1
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Hu H, Li J, Luo S, Tian Y, Wang J, Zhao YL, Zhang R, Zhu J. Design of 2,5-furandicarboxylic based polyesters degraded in different environmental conditions: Comprehensive experimental and theoretical study. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127752. [PMID: 34906869 DOI: 10.1016/j.jhazmat.2021.127752] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Nowadays, the promotion and application of aliphatic-aromatic copolyesters, such as poly (butylene adipate-co-terephthalate) (PBAT), are growing into a general trend. Although the structures of diacids exerted substantial impacts on degradation behavior, the underlying mechanisms have rarely been studied. In this work, 2,5-Furandicarboxylic acid was combined with succinic acid (PBSF), adipic acid (PBAF) and diglycolic acid (PBDF) to prepare three kinds of copolyesters. They showed unique degradation behaviors in buffer, enzyme environment and artificial seawater. These characteristics are closely related to the structural compositions of diacids. PBAFs displayed impressive biodegradability when catalyzed by Candida antarctica lipase B (CALB), while the more hydrophilic PBDFs exhibited faster hydrolysis in both buffer and artificial seawater. PBSFs, with hydrophobic and short segments, obtained a relatively slower rate of hydrolysis and enzymatic degradation. The reactivity sites and hydrolytic pathway were revealed by the combination of DFT calculation and Fukui function analysis. MD simulations, QM/MM optimizations and theozyme calculations showed that PBAF-CALB was prone to form a pre-reaction state, leading to the reduced energy barrier in the acylation process. This work revealed the effects of different structural features of diacids on polymer degradation and paved a way to design target biodegradable polymers in different degradation conditions.
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Affiliation(s)
- Han Hu
- Key Laboratory of Bio-based Polymeric Materials Technology and Application of Zhejiang Province, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, China
| | - Jiayi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shenggan Luo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Tian
- Key Laboratory of Bio-based Polymeric Materials Technology and Application of Zhejiang Province, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, China
| | - Jinggang Wang
- Key Laboratory of Bio-based Polymeric Materials Technology and Application of Zhejiang Province, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States.
| | - Ruoyu Zhang
- Key Laboratory of Bio-based Polymeric Materials Technology and Application of Zhejiang Province, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, China.
| | - Jin Zhu
- Key Laboratory of Bio-based Polymeric Materials Technology and Application of Zhejiang Province, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, China.
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2
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Li X, Li X, Zhang QY, Lv P, Jia Y, Wei D. Cofactor-free ActVA-Orf6 monooxygenase catalysis via proton-coupled electron transfer: A QM/MM study. Org Biomol Chem 2022; 20:5525-5534. [DOI: 10.1039/d2ob00848c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Uncovering the comprehensive catalytic mechanism for the activation of triplet O2 through metal-free and cofactor-free oxidases and oxygenases remains one of the most challenging questions in the area of enzymatic...
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3
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Carvalho HF, Ferrario V, Pleiss J. Molecular Mechanism of Methanol Inhibition in CALB-Catalyzed Alcoholysis: Analyzing Molecular Dynamics Simulations by a Markov State Model. J Chem Theory Comput 2021; 17:6570-6582. [PMID: 34494846 DOI: 10.1021/acs.jctc.1c00559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipases are widely used enzymes that catalyze hydrolysis and alcoholysis of fatty acid esters. At high concentrations of small alcohols such as methanol or ethanol, many lipases are inhibited by the substrate. The molecular basis of the inhibition of Candida antarctica lipase B (CALB) by methanol was investigated by unbiased molecular dynamics (MD) simulations, and the substrate binding kinetics was analyzed by Markov state models (MSMs). The modeled fluxes of productive methanol binding at concentrations between 50 mM and 5.5 M were in good agreement with the experimental activity profile of CALB, with a peak at 300 mM. The kinetic and structural analysis uncovered the molecular basis of CALB inhibition. Beyond 300 mM, the kinetic bottleneck results from crowding of methanol in the substrate access channel, which is caused by the gradual formation of methanol patches close to Leu140 (helix α5), Leu278, and Ile285 (helix α10) at a distance of 4-5 Å from the active site. Our findings demonstrate the usefulness of unbiased MD simulations to study enzyme-substrate interactions at realistic substrate concentrations and the feasibility of scale-bridging by an MSM analysis to derive kinetic information.
