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Zhang S, Zheng R, Long J, Zhu Y, Tan T. Computational design of carboxylase for the synthesis of 4-hydroxyisophthalic acid from p-hydroxybenzoic acid by fixing CO 2. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 366:121703. [PMID: 38996602 DOI: 10.1016/j.jenvman.2024.121703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 06/11/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024]
Abstract
Carbon dioxide (CO2) emissions constitute the primary contribution to global climate change. Synthetic CO2 fixation represents an exceptionally appealing and sustainable method for carbon neutralization. Unlike the limitations of chemical catalysis, biological CO2 fixation displays high selectivity and the ability to operate under mild conditions. The superfamily of amidohydrolases has demonstrated the ability to synthesize a range of aromatic monocarboxylic acids. However, there is a scarcity of reported carboxylases capable of synthesizing aromatic dicarboxylic acids. Among these, 4-hydroxyisophthalic acid holds significant potential for applications across various fields, yet no enzyme has been reported for its synthesis. In this study, we developed for the first time that exhibits starting activity in fixing CO2 to synthesize 4-hydroxyisophthalic acid. Furthermore, we have devised a computational strategy that effectively enhances the catalytic activity of this enzyme. A focused library comprising only 13 variants was generated. Experimental validation confirmed a threefold improvement in the carboxylation activity of the optimal variant (L47M). The computational enzyme design strategy proposed in this paper demonstrates broad applicability in developing carboxylases for synthesizing other aromatic dicarboxylic acids. This lays the groundwork for leveraging biocatalysis in industrial synthesis for CO2 fixation.
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Affiliation(s)
- Shiding Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ruonan Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jianyu Long
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yushan Zhu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Tianwei Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, China.
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Huang X, Zhou J, Yang D, Zhang J, Xia X, Chen YE, Xu J. Decoding CRISPR-Cas PAM recognition with UniDesign. Brief Bioinform 2023; 24:bbad133. [PMID: 37078688 PMCID: PMC10199764 DOI: 10.1093/bib/bbad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/09/2023] [Accepted: 03/16/2023] [Indexed: 04/21/2023] Open
Abstract
The critical first step in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (CRISPR-Cas) protein-mediated gene editing is recognizing a preferred protospacer adjacent motif (PAM) on target DNAs by the protein's PAM-interacting amino acids (PIAAs). Thus, accurate computational modeling of PAM recognition is useful in assisting CRISPR-Cas engineering to relax or tighten PAM requirements for subsequent applications. Here, we describe a universal computational protein design framework (UniDesign) for designing protein-nucleic acid interactions. As a proof of concept, we applied UniDesign to decode the PAM-PIAA interactions for eight Cas9 and two Cas12a proteins. We show that, given native PIAAs, the UniDesign-predicted PAMs are largely identical to the natural PAMs of all Cas proteins. In turn, given natural PAMs, the computationally redesigned PIAA residues largely recapitulated the native PIAAs (74% and 86% in terms of identity and similarity, respectively). These results demonstrate that UniDesign faithfully captures the mutual preference between natural PAMs and native PIAAs, suggesting it is a useful tool for engineering CRISPR-Cas and other nucleic acid-interacting proteins. UniDesign is open-sourced at https://github.com/tommyhuangthu/UniDesign.
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Affiliation(s)
- Xiaoqiang Huang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jun Zhou
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Dongshan Yang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jifeng Zhang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Xiaofeng Xia
- Research & Development, ATGC Inc., 100 E Lancaster Avenue, LIMR Building Lab 129, Wynnewood, PA 19096, USA
| | - Yuqing Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
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Zlobin A, Golovin A. Between Protein Fold and Nucleophile Identity: Multiscale Modeling of the TEV Protease Enzyme-Substrate Complex. ACS OMEGA 2022; 7:40279-40292. [PMID: 36385818 PMCID: PMC9647873 DOI: 10.1021/acsomega.2c05201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
The cysteine protease from the tobacco etch virus (TEVp) is a well-known and widely utilized enzyme. TEVp's chymotrypsin-like fold is generally associated with serine catalytic triads that differ in terms of a reaction mechanism from the most well-studied papain-like cysteine proteases. The question of what dominates the TEVp mechanism, nucleophile identity, or structural composition has never been previously addressed. Here, we use enhanced sampling multiscale modeling to uncover that TEVp combines the features of two worlds in such a way that potentially hampers its activity. We show that TEVp cysteine is strictly in the anionic form in a free enzyme similar to papain. Peptide binding shifts the equilibrium toward the nucleophile's protonated form, characteristic of chymotrypsin-like proteases, although the cysteinyl anion form is still present and interconversion is rapid. This way cysteine protonation generates enzyme states that are a diversion from the most effective course of action, with only 13.2% of Michaelis complex sub-states able to initiate the reaction. As a result, we propose an updated view on the reaction mechanism catalyzed by TEVp. We also demonstrate that AlphaFold is able to construct protease-substrate complexes with high accuracy. We propose that our findings open a way for its industrious use in enzymological tasks. Unique features of TEVp discovered in this work open a discussion on the evolutionary history and trade-offs of optimizing serine triad-associated folds to cysteine as a nucleophile.
