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Cheng Q, DeYonker NJ. A Case Study of the Glycoside Hydrolase Enzyme Mechanism Using an Automated QM-Cluster Model Building Toolkit. Front Chem 2022; 10:854318. [PMID: 35402371 PMCID: PMC8987026 DOI: 10.3389/fchem.2022.854318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/08/2022] [Indexed: 12/03/2022] Open
Abstract
Glycoside hydrolase enzymes are important for hydrolyzing the β-1,4 glycosidic bond in polysaccharides for deconstruction of carbohydrates. The two-step retaining reaction mechanism of Glycoside Hydrolase Family 7 (GH7) was explored with different sized QM-cluster models built by the Residue Interaction Network ResidUe Selector (RINRUS) software using both the wild-type protein and its E217Q mutant. The first step is the glycosylation, in which the acidic residue 217 donates a proton to the glycosidic oxygen leading to bond cleavage. In the subsequent deglycosylation step, one water molecule migrates into the active site and attacks the anomeric carbon. Residue interaction-based QM-cluster models lead to reliable structural and energetic results for proposed glycoside hydrolase mechanisms. The free energies of activation for glycosylation in the largest QM-cluster models were predicted to be 19.5 and 31.4 kcal mol−1 for the wild-type protein and its E217Q mutant, which agree with experimental trends that mutation of the acidic residue Glu217 to Gln will slow down the reaction; and are higher in free energy than the deglycosylation transition states (13.8 and 25.5 kcal mol−1 for the wild-type protein and its mutant, respectively). For the mutated protein, glycosylation led to a low-energy product. This thermodynamic sink may correspond to the intermediate state which was isolated in the X-ray crystal structure. Hence, the glycosylation is validated to be the rate-limiting step in both the wild-type and mutated enzyme.
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Affiliation(s)
- Qianyi Cheng
- *Correspondence: Qianyi Cheng, ; Nathan John DeYonker,
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2
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Mechanism and biomass association of glucuronoyl esterase: an α/β hydrolase with potential in biomass conversion. Nat Commun 2022; 13:1449. [PMID: 35304453 PMCID: PMC8933493 DOI: 10.1038/s41467-022-28938-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 02/11/2022] [Indexed: 12/02/2022] Open
Abstract
Glucuronoyl esterases (GEs) are α/β serine hydrolases and a relatively new addition in the toolbox to reduce the recalcitrance of lignocellulose, the biggest obstacle in cost-effective utilization of this important renewable resource. While biochemical and structural characterization of GEs have progressed greatly recently, there have yet been no mechanistic studies shedding light onto the rate-limiting steps relevant for biomass conversion. The bacterial GE OtCE15A possesses a classical yet distinctive catalytic machinery, with easily identifiable catalytic Ser/His completed by two acidic residues (Glu and Asp) rather than one as in the classical triad, and an Arg side chain participating in the oxyanion hole. By QM/MM calculations, we identified deacylation as the decisive step in catalysis, and quantified the role of Asp, Glu and Arg, showing the latter to be particularly important. The results agree well with experimental and structural data. We further calculated the free-energy barrier of post-catalysis dissociation from a complex natural substrate, suggesting that in industrial settings non-catalytic processes may constitute the rate-limiting step, and pointing to future directions for enzyme engineering in biomass utilization. Zong and coworkers combine computational and experimental methods to decipher in detail the mechanism of action of glucuronoyl esterases, enzymes with significant biotechnological potential for decoupling lignin from polysaccharides in biomass.