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Affiliation(s)
- Henrique F Carvalho
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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4
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Zhang XJ, Qi FY, Qi JM, Yang F, Shen JW, Cai X, Liu ZQ, Zheng YG. Efficient enzymatic synthesis of L-ascorbyl palmitate using Candida antarctica lipase B-embedded metal-organic framework. Biotechnol Prog 2021; 38:e3218. [PMID: 34601810 DOI: 10.1002/btpr.3218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/09/2022]
Abstract
The Candida antarctica lipase B (CALB) was embedded in the metal-organic framework, zeolitic imidazolate framework-8 (ZIF-8), and applied in the enzymatic synthesis of L-ascorbic acid palmitate (ASP) for the first time. The obtained CALB@ZIF-8 achieved the enzyme loading of 80 mg g-1 with 11.3 U g-1 (dry weight) unit activity, 59.8% activity recovery, and 92.7% immobilization yield. Under the optimal condition, ASP was synthesized with over 75.9% conversion of L-ascorbic acid in a 10-batch reaction. Continuous synthesis of ASP was subsequently performed in a packed bed bioreactor with an outstanding average space-time yield of 58.1 g L-1 h-1 , which was higher than ever reported continuous ASP biosynthesis reactions.
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Affiliation(s)
- Xiao-Jian Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Feng-Yu Qi
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jia-Mei Qi
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Fei Yang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jiang-Wei Shen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xue Cai
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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5
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Rincón D, Doerr M, Daza MC. Hydrogen Bonds and n → π* Interactions in the Acetylation of Propranolol Catalyzed by Candida antarctica Lipase B: A QTAIM Study. ACS OMEGA 2021; 6:20992-21004. [PMID: 34423207 PMCID: PMC8375099 DOI: 10.1021/acsomega.1c02559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Enzyme-substrate interactions play a crucial role in enzymatic catalysis. Quantum theory of atoms in molecules (QTAIM) calculations are extremely useful in computational studies of these interactions because they provide very detailed information about the strengths and types of molecular interactions. QTAIM also provides information about the intramolecular changes that occur in the catalytic reaction. Here, we analyze the enzyme-substrate interactions and the topological properties of the electron density in the enantioselective step of the acylation of (R,S)-propranolol, an aminoalcohol with therapeutic applications, catalyzed by Candida antarctica lipase B. Eight reaction paths (four for each enantiomer) are investigated and the energies, atomic charges, hydrogen bonds, and n → π* interactions of propranolol, the catalytic triad (composed of D187, H224, and S105), and the oxyanion hole are analyzed. It is found that D187 acts as an electron density reservoir for H224, and H224 acts as an electron density reservoir for the active site of the protein. It releases electron density when the tetrahedral intermediate is formed from the Michaelis complex and receives it when the enzyme-product complex is formed. Hydrogen bonds can be grouped into noncovalent and covalent hydrogen bonds. The latter are stronger and more important for the reaction than the former. We also found weak n → π* interactions, which are characterized by QTAIM and the natural bond orbital (NBO) analysis.
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6
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Valderrama DIB, Daza MC, Doerr M. Finite-temperature effect in the O-acylation of (R,S)-propranolol catalyzed by Candida antarctica lipase B. J Mol Graph Model 2021; 107:107951. [PMID: 34111759 DOI: 10.1016/j.jmgm.2021.107951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/03/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022]
Abstract
CalB is a triacylglycerol hydrolase (E.C.3.1.1.3) used in the O-acylation of the beta-adrenergic blocking agent (R,S)-propranolol. The catalytic mechanism involves two steps: enzyme acylation and enzyme deacylation. The enantioselectivity of the O-acylation of (R,S)-propranolol originates from the second step, where the acyl-enzyme transfers the acyl group to the racemic substrate. This step occurs via an initial Michaelis complex (MCC) and a tetrahedral intermediate (TI-2). To gain more insight into the molecular basis of this reaction, we performed an exhaustive conformational sampling along the reaction coordinate of the enantioselective step of the reaction (MCC→TI-2→EPC) applying a QM/MM MD protocol (SCC-DFTB/CHARMM) in combination with umbrella sampling and the weighted histogram analysis method. To identify finite temperature effects we compare the PMF and the potential energy pathway. It is found that the effect of the finite temperature in this reaction is a destabilization of the tetrahedral intermediate and an increase of the barrier height of its formation. This increase is higher for the S-enantiomer.