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Affiliation(s)
- Alexander Zlobin
- Belozersky
Institute of Physico-Chemical Biology, Lomonosov
Moscow State University, 119991 Moscow, Russia
- Shemyakin
and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Andrey Golovin
- Belozersky
Institute of Physico-Chemical Biology, Lomonosov
Moscow State University, 119991 Moscow, Russia
- Shemyakin
and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Sirius
University of Science and Technology, 354340 Sochi, Russia
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4
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Hou Q, Li N, Chao Y, Li S, Zhang L. Design and regulation of the surface and interfacial behavior of protein molecules. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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5
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Huang Q, Wang K, Li H, Yi S, Zhao X. Enhancing cellulosic ethanol production through coevolution of multiple enzymatic characteristics of β-glucosidase from Penicillium oxalicum 16. Appl Microbiol Biotechnol 2020; 104:8299-8308. [PMID: 32857198 DOI: 10.1007/s00253-020-10858-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/04/2020] [Accepted: 08/23/2020] [Indexed: 01/04/2023]
Abstract
In previous studies, we isolated a novel β-glucosidase from Penicillium oxalicum 16 (16BGL), which is useful for producing cellulosic ethanol. However, 16BGL has a relatively low enzyme activity and product tolerance; besides, a huge gap exists between the optimum temperature of 16BGL (70 °C) and the fermentation temperature for producing cellulosic ethanol (40 °C). Here, we present a directed evolution-based study, which combines one-round error-prone PCR with three rounds of high-throughput screening, for coevolving multiple enzymatic characteristics of 16BGL. We identified an improved variant Y-1-B1 with a triple mutant (G414S/D421V/T441S). Y-1-B1 had an optimum temperature of 50 °C, much closer to the fermentation temperature. The catalytic efficiency of Y-1-B1 for hydrolyzing pNPG was 1355 mM-1 s-1 at 50 °C and pH 5, significantly higher than that of 16BGL (807 mM-1 s-1). Y-1-B1 also achieved a slightly reduced strength of product inhibition of 1.1 at a glucose concentration of 20 mM, compared with the ratio of 1.3 for 16BGL. A maximum titer of 6.9 g/L for ethanol production was achieved in the reaction with Y-1-B1, which was 22% higher than that achieved with 16BGL. Structure modeling revealed that the mutations are distant from the active-site pocket. Therefore, we performed molecular dynamics (MD) simulations to understand why these mutations can improve catalytic efficiency. MD simulation revealed that the nucleophilic residue Asp261 had a much closer contact with the glucosidic center of pNPG in the simulation with Y-1-B1 than that with 16BGL, suggesting that the mutant is more favorable for catalysis. KEY POINTS: • Multiple enzymatic properties of Penicillium oxalicum 16 BGL were coevolved. • A catalytically efficient triple mutant G414S/D421V/T441S was reported. • Molecular dynamics simulation supported the enhanced catalytic activity.
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Affiliation(s)
- Qiuxia Huang
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Kexin Wang
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Hanxin Li
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Shi Yi
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Xihua Zhao
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China.
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Yang J, Wei Y, Li G, Zhou S, Deng Y. Computer-aided engineering of adipyl-CoA synthetase for enhancing adipic acid synthesis. Biotechnol Lett 2020; 42:2693-2701. [PMID: 32737718 DOI: 10.1007/s10529-020-02978-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/27/2020] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To enhance adipic acid production, a computer-aided approach was employed to engineer the adipyl-CoA synthetase from Thermobifida fusca by combining sequence analysis, protein structure modeling, in silico site-directed mutagenesis, and molecular dynamics simulation. RESULTS Two single mutants of T. fusca adipyl-CoA synthetase, E210βN and E210βQ, achieved a specific enzyme activity of 1.95 and 1.84 U/mg, respectively, which compared favorably with the 1.48 U/mg for the wild-type. The laboratory-level fermentation experiments showed that E210βN and E210βQ achieved a maximum adipic acid titer of 0.32 and 0.3 g/L. In contrast, the wild-type enzyme yielded a titer of 0.15 g/L under the same conditions. Molecular dynamics (MD) simulations revealed that the mutants (E210βN and E210βQ) could accelerate the dephosphorylation process in catalysis and enhance enzyme activity. CONCLUSIONS The combined computational-experimental approach provides an effective strategy for enhancing enzymatic characteristics, and the mutants may find a useful application for producing adipic acid.
