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Guan ZB, Deng XT, Zhang ZH, Xu GC, Cheng WL, Liao XR, Cai YJ. Engineering Glucosamine-6-Phosphate Synthase to Achieve Efficient One-Step Biosynthesis of Glucosamine. ACS Chem Biol 2024; 19:1237-1242. [PMID: 38723147 DOI: 10.1021/acschembio.4c00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
As an important functional monosaccharide, glucosamine (GlcN) is widely used in fields such as medicine, food nutrition, and health care. Here, we report a distinct GlcN biosynthesis method that utilizes engineered Bacillus subtilis glucosamine-6-phosphate synthase (BsGlmS) to convert D-fructose to directly generate GlcN. The best variant obtained by using a combinatorial active-site saturation test/iterative saturation mutagenesis (CAST/ISM) strategy was a quadruple mutant S596D/V597G/S347H/G299Q (BsGlmS-BK19), which has a catalytic activity 1736-fold that of the wild type toward D-fructose. Upon using mutant BK19 as a whole-cell catalyst, D-fructose was converted into GlcN with 65.32% conversion in 6 h, whereas the wild type only attained a conversion rate of 0.31% under the same conditions. Molecular docking and molecular dynamics simulations were implemented to provide insights into the mechanism underlying the enhanced activity of BK19. Importantly, the BsGlmS-BK19 variant specifically catalyzes D-fructose without the need for phosphorylated substrates, representing a significant advancement in GlcN biosynthesis.
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Affiliation(s)
- Zheng-Bing Guan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Xue-Ting Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zi-Hao Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Guo-Chao Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Wan-Li Cheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Xiang-Ru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Yu-Jie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
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2
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Świderek K, Martí S, Arafet K, Moliner V. Computational study of the mechanism of a polyurethane esterase A (PueA) from Pseudomonas chlororaphis. Faraday Discuss 2024. [PMID: 38836643 DOI: 10.1039/d4fd00022f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The effective management of plastic waste has become a global imperative, given our reliance on a linear model in which plastics are manufactured, used once, and then discarded. This has led to the pervasive accumulation of plastic debris in landfills and environmental contamination. Recognizing this issue, numerous initiatives are underway to address the environmental repercussions associated with plastic disposal. In this study, we investigate the possible molecular mechanism of polyurethane esterase A (PueA), which has been previously identified as responsible for the degradation of a polyester polyurethane (PU) sample in Pseudomonas chlororaphis, as an effort to develop enzymatic biodegradation solutions. After generating the unsolved 3D structure of the protein by AlphaFold2 from its known genome, the enzymatic hydrolysis of the same model PU compound previously used in experiments has been explored employing QM/MM molecular dynamics simulations. This required a preliminary analysis of the 3D structure of the apo-enzyme, identifying the putative active site, and the search for the optimal protein-substrate binding site. Finally, the resulting free energy landscape indicates that wild-type PueA can degrade PU chains, although with low-level activity. The reaction takes place by a characteristic four-step path of the serine hydrolases, involving an acylation followed by a diacylation step. Energetics and structural analysis of the evolution of the active site along the reaction suggests that PueA can be considered a promising protein scaffold for further development to achieve efficient biodegradation of PU.
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Affiliation(s)
- Katarzyna Świderek
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain.
| | - Sergio Martí
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain.
| | - Kemel Arafet
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain.
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain.
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3
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Ruiz-Pernía JJ, Świderek K, Bertran J, Moliner V, Tuñón I. Electrostatics as a Guiding Principle in Understanding and Designing Enzymes. J Chem Theory Comput 2024; 20:1783-1795. [PMID: 38410913 PMCID: PMC10938506 DOI: 10.1021/acs.jctc.3c01395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
Enzyme design faces challenges related to the implementation of the basic principles that govern the catalytic activity in natural enzymes. In this work, we revisit basic electrostatic concepts that have been shown to explain the origin of enzymatic efficiency like preorganization and reorganization. Using magnitudes such as the electrostatic potential and the electric field generated by the protein, we explain how these concepts work in different enzymes and how they can be used to rationalize the consequences of point mutations. We also discuss examples of protein design in which electrostatic effects have been implemented. For the near future, molecular simulations, coupled with the use of machine learning methods, can be used to implement electrostatics as a guiding principle for enzyme designs.
