1
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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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Naidoo KJ, Bruce-Chwatt T, Senapathi T, Hillebrand M. Multidimensional Free Energy and Accelerated Quantum Library Methods Provide a Gateway to Glycoenzyme Conformational, Electronic, and Reaction Mechanisms. Acc Chem Res 2021; 54:4120-4130. [PMID: 34726899 DOI: 10.1021/acs.accounts.1c00477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Enzyme reactions are complex to simulate accurately, and none more so than glycoenzymes (glycosyltransferase and glycosidases). A rigorous sampling of the protein frame and the conformationally plural carbohydrate substrate coupled with an unbiased treatment of the electron dynamics is needed to discover the true reaction landscapes. Here, we demonstrate the effectiveness of two computational methods ported in libraries that we have developed. The first is a flat histogram free energy method called FEARCF capable of multidimensional sampling and rapidly converging to a complete coverage of phase space. The second, the Quantum Supercharger Library (QSL), is a method that accelerates the computation of the ab initio electronic wave function as well as the integral derivatives on graphical processing units (GPUs). These QSL accelerated computations form the core components needed for direct quantum dynamics and QM/MM dynamics when coupled with legacy codes such as GAMESS and NWCHEM, making state of the art hyper-parallel electronic computations in chemistry and chemical biology possible. The combination of QSL (acceleration of ab initio QM computation) and FEARCF (multidimensional hyper-parallel reaction dynamics) makes the simulation of ab initio QM/MM reaction dynamics of enzyme catalysis feasible. Enzymes that process carbohydrates pose an added challenge as their pyranose ring substrates span multidimensional conformational space whose sampling is an intimate function of the catalytic mechanism. Here, we use the pairing of FEARCF and QSL to simulate the catalytic effect of the glycoenzyme β-N-acetylglucosamine transferase (OGT). The reaction mechanism is discovered from a variable three bond reaction surface using SCCDFTB. The role of the OGT in distorting the pyranose ring of β-N-acetylglucosamine (GlcNAc) away from the equilibrium 4C1 chair conformation toward the E3 envelope needed for the transition state is discovered from its pucker free energy hypersurfaces (or free energy volume, FEV). A complete GlcNAc ring pucker HF 6-31g FEV is constructed from ab initio QM dynamics in vacuum and ab initio QM/MM dynamics in the OGT catalytic domain. The OGT is shown to clearly lower the pathway toward the transition state E3 ring conformer as well as stabilize it by 1.63 kcal/mol. Illustrated here is the use of QSL accelerated ab initio QM/MM dynamics that thoroughly explores carbohydrate catalyzed reactions through a FEARCF multidimensional sampling of the interdependence between reaction and conformational space. This demonstrates how experimentally inaccessible molecular and electronic mechanisms that underpin enzyme catalysis can be discovered by directly modeling the dynamics of these complex reactions.
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Affiliation(s)
- Kevin J Naidoo
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Science, University of Cape Town, Rondebosch 7701, South Africa
| | - Tomás Bruce-Chwatt
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Tharindu Senapathi
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Malcolm Hillebrand
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- Nonlinear Dynamics and Chaos Group, Department of Mathematics, University of Cape Town, Rondebosch 7701, South Africa
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3
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Li Q, Levi SM, Jacobsen EN. Highly Selective β-Mannosylations and β-Rhamnosylations Catalyzed by Bis-thiourea. J Am Chem Soc 2020; 142:11865-11872. [PMID: 32527078 DOI: 10.1021/jacs.0c04255] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We report highly β-selective bis-thioureas-catalyzed 1,2-cis-O-pyranosylations employing easily accessible acetonide-protected donors. A wide variety of alcohol nucleophiles, including complex natural products, glycosides, and amino acids were β-mannosylated and β-rhamnosylated successfully using an operationally simple protocol under mild and neutral conditions. Less nucleophilic acceptors such as phenols were also glycosylated efficiently in excellent yields and with high β-selectivities.
