
- Chemical
and Biological Engineering
Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
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21
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Bu L, Crowley MF, Himmel ME, Beckham GT. Computational investigation of the pH dependence of loop flexibility and catalytic function in glycoside hydrolases. J Biol Chem 2013; 288:12175-86. [PMID: 23504310 DOI: 10.1074/jbc.m113.462465] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulase enzymes cleave glycosidic bonds in cellulose to produce cellobiose via either retaining or inverting hydrolysis mechanisms, which are significantly pH-dependent. Many fungal cellulases function optimally at pH ~5, and their activities decrease dramatically at higher or lower pH. To understand the molecular-level implications of pH in cellulase structure, we use a hybrid, solvent-based, constant pH molecular dynamics method combined with pH-based replica exchange to determine the pK(a) values of titratable residues of a glycoside hydrolase (GH) family 6 cellobiohydrolase (Cel6A) and a GH family 7 cellobiohydrolase (Cel7A) from the fungus Hypocrea jecorina. For both enzymes, we demonstrate that a bound substrate significantly affects the pKa values of the acid residues at the catalytic center. The calculated pK(a) values of catalytic residues confirm their proposed roles from structural studies and are consistent with the experimentally measured apparent pKa values. Additionally, GHs are known to impart a strained pucker conformation in carbohydrate substrates in active sites for catalysis, and results from free energy calculations combined with constant pH molecular dynamics suggest that the correct ring pucker is stable near the optimal pH for both Cel6A and Cel7A. Much longer molecular dynamics simulations of Cel6A and Cel7A with fixed protonation states based on the calculated pK(a) values suggest that pH affects the flexibility of tunnel loops, which likely affects processivity and substrate complexation. Taken together, this work demonstrates several molecular-level effects of pH on GH enzymes important for cellulose turnover in the biosphere and relevant to biomass conversion processes.
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Affiliation(s)
- Lintao Bu
- National Bioenergy Center, Colorado School of Mines, Golden, Colorado 80401, USA.
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22
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Langan P, Evans BR, Foston M, Heller WT, O'Neill H, Petridis L, Pingali SV, Ragauskas AJ, Smith JC, Urban VS, Davison BH. Neutron Technologies for Bioenergy Research. Ind Biotechnol (New Rochelle N Y) 2012. [DOI: 10.1089/ind.2012.0012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Paul Langan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Barbara R. Evans
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Marcus Foston
- Institute of Paper Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - William T. Heller
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN
| | - Loukas Petridis
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Sai Venkatesh Pingali
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Arthur J. Ragauskas
- Institute of Paper Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Jeremy C. Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Volker S. Urban
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Brian H. Davison
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN
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23
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Garnett JA, Simpson PJ, Taylor J, Benjamin SV, Tagliaferri C, Cota E, Chen YYM, Wu H, Matthews S. Structural insight into the role of Streptococcus parasanguinis Fap1 within oral biofilm formation. Biochem Biophys Res Commun 2012; 417:421-6. [PMID: 22166217 PMCID: PMC3518267 DOI: 10.1016/j.bbrc.2011.11.131] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 11/28/2011] [Indexed: 12/22/2022]
Abstract
The fimbriae-associated protein 1 (Fap1) is a major adhesin of Streptococcus parasanguinis, a primary colonizer of the oral cavity that plays an important role in the formation of dental plaque. Fap1 is an extracellular adhesive surface fibre belonging to the serine-rich repeat protein (SRRP) family, which plays a central role in the pathogenesis of streptococci and staphylococci. The N-terminal adhesive region of Fap1 (Fap1-NR) is composed of two domains (Fap1-NR(α) and Fap1-NR(β)) and is projected away from the bacterial surface via the extensive serine-rich repeat region, for adhesion to the salivary pellicle. The adhesive properties of Fap1 are modulated through a pH switch in which a reduction in pH results in a rearrangement between the Fap1-NR(α) and Fap1-NR(β) domains, which assists in the survival of S. parasanguinis in acidic environments. We have solved the structure of Fap1-NR(α) at pH 5.0 at 3.0Ǻ resolution and reveal how subtle rearrangements of the 3-helix bundle combined with a change in electrostatic potential mediates 'opening' and activation of the adhesive region. Further, we show that pH-dependent changes are critical for biofilm formation and present an atomic model for the inter-Fap1-NR interactions which have been assigned an important role in the biofilm formation.
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Affiliation(s)
- James A. Garnett
- Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Peter J. Simpson
- Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Jonathan Taylor
- Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Stefi V. Benjamin
- Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Camille Tagliaferri
- Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Ernesto Cota
- Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Yi-Ywan M. Chen
- Department of Microbiology & Immunology, and Research Center for Pathogenic Bacteria, Chang Gung University, Tao-Yuan, Taiwan
| | - Hui Wu
- Department of Pediatric Dentistry, University of Alabama at Birmingham, School of Dentistry, Birmingham, AL 35294
| | - Stephen Matthews
- Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
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24
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In Silico Strategies Toward Enzyme Function and Dynamics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012. [DOI: 10.1016/b978-0-12-398312-1.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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