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Affiliation(s)
| | - Katarzyna Świderek
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Joan Bertran
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Vicent Moliner
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
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4
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Pan X, Van R, Pu J, Nam K, Mao Y, Shao Y. Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions. J Chem Theory Comput 2023; 19:8234-8244. [PMID: 37943896 PMCID: PMC10835707 DOI: 10.1021/acs.jctc.3c00973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
In enzyme mechanistic studies and mutant design, it is highly desirable to know the individual residue contributions to the reaction free energy and barrier. In this work, we show that such free energy contributions from each residue can be readily obtained by postprocessing ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulation trajectories. Specifically, through a mean force integration along the minimum free energy pathway, one can obtain the electrostatic, polarization, and van der Waals contributions from each residue to the free energy barrier. Separately, a similar analysis procedure allows us to assess the contribution from different collective variables along the reaction coordinate. The chorismate mutase reaction is used to demonstrate the utilization of these two trajectory analysis tools.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Richard Van
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, United States
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yuezhi Mao
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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Ge F, Chen G, Qian M, Xu C, Liu J, Cao J, Li X, Hu D, Xu Y, Xin Y, Wang D, Zhou J, Shi H, Tan Z. Artificial Intelligence Aided Lipase Production and Engineering for Enzymatic Performance Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14911-14930. [PMID: 37800676 DOI: 10.1021/acs.jafc.3c05029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
With the development of artificial intelligence (AI), tailoring methods for enzyme engineering have been widely expanded. Additional protocols based on optimized network models have been used to predict and optimize lipase production as well as properties, namely, catalytic activity, stability, and substrate specificity. Here, different network models and algorithms for the prediction and reforming of lipase, focusing on its modification methods and cases based on AI, are reviewed in terms of both their advantages and disadvantages. Different neural networks coupled with various algorithms are usually applied to predict the maximum yield of lipase by optimizing the external cultivations for lipase production, while one part is used to predict the molecule variations affecting the properties of lipase. However, few studies have directly utilized AI to engineer lipase by affecting the structure of the enzyme, and a set of research gaps needs to be explored. Additionally, future perspectives of AI application in enzymes, including lipase engineering, are deduced to help the redesign of enzymes and the reform of new functional biocatalysts. This review provides a new horizon for developing effective and innovative AI tools for lipase production and engineering and facilitating lipase applications in the food industry and biomass conversion.
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Affiliation(s)
- Feiyin Ge
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Gang Chen
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Minjing Qian
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Cheng Xu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jiao Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jiaqi Cao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Xinchao Li
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Die Hu
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, People's Republic of China
| | - Yangsen Xu
- Dongtai Hanfangyuan Biotechnology Co. Ltd., Yancheng 224241, People's Republic of China
| | - Ya Xin
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Dianlong Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jia Zhou
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Hao Shi
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Zhongbiao Tan
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
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Świderek K, Velasco-Lozano S, Galmés MÀ, Olazabal I, Sardon H, López-Gallego F, Moliner V. Mechanistic studies of a lipase unveil effect of pH on hydrolysis products of small PET modules. Nat Commun 2023; 14:3556. [PMID: 37321996 PMCID: PMC10272158 DOI: 10.1038/s41467-023-39201-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Biocatalysis is a key technology enabling plastic recycling. However, despite advances done in the development of plastic-degrading enzymes, the molecular mechanisms that govern their catalytic performance are poorly understood, hampering the engineering of more efficient enzyme-based technologies. In this work, we study the hydrolysis of PET-derived diesters and PET trimers catalyzed by the highly promiscuous lipase B from Candida antarctica (CALB) through QM/MM molecular dynamics simulations supported by experimental Michaelis-Menten kinetics. The computational studies reveal the role of the pH on the CALB regioselectivity toward the hydrolysis of bis-(hydroxyethyl) terephthalate (BHET). We exploit this insight to perform a pH-controlled biotransformation that selectively hydrolyzes BHET to either its corresponding diacid or monoesters using both soluble and immobilized CALB. The discoveries presented here can be exploited for the valorization of BHET resulting from the organocatalytic depolymerization of PET.
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Affiliation(s)
- Katarzyna Świderek
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castellón, Spain.
| | - Susana Velasco-Lozano
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón, 182, 20014 Donostia-San Sebastián, Spain
| | - Miquel À Galmés
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castellón, Spain
| | - Ion Olazabal
- POLYMAT, Department of Polymer Science and Technology, University of the Basque Country UPV/EHU, Manuel de Lardizabal, 3, 20018, Donostia-San Sebastián, Spain
| | - Haritz Sardon
- POLYMAT, Department of Polymer Science and Technology, University of the Basque Country UPV/EHU, Manuel de Lardizabal, 3, 20018, Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón, 182, 20014 Donostia-San Sebastián, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castellón, Spain.
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7
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Galmés MÀ, Nödling AR, He K, Luk LYP, Świderek K, Moliner V. Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases. Chem Sci 2022; 13:4779-4787. [PMID: 35655887 PMCID: PMC9067594 DOI: 10.1039/d2sc00778a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
While there has been emerging interest in designing new enzymes to solve practical challenges, computer-based options to redesign catalytically active proteins are rather limited. Here, a rational QM/MM molecular dynamics strategy based on combining the best electrostatic properties of enzymes with activity in a common reaction is presented. The computational protocol has been applied to the re-design of the protein scaffold of an existing promiscuous esterase from Bacillus subtilis Bs2 to enhance its secondary amidase activity. After the alignment of Bs2 with a non-homologous amidase Candida antarctica lipase B (CALB) within rotation quaternions, a relevant spatial aspartate residue of the latter was transferred to the former as a means to favor the electrostatics of transition state formation, where a clear separation of charges takes place. Deep computational insights, however, revealed a significant conformational change caused by the amino acid replacement, provoking a shift in the pK a of the inserted aspartate and counteracting the anticipated catalytic effect. This prediction was experimentally confirmed with a 1.3-fold increase in activity. The good agreement between theoretical and experimental results, as well as the linear correlation between the electrostatic properties and the activation energy barriers, suggest that the presented computational-based investigation can transform in an enzyme engineering approach.
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Affiliation(s)
- Miquel À Galmés
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castellón Spain +34 964728084
| | - Alexander R Nödling
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Kaining He
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Louis Y P Luk
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Katarzyna Świderek
- Department of Physical and Analytical Chemistry, Universitat Jaume I 12071 Castellón Spain +34 964728070
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castellón Spain +34 964728084
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