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Zong Z, Li Q, Hong Z, Fu H, Cai W, Chipot C, Jiang H, Zhang D, Chen S, Shao X. Lysine Mutation of the Claw-Arm-Like Loop Accelerates Catalysis by Cellobiohydrolases. J Am Chem Soc 2019; 141:14451-14459. [DOI: 10.1021/jacs.9b08477] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Zhiyou Zong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Qiyu Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhangyong Hong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Haohao Fu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Wensheng Cai
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana—Champaign, LPCT, UMR 7019 Universiteé de Lorraine CNRS, Vandœuvre-lès-Nancy F-54500, France
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Dongyuan Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Shulin Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Xueguang Shao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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4
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Yao L, Yoo CG, Meng X, Li M, Pu Y, Ragauskas AJ, Yang H. A structured understanding of cellobiohydrolase I binding to poplar lignin fractions after dilute acid pretreatment. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:96. [PMID: 29632555 PMCID: PMC5883885 DOI: 10.1186/s13068-018-1087-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 01/11/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Cellulase adsorption to lignin is considered a cost barrier for bioethanol production; however, its detailed association mechanism is still not fully understood. In this study, two natural poplar variants with high and low sugar release performance were selected as the low and high recalcitrant raw materials (named L and H, respectively). Three different lignin fractions were extracted using ethanol, followed by p-dioxane and then cellulase treatment from the dilute acid pretreated poplar solids (fraction 1, 2, and 3, respectively). RESULTS Each lignin fraction had different physicochemical properties. Ethanol-extracted lignin had the lowest weight average molecular weight, while the molecular weights for the other two lignin fractions were similar. 31P NMR analysis revealed that lignin fraction with higher molecular weight contained more aliphatic hydroxyl groups and less phenolic hydroxyl groups. Semi-quantitative analysis by 2D HSQC NMR indicated that the lignin fractions isolated from the natural variants had different contents of syringyl (S), guaiacyl (G) and interunit linkages. Lignin extracted by ethanol contained the largest amount of S units, the smallest amounts of G and p-hydroxybenzoate (PB) subunits, while the contents of these lignin subunits in the other two lignin fractions were similar. The lignin fraction obtained after cellulase treatment was primarily comprised of β-O-4 linkages with small amounts of β-5 and β-β linkages. The binding strength of these three lignin fractions obtained by Langmuir equations were in the order of L1 > L3 > L2 for the low recalcitrance poplar and H1 > H2 > H3 for the high recalcitrance poplar. CONCLUSIONS Overall, adsorption ability of lignin was correlated with the sugar release of poplar. Structural features of lignin were associated with its binding to CBH. For natural poplar variants, lignin fractions with lower molecular weight and polydispersity index (PDI) exhibited more CBH adsorption ability. Lignins with more phenolic hydroxyl groups had higher CBH binding strength. It was also found that lignin fractions with more condensed aromatics adsorbed more CBH likely attributed to stronger hydrophobic interactions.
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Affiliation(s)
- Lan Yao
- School of Pulp & Paper Engineering, Hubei University of Technology, Wuhan, 430068 China
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan, 430068 China
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN 37996-2200 USA
| | - Chang Geun Yoo
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xianzhi Meng
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN 37996-2200 USA
| | - Mi Li
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yunqiao Pu
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Arthur J. Ragauskas
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN 37996-2200 USA
- Department of Forestry, Wildlife and Fisheries, Center for Renewable Carbon, Institute of Agriculture, The University of Tennessee, Knoxville, TN 37996-2200 USA
| | - Haitao Yang
- School of Pulp & Paper Engineering, Hubei University of Technology, Wuhan, 430068 China
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan, 430068 China
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5
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Yan S, Yao L, Kang B, Lee JY. Solvent effect on hydrogen bonded Tyr⋯Asp⋯Arg triads: Enzymatic catalyzed model system. Comput Biol Chem 2016; 65:140-147. [PMID: 27825065 DOI: 10.1016/j.compbiolchem.2016.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/06/2016] [Accepted: 10/29/2016] [Indexed: 10/20/2022]
Abstract
The hydrogen bond plays a vital role in structural arrangement, intermediate state stabilization, materials function, and biological activity of certain enzymatic reactions. The solvent and electronic effects on hydrogen bonds are illustrated employing the polarizable contimuum model at B3LYP/6-311++G(d,p) level. Geometry optimizations reflect the significant solvent and electronic effect. The proton departs spontaneously upon oxidation from the hydroxyl group of tyrosyl in hydrogen bonded Tyr⋯Asp⋯Arg triads in both gas phase and solvents. The electron transfer isomers are observed for anionic triads, no matter what the solvent is. The difference of distance between two hydrogen bonds is enlarged in solvent as compared to that in gas phase. The electronic effect on IR spectra is distinctive. The tyrosyl fragment tends to be oxidized and the arginine moiety is easier to bind an excess electron. The variations of chemical shift and spin-spin coupling constant are more significant upon electron transfer than upon solvent dielectric constant. The augmentation of solvent dielectric constant stabilizes the system, enhances the difference of isomers, and increases the vertical ionization potential and vertical electron affinity values.