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Affiliation(s)
- Daniel I Barrera Valderrama
- Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia; Departamento de Química, Universidad de Pamplona, Km 1 Vía Bucaramanga, Pamplona, Colombia
| | - Martha C Daza
- Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia
| | - Markus Doerr
- Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia.
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7
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Figueiredo PR, Almeida BC, Dourado DFAR, Sousa AF, Silvestre AJD, Carvalho ATP. Enzymatic Synthesis of Poly(caprolactone): A QM/MM Study. ChemCatChem 2020. [DOI: 10.1002/cctc.202000780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pedro R. Figueiredo
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
| | - Beatriz C. Almeida
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
| | - Daniel F. A. R. Dourado
- Almac Sciences Department of Biocatalysis and Isotope Chemistry Almac House 20 Seagoe Industrial Estate Craigavon BT63 5QD Northern Ireland UK
| | | | | | - Alexandra T. P. Carvalho
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
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8
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Wang R, Wang S, Xu Y, Yu X. Enhancing the thermostability of Rhizopus chinensis lipase by rational design and MD simulations. Int J Biol Macromol 2020; 160:1189-1200. [PMID: 32485250 DOI: 10.1016/j.ijbiomac.2020.05.243] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 01/16/2023]
Abstract
To improve the thermostability of r27RCL from Rhizopus chinensis and broaden its industrial applications, we used rational design (FoldX) according to ΔΔG calculation to predict mutations. Four thermostable variants S142A, D217V, Q239F, and S250Y were screened out and then combined together to generate a quadruple-mutation (S142A/D217V/Q239F/S250Y) variant, called m31. m31 exhibited enhanced thermostability with a 41.7-fold longer half-life at 60 °C, a 5 °C higher of topt, and 15.8 °C higher of T5030 compared to that of r27RCL expressed in Pichiapastoris. Molecular dynamics simulations were conducted to analyze the mechanism of the thermostable mutant. The results indicated that the rigidity of m31 was improved due to the decreased solvent accessible surface area, a newly formed salt bridge of Glu292:His171, and the increased ΔΔG of m31. According to the root-mean-square-fluctuation analysis, three positive mutations S142A, D217V, and Q239F located in the thermal weak regions and greatly decreased the distribution of thermal-fluctuated regions of m31, compared to that of r27RCL. These results suggested that to simultaneously implement MD simulations and ΔΔG-based rational approaches will be more accurate and efficient for the improvement of enzyme thermostability.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Pharmaceutical Science, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Shang Wang
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaowei Yu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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9
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Sheng X, Kazemi M, Planas F, Himo F. Modeling Enzymatic Enantioselectivity using Quantum Chemical Methodology. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00983] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Masoud Kazemi
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Ferran Planas
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
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10
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Mangiagalli M, Carvalho H, Natalello A, Ferrario V, Pennati ML, Barbiroli A, Lotti M, Pleiss J, Brocca S. Diverse effects of aqueous polar co-solvents on Candida antarctica lipase B. Int J Biol Macromol 2020; 150:930-940. [DOI: 10.1016/j.ijbiomac.2020.02.145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 02/04/2023]
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11
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Figueiredo P, Almeida BC, Carvalho ATP. Enzymatic Polymerization of PCL-PEG Co-polymers for Biomedical Applications. Front Mol Biosci 2019; 6:109. [PMID: 31681797 PMCID: PMC6811512 DOI: 10.3389/fmolb.2019.00109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/04/2019] [Indexed: 11/25/2022] Open
Abstract
Biodegradable polymers, obtained via chemical synthesis, are currently employed in a wide range of biomedical applications. However, enzymatic polymerization is an attractive alternative because it is more sustainable and safer. Many lipases can be employed in ring-opening polymerization (ROP) of biodegradable polymers. Nevertheless, the harsh conditions required in industrial context are not always compatible with their enzymatic activity. In this work, we have studied a thermophilic carboxylesterase and the commonly used Lipase B from Candida antarctica (CaLB) for tailored synthesis of amphiphilic polyesters for biomedical applications. We have conducted Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) MD simulations of the synthesis of Polycaprolactone-Polyethylene Glycol (PCL-PEG) model co-polymers. Our insights about the reaction mechanisms are important for the design of customized enzymes capable to synthesize different polyesters for biomedical applications.