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Affiliation(s)
- Qiuhan Li
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Samuel M Levi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Eric N Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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4
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Alonso-Gil S. Mimicking the transition state of reactions of glycoside hydrolases: Updating the conformational space of the oxocarbenium cation. J Carbohydr Chem 2020. [DOI: 10.1080/07328303.2020.1766481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Santiago Alonso-Gil
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague 8, Czech Republic
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5
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Bharadwaj VS, Knott BC, Ståhlberg J, Beckham GT, Crowley MF. The hydrolysis mechanism of a GH45 cellulase and its potential relation to lytic transglycosylase and expansin function. J Biol Chem 2020; 295:4477-4487. [PMID: 32054684 DOI: 10.1074/jbc.ra119.011406] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/12/2020] [Indexed: 11/06/2022] Open
Abstract
Family 45 glycoside hydrolases (GH45) are endoglucanases that are integral to cellulolytic secretomes, and their ability to break down cellulose has been successfully exploited in textile and detergent industries. In addition to their industrial relevance, understanding the molecular mechanism of GH45-catalyzed hydrolysis is of fundamental importance because of their structural similarity to cell wall-modifying enzymes such as bacterial lytic transglycosylases (LTs) and expansins present in bacteria, plants, and fungi. Our understanding of the catalytic itinerary of GH45s has been incomplete because a crystal structure with substrate spanning the -1 to +1 subsites is currently lacking. Here we constructed and validated a putative Michaelis complex in silico and used it to elucidate the hydrolytic mechanism in a GH45, Cel45A from the fungus Humicola insolens, via unbiased simulation approaches. These molecular simulations revealed that the solvent-exposed active-site architecture results in lack of coordination for the hydroxymethyl group of the substrate at the -1 subsite. This lack of coordination imparted mobility to the hydroxymethyl group and enabled a crucial hydrogen bond with the catalytic acid during and after the reaction. This suggests the possibility of a nonhydrolytic reaction mechanism when the catalytic base aspartic acid is missing, as is the case in some LTs (murein transglycosylase A) and expansins. We calculated reaction free energies and demonstrate the thermodynamic feasibility of the hydrolytic and nonhydrolytic reaction mechanisms. Our results provide molecular insights into the hydrolysis mechanism in HiCel45A, with possible implications for elucidating the elusive catalytic mechanism in LTs and expansins.
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Affiliation(s)
- Vivek S Bharadwaj
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Brandon C Knott
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P. O. Box 7015, 750 07 Uppsala, Sweden
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Michael F Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
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6
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Yang Y, Liu Y, Ning L, Wang L, Mu Y, Li W. Binding Process and Free Energy Characteristics of Cellulose Chain into the Catalytic Domain of Cellobiohydrolase TrCel7A. J Phys Chem B 2019; 123:8853-8860. [PMID: 31557037 DOI: 10.1021/acs.jpcb.9b05023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It was observed in experiments that the catalytic domain (CD) of Trichoderma reesei Cel7A (TrCel7A) hydrolyzes crystalline cellulose in a processive manner, but the underlying binding mechanism is still unknown. Here, through replica-exchange molecular dynamics simulations, we find that the loading and sucking-in process of the cellulose chain into CD is entropy-driven and enthalpy-unfavorable, which firmly relate to the desolvation of the binding channel of CD. During the loading process, hydrophobic interactions play a dominant role because several aromatic residues have been identified to guide the cellulose chain processing. At the active site, a transition from enthalpy- to entropy-driven is detected for the driving force. Such a finding reveals the indispensability of the catalytic reaction of the glycosidic bond to provide the energy to drive the movements of the cellulose chain. Our study reveals the interaction pictures between the cellulose chain and TrCel7A at the atomic level, which helps better understand the catalytic mechanism of TrCel7A.