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Affiliation(s)
- Shihai Yan
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Lishan Yao
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.
| | - Baotao Kang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China.
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, 440746, Republic of Korea, Republic of Korea.
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6
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Sørensen TH, Windahl MS, McBrayer B, Kari J, Olsen JP, Borch K, Westh P. Loop variants of the thermophileRasamsonia emersoniiCel7A with improved activity against cellulose. Biotechnol Bioeng 2016; 114:53-62. [DOI: 10.1002/bit.26050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Trine Holst Sørensen
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
| | | | | | - Jeppe Kari
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
| | - Johan Pelck Olsen
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
| | | | - Peter Westh
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
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7
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Wang Y, Song X, Zhang S, Li J, Shu Z, He C, Huang Q, Yao L. Improving the activity of Trichoderma reesei cel7B through stabilizing the transition state. Biotechnol Bioeng 2015; 113:1171-7. [PMID: 26616246 DOI: 10.1002/bit.25887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 11/11/2015] [Accepted: 11/17/2015] [Indexed: 11/10/2022]
Abstract
Trichoderma reesei (Tr.) cellulases, which convert cellulose to reducing sugars, are a promising catalyst used in the lignocellulosic biofuel production. Improving Tr. cellulases activity, though very difficult, is highly desired due to the recalcitrance of lignocellulose. Meanwhile, it is preferable to enhance the cellulase's promiscuity so that substrates other than cellulose can also be hydrolyzed. In this work, an attempt is made to improve the catalytic activity of a major endogluanase Tr. Cel7B against xylan which crosslinks with cellulose in lignocellulose. By using quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, the transition state of the xylo-oligosaccharide hydrolysis is identified. Then, mutations are introduced and their effect on the transition state stabilization is ranked based on the free energy calculations. Seven top ranked mutants are evaluated experimentally. Three mutants A208Q, A222D, and G230R show a higher activity than the wild-type Tr. Cel7B in the hydrolysis of xylan (by up to 47%) as well as filter paper (by up to 50%). The combination of the single mutants can further improve the enzyme activity. Our work demonstrates that the free energy method is effective in engineering the Tr. Cel7B activity against xylan and cellulose, and thus may also be useful for improving the activity of other Tr. cellulases. Biotechnol. Bioeng. 2016;113: 1171-1177. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Yefei Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Xiangfei Song
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Shujun Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Jingwen Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Zhiyu Shu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Chunyan He
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Qingshan Huang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Lishan Yao
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China. .,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.
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8
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Hamid SBA, Islam MM, Das R. Cellulase biocatalysis: key influencing factors and mode of action. CELLULOSE 2015; 22:2157-2182. [DOI: 10.1007/s10570-015-0672-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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9
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Sørensen TH, Cruys-Bagger N, Borch K, Westh P. Free Energy Diagram for the Heterogeneous Enzymatic Hydrolysis of Glycosidic Bonds in Cellulose. J Biol Chem 2015; 290:22203-11. [PMID: 26183776 DOI: 10.1074/jbc.m115.659656] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 01/25/2023] Open
Abstract
Kinetic and thermodynamic data have been analyzed according to transition state theory and a simplified reaction scheme for the enzymatic hydrolysis of insoluble cellulose. For the cellobiohydrolase Cel7A from Hypocrea jecorina (Trichoderma reesei), we were able to measure or collect relevant values for all stable and activated complexes defined by the reaction scheme and hence propose a free energy diagram for the full heterogeneous process. For other Cel7A enzymes, including variants with and without carbohydrate binding module (CBM), we obtained activation parameters for the association and dissociation of the enzyme-substrate complex. The results showed that the kinetics of enzyme-substrate association (i.e. formation of the Michaelis complex) was almost entirely entropy-controlled and that the activation entropy corresponded approximately to the loss of translational and rotational degrees of freedom of the dissolved enzyme. This implied that the transition state occurred early in the path where the enzyme has lost these degrees of freedom but not yet established extensive contact interactions in the binding tunnel. For dissociation, a similar analysis suggested that the transition state was late in the path where most enzyme-substrate contacts were broken. Activation enthalpies revealed that the rate of dissociation was far more temperature-sensitive than the rates of both association and the inner catalytic cycle. Comparisons of one- and two-domain variants showed that the CBM had no influence on the transition state for association but increased the free energy barrier for dissociation. Hence, the CBM appeared to promote the stability of the complex by delaying dissociation rather than accelerating association.