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Affiliation(s)
| | | | - Alexandra T. P. Carvalho
- Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
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12
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Kazemi M, Sheng X, Himo F. Origins of Enantiopreference of
Mycobacterium smegmatis
Acyl Transferase: A Computational Analysis. Chemistry 2019; 25:11945-11954. [DOI: 10.1002/chem.201902351] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Masoud Kazemi
- Department of Organic ChemistryArrhenius Laboratory Stockholm University 10691 Stockholm Sweden
| | - Xiang Sheng
- Department of Organic ChemistryArrhenius Laboratory Stockholm University 10691 Stockholm Sweden
| | - Fahmi Himo
- Department of Organic ChemistryArrhenius Laboratory Stockholm University 10691 Stockholm Sweden
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13
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Artificial cysteine-lipases with high activity and altered catalytic mechanism created by laboratory evolution. Nat Commun 2019; 10:3198. [PMID: 31324776 PMCID: PMC6642262 DOI: 10.1038/s41467-019-11155-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/24/2019] [Indexed: 11/13/2022] Open
Abstract
Engineering artificial enzymes with high activity and catalytic mechanism different from naturally occurring enzymes is a challenge in protein design. For example, many attempts have been made to obtain active hydrolases by introducing a Ser → Cys exchange at the respective catalytic triads, but this generally induced a breakdown of activity. We now report that this long-standing dogma no longer pertains, provided additional mutations are introduced by directed evolution. By employing Candida antarctica lipase B (CALB) as the model enzyme with the Ser-His-Asp catalytic triad, a highly active cysteine-lipase having a Cys-His-Asp catalytic triad and additional mutations W104V/A281Y/A282Y/V149G can be evolved, showing a 40-fold higher catalytic efficiency than wild-type CALB in the hydrolysis of 4-nitrophenyl benzoate, and tolerating bulky substrates. Crystal structures, kinetics, MD simulations and QM/MM calculations reveal dynamic features and explain all results, including the preference of a two-step mechanism involving the zwitterionic pair Cys105−/His224+ rather than a concerted process. Candida antarctica lipase B (CALB) is a serine lipase. Here, the authors use directed evolution to exchange serine with cysteine in the catalytic triad of the enzyme, thereby obtaining a highly active CALB variant that — unlike the wild type — accommodates bulky substrates.
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14
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van Rijn JPM, Escorcia AM, Thiel W. QM/MM study of the taxadiene synthase mechanism. J Comput Chem 2019; 40:1902-1910. [DOI: 10.1002/jcc.25846] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/05/2019] [Accepted: 04/15/2019] [Indexed: 01/10/2023]
Affiliation(s)
| | - Andrés M. Escorcia
- Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim Germany
| | - Walter Thiel
- Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim Germany
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15
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Lu Y, Farrow MR, Fayon P, Logsdail AJ, Sokol AA, Catlow CRA, Sherwood P, Keal TW. Open-Source, Python-Based Redevelopment of the ChemShell Multiscale QM/MM Environment. J Chem Theory Comput 2019; 15:1317-1328. [PMID: 30511845 DOI: 10.1021/acs.jctc.8b01036] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language. The redeveloped package is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate with benchmarks on zirconium dioxide nanoparticles of over 160000 atoms.