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Affiliation(s)
- Ju Yang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Yafeng Wei
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Guohui Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.
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Wang K, Huang Q, Li H, Zhao X. Co-evolution of β-glucosidase activity and product tolerance for increasing cellulosic ethanol yield. Biotechnol Lett 2020; 42:2239-2250. [PMID: 32583369 DOI: 10.1007/s10529-020-02935-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 05/30/2020] [Indexed: 12/19/2022]
Abstract
β-Glucosidase (BGL) plays a key role in cellulose hydrolysis. However, it is still a great challenge to enhance product tolerance and enzyme activity of BGL simultaneously. Here, we utilized one round error-prone PCR to engineer the Penicillium oxalicum 16 BGL (16BGL) for improving the cellulosic ethanol yield. We identified a new variant (L-6C), a triple mutant (M280T/V484L/D589E), with enhanced catalytic efficiency ([Formula: see text]) for hydrolyzing pNPG and reduced strength of inhibition ([Formula: see text]) by glucose. To be specific, L-6C achieved a [Formula: see text] of 0.35 at a glucose concentration of 20 mM, which was 3.63 times lower than that attained by 16BGL. The catalytic efficiency for L-6C to hydrolyze pNPG was determined to be 983.68 mM-1 s-1, which was 22% higher than that for 16BGL. However, experiments showed that L-6C had reduced binding affinity (2.88 mM) to pNGP compared with 16BGL (1.69 mM). L-6C produced 6.15 g/L ethanol whose yield increased by about 10% than 16BGL. We performed molecular docking and molecular dynamics (MD) simulation, and binding free energy calculation using the Molecular Mechanics/Poisson Boltzmann surface area (MM/PBSA) method. MD simulation together with the MM/PBSA calculation suggested that L-6C had reduced binding free energy to pNPG, which was consistent with the experimental data.
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Affiliation(s)
- Kexin Wang
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Qiuxia Huang
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Hanxin Li
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Xihua Zhao
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China.
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Strategy for the Biosynthesis of Short Oligopeptides: Green and Sustainable Chemistry. Biomolecules 2019; 9:biom9110733. [PMID: 31766233 PMCID: PMC6920838 DOI: 10.3390/biom9110733] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 02/07/2023] Open
Abstract
Short oligopeptides are some of the most promising and functionally important amide bond-containing components, with widespread applications. Biosynthesis of these oligopeptides may potentially become the ultimate strategy because it has better cost efficiency and environmental-friendliness than conventional solid phase peptide synthesis and chemo-enzymatic synthesis. To successfully apply this strategy for the biosynthesis of structurally diverse amide bond-containing components, the identification and selection of specific biocatalysts is extremely important. Given that perspective, this review focuses on the current knowledge about the typical enzymes that might be potentially used for the synthesis of short oligopeptides. Moreover, novel enzymatic methods of producing desired peptides via metabolic engineering are highlighted. It is believed that this review will be helpful for technological innovation in the production of desired peptides.
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Ferrario V, Fischer M, Zhu Y, Pleiss J. Modelling of substrate access and substrate binding to cephalosporin acylases. Sci Rep 2019; 9:12402. [PMID: 31455800 PMCID: PMC6712217 DOI: 10.1038/s41598-019-48849-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/14/2019] [Indexed: 01/16/2023] Open
Abstract
Semisynthetic cephalosporins are widely used antibiotics currently produced by different chemical steps under harsh conditions, which results in a considerable amount of toxic waste. Biocatalytic synthesis by the cephalosporin acylase from Pseudomonas sp. strain N176 is a promising alternative. Despite intensive engineering of the enzyme, the catalytic activity is still too low for a commercially viable process. To identify the bottlenecks which limit the success of protein engineering efforts, a series of MD simulations was performed to study for two acylase variants (WT, M6) the access of the substrate cephalosporin C from the bulk to the active site and the stability of the enzyme-substrate complex. In both variants, cephalosporin C was binding to a non-productive substrate binding site (E86α, S369β, S460β) at the entrance to the binding pocket, preventing substrate access. A second non-productive binding site (G372β, W376β, L457β) was identified within the binding pocket, which competes with the active site for substrate binding. Noteworthy, substrate binding to the protein surface followed a Langmuir model resulting in binding constants K = 7.4 and 9.2 mM for WT and M6, respectively, which were similar to the experimentally determined Michaelis constants KM = 11.0 and 8.1 mM, respectively.
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Affiliation(s)
- Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Mona Fischer
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Yushan Zhu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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