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Affiliation(s)
- Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education , Shandong Normal University , Jinan 250014 , China
| | | | - Lulu Ning
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | | | - Yuguang Mu
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
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7
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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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8
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Structure and dynamics of Trichoderma harzianum Cel7B suggest molecular architecture adaptations required for a wide spectrum of activities on plant cell wall polysaccharides. Biochim Biophys Acta Gen Subj 2019; 1863:1015-1026. [DOI: 10.1016/j.bbagen.2019.03.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/04/2019] [Accepted: 03/18/2019] [Indexed: 11/19/2022]
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9
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Brás NF, Santos-Martins D, Fernandes PA, Ramos MJ. Mechanistic Pathway on Human α-Glucosidase Maltase-Glucoamylase Unveiled by QM/MM Calculations. J Phys Chem B 2018; 122:3889-3899. [DOI: 10.1021/acs.jpcb.8b01321] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Natércia F. Brás
- REQUIMTE/UCIBIO, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Diogo Santos-Martins
- REQUIMTE/UCIBIO, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE/UCIBIO, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE/UCIBIO, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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10
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Rogers IL, Naidoo KJ. Producing DFT/MM enzyme reaction trajectories from SCC-DFTB/MM driving forces to probe the underlying electronics of a glycosyltransferase reaction. J Comput Chem 2017; 38:1789-1798. [PMID: 28488320 DOI: 10.1002/jcc.24820] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/14/2017] [Accepted: 04/03/2017] [Indexed: 02/05/2023]
Abstract
The SCC-DFTB/MIO/CHARMM free energy surface for a glycosyltransferase, TcTS, is benchmarked against a DFT/MM reaction trajectory using the same CHARMM MM force field ported to the NWChem package. The popular B3LYP functional, against which the MIO parameter set was parameterized is used to optimize TS structures and run DFT reaction dynamics. A novel approach was used to generate reaction forces from a SCC-DFTB/MIO/CHARMM reaction surface to drive B3LYP/6-31G/MM and B3LYP/6-31G(d)/MM reaction trajectories. Although TS structures compare favorably, differences stemming primarily from a minimal basis set approximation prevented a successful 6-31G(d) FEARCF reaction dynamics trajectory. None the less, the dynamic evolution of the B3LYP/6-31G/MM-computed electron density provided an opportunity to perform NBO analysis along the reaction trajectory. Here, we illustrate that a successful ab initio reaction trajectory is computationally accessible when the underlying potential energy function of the semi-empirical method used to produce driving forces is sufficiently close to the ab initio potential. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Ian L Rogers
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Kevin J Naidoo
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
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11
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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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12
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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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13
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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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14
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Reilly PJ, Rovira C. Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter J. Reilly
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011-2230, United States
| | - Carme Rovira
- Departament de Química Orgànica
and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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15
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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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16
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Ardèvol A, Rovira C. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations. J Am Chem Soc 2015; 137:7528-47. [DOI: 10.1021/jacs.5b01156] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Albert Ardèvol
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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17
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Renison CA, Fernandes KD, Naidoo KJ. Quantum supercharger library: Hyper-parallel integral derivatives algorithms forab initioQM/MM dynamics. J Comput Chem 2015; 36:1410-9. [DOI: 10.1002/jcc.23938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 01/23/2023]
Affiliation(s)
- C. Alicia Renison
- Scientific Computing Research Unit and Department of Chemistry; University of Cape Town; Rondebosch, Cape Town 7701 South Africa
| | - Kyle D. Fernandes
- Scientific Computing Research Unit and Department of Chemistry; University of Cape Town; Rondebosch, Cape Town 7701 South Africa
| | - Kevin J. Naidoo
- Scientific Computing Research Unit and Department of Chemistry; University of Cape Town; Rondebosch, Cape Town 7701 South Africa
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18
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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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19
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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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20
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Silveira RL, Skaf MS. Molecular Dynamics Simulations of Family 7 Cellobiohydrolase Mutants Aimed at Reducing Product Inhibition. J Phys Chem B 2014; 119:9295-303. [DOI: 10.1021/jp509911m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Rodrigo L. Silveira
- Institute
of Chemistry, University of Campinas, Cx. P. 6154 Campinas, SP, 13084-862, Brazil
| | - Munir S. Skaf
- Institute
of Chemistry, University of Campinas, Cx. P. 6154 Campinas, SP, 13084-862, Brazil
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21
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Rogers IL, Naidoo KJ. Profiling Transition-State Configurations on the Trypanosoma cruzi trans-Sialidase Free-Energy Reaction Surfaces. J Phys Chem B 2014; 119:1192-201. [DOI: 10.1021/jp506824r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ian L. Rogers
- Scientific
Computing Research Unit and ‡Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J. Naidoo
- Scientific
Computing Research Unit and ‡Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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22
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Knott BC, Crowley MF, Himmel ME, Ståhlberg J, Beckham GT. Carbohydrate-protein interactions that drive processive polysaccharide translocation in enzymes revealed from a computational study of cellobiohydrolase processivity. J Am Chem Soc 2014; 136:8810-9. [PMID: 24869982 DOI: 10.1021/ja504074g] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Translocation of carbohydrate polymers through protein tunnels and clefts is a ubiquitous biochemical phenomenon in proteins such as polysaccharide synthases, glycoside hydrolases, and carbohydrate-binding modules. Although static snapshots of carbohydrate polymer binding in proteins have long been studied via crystallography and spectroscopy, the molecular details of polysaccharide chain processivity have not been elucidated. Here, we employ simulation to examine how a cellulose chain translocates by a disaccharide unit during the processive cycle of a glycoside hydrolase family 7 cellobiohydrolase. Our results demonstrate that these biologically and industrially important enzymes employ a two-step mechanism for chain threading to form a Michaelis complex and that the free energy barrier to chain threading is significantly lower than the hydrolysis barrier. Taken with previous studies, our findings suggest that the rate-limiting step in enzymatic cellulose degradation is the glycosylation reaction, not chain processivity. Based on the simulations, we find that strong electrostatic interactions with polar residues that are conserved in GH7 cellobiohydrolases, but not in GH7 endoglucanases, at the leading glucosyl ring provide the thermodynamic driving force for polysaccharide chain translocation. Also, we consider the role of aromatic-carbohydrate interactions, which are widespread in carbohydrate-active enzymes and have long been associated with processivity. Our analysis suggests that the primary role for these aromatic residues is to provide tunnel shape and guide the carbohydrate chain to the active site. More broadly, this work elucidates the role of common protein motifs found in carbohydrate-active enzymes that synthesize or depolymerize polysaccharides by chain translocation mechanisms coupled to catalysis.