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Affiliation(s)
- You Lu
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
| | - Matthew R Farrow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
| | - Pierre Fayon
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
| | - Andrew J Logsdail
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom.,Cardiff Catalysis Institute, School of Chemistry , Cardiff University , Cardiff CF10 3AT , United Kingdom
| | - Alexey A Sokol
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
| | - C Richard A Catlow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom.,Cardiff Catalysis Institute, School of Chemistry , Cardiff University , Cardiff CF10 3AT , United Kingdom.,UK Catalysis Hub, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Oxon OX11 0QX , United Kingdom
| | - Paul Sherwood
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
| | - Thomas W Keal
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , United Kingdom
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16
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QM/MM study of the stereospecific proton exchange of glutathiohydroxyacetone by glyoxalase I. RESULTS IN CHEMISTRY 2019. [DOI: 10.1016/j.rechem.2019.100011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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17
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Cheng Q, Liu G, Zhang P, Xu W, Tang K. Lipase-catalyzed hydrolysis of (R,S)-2,3-diphenylpropionic methyl ester enhanced by hydroxypropyl-β-cyclodextrin. Biotechnol Prog 2018; 34:1355-1362. [PMID: 30281958 DOI: 10.1002/btpr.2716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 08/09/2018] [Indexed: 01/06/2023]
Abstract
The enantioselective hydrolysis of (R,S)-2,3-diphenylpropionic methyl ester ((R,S)-2,3-2-PPAME) catalyzed by lipase to (R)-2,3-diphenylpropionic acid ((R)-2,3-2-PPA) was studied in an aqueous system. The catalytic effects of different types of lipase were compared, and Candida antarctica lipase A (CALA) with higher catalytic activity and enantioselectivity was selected. Hydroxypropyl-β-cyclodextrin (HP-β-CD) was added to the aqueous system to increase the solubility of 2,3-2-PPAME, which resulted in an increase of 35.56% in substrate conversion remaining the high enantiomeric excess. The factors influencing the substrate conversion and the optical purity of product such as temperature, pH, concentrations of CALA and HP-β-CD, substrate loading, and reaction time were optimized. The optimal conditions for this reaction were obtained, including pH of 5.5, 30 mg/mL CALA, 25 mmol/L HP-β-CD, 0.12 mmol substrate, temperature at 60 °C, agitation speed at 400 rpm, and 48 h for reaction time. Under these optimal conditions, the substrate conversion was up to 44.70% and the optical purity of the product (R)-2,3-2-PPA was up to 98.20%. This work provides an efficient alternative method for lipase-catalyzed enantioselective hydrolysis of 2,3-2-PPAME to (R)-2,3-2-PPA by β-cyclodextrin inclusion in an aqueous reaction system of hydrolysis. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:1355-1362, 2018.
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Affiliation(s)
- Qing Cheng
- Dept. of Chemistry and Chemical Engineering, Hunan Inst. of Science and Technology, Yueyang, Hunan, China
| | - Guangyong Liu
- Dept. of Chemistry and Chemical Engineering, Hunan Inst. of Science and Technology, Yueyang, Hunan, China
| | - Panliang Zhang
- Dept. of Chemistry and Chemical Engineering, Hunan Inst. of Science and Technology, Yueyang, Hunan, China
| | - Weifeng Xu
- Dept. of Chemistry and Chemical Engineering, Hunan Inst. of Science and Technology, Yueyang, Hunan, China
| | - Kewen Tang
- Dept. of Chemistry and Chemical Engineering, Hunan Inst. of Science and Technology, Yueyang, Hunan, China
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Escorcia AM, Stein M. QM/MM Investigation of the Role of a Second Coordination Shell Arginine in [NiFe]-Hydrogenases. Front Chem 2018; 6:164. [PMID: 29868565 PMCID: PMC5962704 DOI: 10.3389/fchem.2018.00164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/23/2018] [Indexed: 01/01/2023] Open
Abstract
[NiFe]-hydrogenases are highly efficient catalysts for the heterolytic splitting of molecular hydrogen (H2). The heterobimetallic cysteine-coordinated active site of these enzymes is covered by a highly conserved arginine residue, whose role in the reaction is not fully resolved yet. The structural and catalytic role of this arginine is investigated here using QM/MM calculations with various exchange-correlation functionals. All of them give a very consistent picture of the thermodynamics of H2 oxidation. The concept of the presence of a neutral arginine and its direct involvement as a Frustrated Lewis Pair (FLP) in the reaction is critically evaluated. The arginine, however, would exist in its standard protonation state and perform a critical role in positioning and slightly polarizing the substrate H2. It is not directly involved in the heterolytic processing of H2 but guides its approach and reduces its flexibility during binding. Upon substitution of the positively charged arginine by a charge-conserving lysine residue, the H2 binding position remains unaffected. However, critical hydrogen bonding interactions with nearby aspartate residues are lost. In addition, the H2 polarization is unfavorable and the reduced side-chain volume may negatively affect the kinetics of the catalytic process.