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Affiliation(s)
- Trine Holst Sørensen
- From Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
| | - Nicolaj Cruys-Bagger
- From Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Peter Westh
- From Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
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10
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Song X, Wang Y, Zhang S, Yan S, Li T, Yao L. Characterization of the Dielectric Constant in the Trichoderma reesei Cel7B Active Site. J Chem Inf Model 2015; 55:1369-76. [PMID: 26114648 DOI: 10.1021/acs.jcim.5b00155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An attempt is made to evaluate the dielectric constant of the Trichoderma reesei Cel7B active site. Through kinetic measurements, the pKa value of the catalytic acid E201 is determined. Mutations (away from E201) with net charge changes are introduced to perturb the E201 pKa. It is shown that the mutation with a +1 charge change (including G225R, G230R, and A335R) decreases the pKa of E201, whereas the mutation with a -1 charge change (including Q149E, A222D, G225D, and G230D) increases the pKa. This effect is consistent with the electrostatic interaction between the changed charge and the E201 side chain. The fitting of the experimental data yields an apparent dielectric constant of 25-80. Molecular dynamics simulations with explicit water molecules indicate that the high solvent accessibility of the active site contributes largely to the high dielectric constant. ONIOM calculations show that high dielectric constant benefits the catalysis through decreasing the energy of the transition state relative to that of the enzyme substrate complex.
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Affiliation(s)
- Xiangfei Song
- †Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266061, China
| | - Yefei Wang
- †Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266061, China
| | - Shujun Zhang
- †Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266061, China
| | - Shihai Yan
- ‡College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Tong Li
- †Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266061, China
| | - Lishan Yao
- †Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266061, China
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11
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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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12
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Schutt TC, Bharadwaj VS, Granum DM, Maupin CM. The impact of active site protonation on substrate ring conformation in Melanocarpus albomyces cellobiohydrolase Cel7B. Phys Chem Chem Phys 2015; 17:16947-58. [DOI: 10.1039/c5cp01801c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding how the protonation state of active site residues impacts the enzyme's structure and substrate conformation is important for improving the efficiency and economic viability of the degradation of cellulosic materials as feedstock for liquid fuel and value-added chemicals.
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Affiliation(s)
- Timothy C. Schutt
- Chemical and Biological Engineering Department
- Colorado School of Mines
- Golden
- USA
| | - Vivek S. Bharadwaj
- Chemical and Biological Engineering Department
- Colorado School of Mines
- Golden
- USA
| | - David M. Granum
- Chemical and Biological Engineering Department
- Colorado School of Mines
- Golden
- USA
| | - C. Mark Maupin
- Chemical and Biological Engineering Department
- Colorado School of Mines
- Golden
- USA
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13
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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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14
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. ENTROPY 2013. [DOI: 10.3390/e16010163] [Citation(s) in RCA: 291] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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15
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Knott BC, Haddad Momeni M, Crowley MF, Mackenzie LF, Götz AW, Sandgren M, Withers SG, Ståhlberg J, Beckham GT. The Mechanism of Cellulose Hydrolysis by a Two-Step, Retaining Cellobiohydrolase Elucidated by Structural and Transition Path Sampling Studies. J Am Chem Soc 2013; 136:321-9. [DOI: 10.1021/ja410291u] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Majid Haddad Momeni
- Department
of Molecular Biology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | | | - Lloyd F. Mackenzie
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | - Andreas W. Götz
- San
Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Mats Sandgren
- Department
of Molecular Biology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Stephen G. Withers
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | - Jerry Ståhlberg
- Department
of Molecular Biology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
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16
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Zhang Y, Yan S, Yao L. A Mechanistic Study of Trichoderma reesei Cel7B Catalyzed Glycosidic Bond Cleavage. J Phys Chem B 2013; 117:8714-22. [DOI: 10.1021/jp403999s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yu Zhang
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Shihai Yan
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Lishan Yao
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
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17
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Pan XL, Liu W, Liu JY. Mechanism of the Glycosylation Step Catalyzed by Human α-Galactosidase: A QM/MM Metadynamics Study. J Phys Chem B 2013; 117:484-9. [DOI: 10.1021/jp308747c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Xiao-Liang Pan
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of
Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Wei Liu
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of
Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Jing-Yao Liu
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of
Theoretical Chemistry, Jilin University, Changchun 130023, China
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