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Affiliation(s)
- Brandon C Knott
- National Bioenergy Center and ‡Biosciences Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
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23
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Ivchenko O, Whittleston CS, Carr JM, Imhof P, Goerke S, Bachert P, Wales DJ. Proton transfer pathways, energy landscape, and kinetics in creatine-water systems. J Phys Chem B 2014; 118:1969-75. [PMID: 24476099 DOI: 10.1021/jp410172k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We study the exchange processes of the metabolite creatine, which is present in both tumorous and normal tissues and has NH2 and NH groups that can transfer protons to water. Creatine produces chemical exchange saturation transfer (CEST) contrast in magnetic resonance imaging (MRI). The proton transfer pathway from zwitterionic creatine to water is examined using a kinetic transition network constructed from the discrete path sampling approach and an approximate quantum-chemical energy function, employing the self-consistent-charge density-functional tight-binding (SCC-DFTB) method. The resulting potential energy surface is visualized by constructing disconnectivity graphs. The energy landscape consists of two distinct regions corresponding to the zwitterionic creatine structures and deprotonated creatine. The activation energy that characterizes the proton transfer from the creatine NH2 group to water was determined from an Arrhenius fit of rate constants as a function of temperature, obtained from harmonic transition state theory. The result is in reasonable agreement with values obtained in water exchange spectroscopy (WEX) experiments.
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Affiliation(s)
- Olga Ivchenko
- Department of Medical Physics in Radiology, Deutsches Krebsforschungszentrum (DKFZ, German Cancer Research Center) , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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24
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Mayes HB, Broadbelt LJ, Beckham GT. How Sugars Pucker: Electronic Structure Calculations Map the Kinetic Landscape of Five Biologically Paramount Monosaccharides and Their Implications for Enzymatic Catalysis. J Am Chem Soc 2014; 136:1008-22. [DOI: 10.1021/ja410264d] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- National
Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Linda J. Broadbelt
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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25
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Granum DM, Vyas S, Sambasivarao SV, Maupin CM. Computational Evaluations of Charge Coupling and Hydrogen Bonding in the Active Site of a Family 7 Cellobiohydrolase. J Phys Chem B 2014; 118:434-48. [DOI: 10.1021/jp408536s] [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 and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Shubham Vyas
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Somisetti V. Sambasivarao
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - C. Mark Maupin
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
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26
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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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27
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Fleming KL, Pfaendtner J. Characterizing the Catalyzed Hydrolysis of β-1,4 Glycosidic Bonds Using Density Functional Theory. J Phys Chem A 2013; 117:14200-8. [DOI: 10.1021/jp4081178] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kelly L. Fleming
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Jim Pfaendtner
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
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28
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Lu T, Zhang Z, Zhang C. Glycosyl rotation and distortion by key residues in Endocellulase Cel6A from Theromobifida fusca. Glycobiology 2013; 24:247-51. [PMID: 24287179 DOI: 10.1093/glycob/cwt105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Endocellulases are one kind of the important biodegrading cellulose enzymes. Experimental results show that a rotated and distorted preactivated structure exists before the substrate entering the transition state. The molecular dynamic simulation of endocellulase Cel6A models revealed a correlation between the rotation and distortion of pyranoside ring in -1 glycosyl unit of the substrate. The two key residues, Tyr73 and Ser189, in Cal6A cooperate to rotate and distort the pyranoside ring in the cellulose hydrolysis.