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Affiliation(s)
- Andrés M Escorcia
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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Escorcia AM, van Rijn JPM, Cheng GJ, Schrepfer P, Brück TB, Thiel W. Molecular dynamics study of taxadiene synthase catalysis. J Comput Chem 2018; 39:1215-1225. [PMID: 29450907 DOI: 10.1002/jcc.25184] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 01/10/2023]
Abstract
Molecular dynamics (MD) simulations have been performed to study the dynamic behavior of noncovalent enzyme carbocation complexes involved in the cyclization of geranylgeranyl diphosphate to taxadiene catalyzed by taxadiene synthase (TXS). Taxadiene and the observed four side products originate from the deprotonation of carbocation intermediates. The MD simulations of the TXS carbocation complexes provide insights into potential deprotonation mechanisms of such carbocations. The MD results do not support a previous hypothesis that carbocation tumbling is a key factor in the deprotonation of the carbocations by pyrophosphate. Instead water bridges are identified which may allow the formation of side products via multiple proton transfer reactions. A novel reaction path for taxadiene formation is proposed on the basis of the simulations. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Andrés M Escorcia
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
| | | | - Gui-Juan Cheng
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
| | - Patrick Schrepfer
- Professorship of Industrial Biocatalysis, Department of Chemistry, Technical University Munich, Lichtenberg Str. 4, Garching, 85748, Germany
| | - Thomas B Brück
- Professorship of Industrial Biocatalysis, Department of Chemistry, Technical University Munich, Lichtenberg Str. 4, Garching, 85748, Germany
| | - Walter Thiel
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
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Barrera Valderrama DI, Doerr M, Daza Espinosa MC. Función de los confórmeros de ataque cercano en la acilación enantioselectiva del (R,S)-propranolol catalizada por lipasa B de Candida antarctica. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2018. [DOI: 10.15446/rev.colomb.biote.v20n1.73652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
La lipasa B de Candida antarctica (CalB) se ha utilizado en la acilación quimio- y enantioselectiva del racemato (R,S)-propranolol. CalB tiene enantioselectividad moderada (E=63) por el R-propranolol. La enantioselectividad, se origina en la reacción de transferencia del grupo acilo desde la serina catalítica, acilada, al propranolol. La fase inicial de esta reacción involucra la formación de complejos de Michaelis y posteriormente conformaciones de ataque cercano. El análisis de las conformaciones de ataque cercano ha permitido en varios casos explicar el origen de la catálisis o reproducir el efecto catalítico. En este trabajo se profundiza en la comprensión la función de las conformaciones de ataque cercano en la enantioselectividad de la acilación del (R,S)-propranolol catalizada por CalB. Para lo anterior se realizó un estudio detallado de los complejos de Michaelis y de las conformaciones de ataque cercano del paso enantioselectivo de la reacción de acilación del (R,S)-propranolol utilizando un protocolo de dinámica molecular QM/MM (SCCDFTB/CHARMM) utilizando 6 distribuciones de velocidades iniciales y simulaciones de 2,5 ns. Se estudiaron 7 complejos CalB-propranolol. Los enlaces de hidrógeno del sitio activo de CalB acilada relevantes para la actividad catalítica fueron estables en todas las simulaciones. Las poblaciones de los complejos de Michaelis y de las conformaciones de ataque cercano son dependientes de la distribución de las velocidades iniciales de la dinámica molecular. La enantioselectividad moderada de CalB acilada, encontrada experimentalmente, puede ser parcialmente atribuida a la alta población de conformaciones de ataque cercano observada para el S-propranolol.
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Ling B, Wang X, Su H, Liu R, Liu Y. Protonation state and fine structure of the active site determine the reactivity of dehydratase: hydration and isomerization of β-myrcene catalyzed by linalool dehydratase/isomerase from Castellaniella defragrans. Phys Chem Chem Phys 2018; 20:17342-17352. [DOI: 10.1039/c8cp02362j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Linalool dehydratase/isomerase (LinD) from Castellaniella defragrans is a bifunctional enzyme that catalyzes the hydration of β-myrcene to (S)-linalool and isomerization of (S)-linalool to geraniol.
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Affiliation(s)
- Baoping Ling
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu
- China
- School of Chemistry and Chemical Engineering & Environmental Science and Engineering
| | - Xiya Wang
- School of Chemistry and Chemical Engineering & Environmental Science and Engineering
- Shandong University
- Jinan
- China
| | - Hao Su
- School of Chemistry and Chemical Engineering & Environmental Science and Engineering
- Shandong University
- Jinan
- China
| | - Rutao Liu
- School of Chemistry and Chemical Engineering & Environmental Science and Engineering
- Shandong University
- Jinan
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering & Environmental Science and Engineering
- Shandong University
- Jinan
- China
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