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Affiliation(s)
- Tao Lu
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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29
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Kellie JL, Wilson KA, Wetmore SD. Standard role for a conserved aspartate or more direct involvement in deglycosylation? An ONIOM and MD investigation of adenine-DNA glycosylase. Biochemistry 2013; 52:8753-65. [PMID: 24168684 DOI: 10.1021/bi401310w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
8-Oxoguanine (OG) is one of the most frequently occurring forms of DNA damage and is particularly deleterious since it forms a stable Hoogsteen base pair with adenine (A). The repair of an OG:A mispair is initiated by adenine-DNA glycosylase (MutY), which hydrolyzes the sugar-nucleobase bond of the adenine residue before the lesion is processed by other proteins. MutY has been proposed to use a two-part chemical step involving protonation of the adenine nucleobase, followed by SN1 hydrolysis of the glycosidic bond. However, differences between a recent (fluorine recognition complex, denoted as the FLRC) crystal structure and the structure on which most mechanistic conclusions have been based to date (namely, the lesion recognition complex or LRC) raise questions regarding the mechanism used by MutY and the discrete role of various active-site residues. The present work uses both molecular dynamics (MD) and quantum mechanical (ONIOM) models to compare the active-site conformational dynamics in the two crystal structures, which suggests that only the understudied FLRC leads to a catalytically competent reactant. Indeed, all previous computational studies on MutY have been initiated from the LRC structure. Subsequently, for the first time, various mechanisms are examined with detailed ONIOM(M06-2X:PM6) reaction potential energy surfaces (PES) based on the FLRC structure, which significantly extends the mechanistic picture. Specifically, our work reveals that the reaction proceeds through a different route than the commonly accepted mechanism and the catalytic function of various active-site residues (Geobacillus stearothermophilus numbering). Specifically, contrary to proposals based on the LRC, E43 is determined to solely be involved in the initial adenine protonation step and not the deglycosylation reaction as the general base. Additionally, a novel catalytic role is proposed for Y126, whereby this residue plays a significant role in stabilizing the highly charged active site, primarily through interactions with E43. More importantly, D144 is found to explicitly catalyze the nucleobase dissociation step through partial nucleophilic attack. Although this is a more direct role than previously proposed for any other DNA glycosylase, comparison to previous work on other glycosylases justifies the larger contribution in the case of MutY and allows us to propose a unified role for the conserved Asp/Glu in the DNA glycosylases, as well as other enzymes that catalyze nucleotide deglycosylation reactions.
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Affiliation(s)
- Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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30
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Liu J, Zheng M, Zhang C, Xu D. “Amide Resonance” in the Catalysis of 1,2-α-l-Fucosidase from Bifidobacterium bifidum. J Phys Chem B 2013; 117:10080-92. [DOI: 10.1021/jp402110j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jingli Liu
- Key
Laboratory of Green Chemistry and Technology, College
of Chemistry, Ministry of Education, Chengdu, Sichuan 610064, P. R. China
| | - Min Zheng
- Key
Laboratory of Green Chemistry and Technology, College
of Chemistry, Ministry of Education, Chengdu, Sichuan 610064, P. R. China
| | - Chunchun Zhang
- Testing & Analytical Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Dingguo Xu
- Key
Laboratory of Green Chemistry and Technology, College
of Chemistry, Ministry of Education, Chengdu, Sichuan 610064, P. R. China
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31
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Ghattyvenkatakrishna PK, Alekozai EM, Beckham GT, Schulz R, Crowley MF, Uberbacher EC, Cheng X. Initial recognition of a cellodextrin chain in the cellulose-binding tunnel may affect cellobiohydrolase directional specificity. Biophys J 2013; 104:904-12. [PMID: 23442969 DOI: 10.1016/j.bpj.2012.12.052] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/14/2012] [Accepted: 12/27/2012] [Indexed: 10/27/2022] Open
Abstract
Cellobiohydrolases processively hydrolyze glycosidic linkages in individual polymer chains of cellulose microfibrils, and typically exhibit specificity for either the reducing or nonreducing end of cellulose. Here, we conduct molecular dynamics simulations and free energy calculations to examine the initial binding of a cellulose chain into the catalytic tunnel of the reducing-end-specific Family 7 cellobiohydrolase (Cel7A) from Hypocrea jecorina. In unrestrained simulations, the cellulose diffuses into the tunnel from the -7 to the -5 positions, and the associated free energy profiles exhibit no barriers for initial processivity. The comparison of the free energy profiles for different cellulose chain orientations show a thermodynamic preference for the reducing end, suggesting that the preferential initial binding may affect the directional specificity of the enzyme by impeding nonproductive (nonreducing end) binding. Finally, the Trp-40 at the tunnel entrance is shown with free energy calculations to have a significant effect on initial chain complexation in Cel7A.
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32
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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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33
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Gaus M, Cui Q, Elstner M. Density functional tight binding: application to organic and biological molecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1156] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Michael Gaus
- Department of Chemistry and Theoretical Chemistry Institute University of Wisconsin Madison WI 53706 USA
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute University of Wisconsin Madison WI 53706 USA
| | - Marcus Elstner
- Karlsruhe Institute of Technology Physical Chemistry, Kaiserstrasse 12 D‐76131 Karlsruhe Germany
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34
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Barnett CB, Naidoo KJ. PNP diminishes guanosine glycosidic bond strength through restrictive ring pucker as a precursor to phosphorylation. J Phys Chem B 2013; 117:6019-26. [PMID: 23621450 DOI: 10.1021/jp3109013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Purine nucleoside phosphorylase is a transferase that catalyzes the addition of phosphate and removal of a purine base from guanosine and similar nucleosides. Here the interplay between sugar puckering conformation, the enzyme, and the perceived course of the reaction is examined using QM/MM FEARCF dynamics simulations. The enzyme biases the guanosine sugar ring toward a flattened (4)E conformer as a step that is critical to the success of the phosphorylation reaction. The C4' endo conformer allows the nonbonded ring oxygen orbital to align and donate electrons into the antibonding glycosidic bond orbital, thus weakening the bond. This conformational preference is due to sustained and directed noncovalent interactions anchored by the phosphate nucleophile's hydrogen bonds to the sugar C2' and C3' hydroxyls. In so doing, PNP alters the solution sugar ring pucker preferences as part of its catalytic reaction barrier lowering function.
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Affiliation(s)
- Christopher B Barnett
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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35
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Khalili P, Barnett CB, Naidoo KJ. Interpreting medium ring canonical conformers by a triangular plane tessellation of the macrocycle. J Chem Phys 2013; 138:184110. [DOI: 10.1063/1.4803698] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Pegah Khalili
- Scientific Computing Research Unit, University of Cape Town, Cape Town 7701, South Africa
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36
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Lodola A, Capoferri L, Rivara S, Tarzia G, Piomelli D, Mulholland A, Mor M. Quantum mechanics/molecular mechanics modeling of fatty acid amide hydrolase reactivation distinguishes substrate from irreversible covalent inhibitors. J Med Chem 2013; 56:2500-12. [PMID: 23425199 DOI: 10.1021/jm301867x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Carbamate and urea derivatives are important classes of fatty acid amide hydrolase (FAAH) inhibitors that carbamoylate the active-site nucleophile Ser241. In the present work, the reactivation mechanism of carbamoylated FAAH is investigated by means of a quantum mechanics/molecular mechanics (QM/MM) approach. The potential energy surfaces for decarbamoylation of FAAH covalent adducts, derived from the O-aryl carbamate URB597 and from the N-piperazinylurea JNJ1661610, were calculated and compared to that for deacylation of FAAH acylated by the substrate oleamide. Calculations show that a carbamic group bound to Ser241 prevents efficient stabilization of transition states of hydrolysis, leading to large increments in the activation barrier. Moreover, the energy barrier for the piperazine carboxylate was significantly lower than that for the cyclohexyl carbamate derived from URB597. This is consistent with experimental data showing slowly reversible FAAH inhibition for the N-piperazinylurea inhibitor and irreversible inhibition for URB597.
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Affiliation(s)
- Alessio Lodola
- Dipartimento di Farmacia, Università degli Studi di Parma, I-43124 Parma, Italy
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37
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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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38
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Whitfield DM. Plausible transition states for glycosylation reactions. Carbohydr Res 2012; 356:180-90. [DOI: 10.1016/j.carres.2012.03.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 03/27/2012] [Accepted: 03/30/2012] [Indexed: 11/29/2022]
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39
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Naidoo KJ. Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association. Phys Chem Chem Phys 2012; 14:9026-36. [DOI: 10.1039/c2cp23802k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4423-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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