1
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Jiang W, Wu Y, Su R, Xu W, Yang W, Qiu Y, Cai Y, Wang C, Hu L, Gu W, Zhu C. Grain-Boundary-Rich Ceria Metallene Nanozyme with Abundant Metal Site Pairs Boosts Phosphatase-like Activity. NANO LETTERS 2024; 24:9635-9642. [PMID: 39077994 DOI: 10.1021/acs.nanolett.4c02394] [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: 07/31/2024]
Abstract
Natural phosphatases featuring paired metal sites inspire various advanced nanozymes with phosphatase-like activity as alternatives in practical applications. Numerous efforts to create point defects show limited metal site pairs, further resulting in insufficient activity. However, it remains a grand challenge to accurately engineer abundant metal site pairs in nanozymes. Herein, we report a grain-boundary-rich ceria metallene nanozyme (GB-CeO2) with phosphatase-like activity. Grain boundaries acting as the line or interfacial defects can effectively increase the content of Ce4+/Ce3+ site pairs to 72.28%, achieving a 49.28-fold enhancement in activity. Furthermore, abundant grain boundaries optimize the band structure to assist the photoelectron transfer under irradiation, which further increases the content of metal site pairs to 88.96% and finally realizes a 114.39-fold enhanced activity over that of CeO2 without irradiation. Given the different inhibition effects of pesticides on catalysts with and without irradiation, GB-CeO2 was successfully applied to recognize mixed toxic pesticides.
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Affiliation(s)
- Wenxuan Jiang
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Yu Wu
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Rina Su
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Weiqing Xu
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Wenhong Yang
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Yiwei Qiu
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Yujia Cai
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Canglong Wang
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, People's Republic of China
| | - Liuyong Hu
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, Hubei Engineering Technology Research Center of Optoelectronic and New Energy Materials, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
| | - Wenling Gu
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Chengzhou Zhu
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
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2
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Yu J, Fu Y, Cao Z. QM/MM and MM MD Simulations on Enzymatic Degradation of the Nerve Agent VR by Phosphotriesterase. J Phys Chem B 2023; 127:7462-7471. [PMID: 37584503 DOI: 10.1021/acs.jpcb.3c03952] [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: 08/17/2023]
Abstract
V-type nerve agents are hardly degraded by phosphotriesterase (PTE). Interestingly, the PTE variant of BHR-73MNW can effectively improve the hydrolytic efficiency of VR, especially for its Sp-enantiomer. Here, the whole enzymatic degradation of both Sp and Rp enantiomers of VR by the wild-type PTE and its variant BHR-73MNW was investigated by quantum mechanics/molecular mechanics (QM/MM) calculations and MM molecular dynamics simulations. Present results indicate that the degradation of VR can be initiated by the nucleophilic attack of the bridging OH- and the zinc-bound water molecule. The QM/MM-predicted energy barriers for the hydrolytic process of Sp-VR are 19.8 kcal mol-1 by the variant with water as a nucleophile and 22.0 kcal mol-1 by the wild-type PTE with OH- as a nucleophile, and corresponding degraded products are bound to the dinuclear metal site in monodentate and bidentate coordination modes, respectively. The variant effectively increases the volume of the large pocket, allowing more water molecules to enter the active pocket and resulting in the improvement of the degradation efficiency of Sp-VR. The hydrolysis of Rp-VR is triggered only by the hydroxide with an energy span of 20.6 kcal mol-1 for the wild-type PTE and 20.7 kcal mol-1 for the variant BHR-73-MNW PTE. Such mechanistic insights into the stereoselective degradation of VR by PTE and the role of water may inspire further studies to improve the catalytic efficiency of PTE toward the detoxification of nerve agents.
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Affiliation(s)
- Jun Yu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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3
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Wang KY, Zhang J, Hsu YC, Lin H, Han Z, Pang J, Yang Z, Liang RR, Shi W, Zhou HC. Bioinspired Framework Catalysts: From Enzyme Immobilization to Biomimetic Catalysis. Chem Rev 2023; 123:5347-5420. [PMID: 37043332 PMCID: PMC10853941 DOI: 10.1021/acs.chemrev.2c00879] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Indexed: 04/13/2023]
Abstract
Enzymatic catalysis has fueled considerable interest from chemists due to its high efficiency and selectivity. However, the structural complexity and vulnerability hamper the application potentials of enzymes. Driven by the practical demand for chemical conversion, there is a long-sought quest for bioinspired catalysts reproducing and even surpassing the functions of natural enzymes. As nanoporous materials with high surface areas and crystallinity, metal-organic frameworks (MOFs) represent an exquisite case of how natural enzymes and their active sites are integrated into porous solids, affording bioinspired heterogeneous catalysts with superior stability and customizable structures. In this review, we comprehensively summarize the advances of bioinspired MOFs for catalysis, discuss the design principle of various MOF-based catalysts, such as MOF-enzyme composites and MOFs embedded with active sites, and explore the utility of these catalysts in different reactions. The advantages of MOFs as enzyme mimetics are also highlighted, including confinement, templating effects, and functionality, in comparison with homogeneous supramolecular catalysts. A perspective is provided to discuss potential solutions addressing current challenges in MOF catalysis.
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Affiliation(s)
- Kun-Yu Wang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiaqi Zhang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu-Chuan Hsu
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hengyu Lin
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zongsu Han
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiandong Pang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- School
of Materials Science and Engineering, Tianjin Key Laboratory of Metal
and Molecule-Based Material Chemistry, Nankai
University, Tianjin 300350, China
| | - Zhentao Yang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Rong-Ran Liang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wei Shi
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong-Cai Zhou
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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4
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Schnettler JD, Klein OJ, Kaminski TS, Colin PY, Hollfelder F. Ultrahigh-Throughput Directed Evolution of a Metal-Free α/β-Hydrolase with a Cys-His-Asp Triad into an Efficient Phosphotriesterase. J Am Chem Soc 2023; 145:1083-1096. [PMID: 36583539 PMCID: PMC9853848 DOI: 10.1021/jacs.2c10673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Finding new mechanistic solutions for biocatalytic challenges is key in the evolutionary adaptation of enzymes, as well as in devising new catalysts. The recent release of man-made substances into the environment provides a dynamic testing ground for observing biocatalytic innovation at play. Phosphate triesters, used as pesticides, have only recently been introduced into the environment, where they have no natural counterpart. Enzymes have rapidly evolved to hydrolyze phosphate triesters in response to this challenge, converging onto the same mechanistic solution, which requires bivalent cations as a cofactor for catalysis. In contrast, the previously identified metagenomic promiscuous hydrolase P91, a homologue of acetylcholinesterase, achieves slow phosphotriester hydrolysis mediated by a metal-independent Cys-His-Asp triad. Here, we probe the evolvability of this new catalytic motif by subjecting P91 to directed evolution. By combining a focused library approach with the ultrahigh throughput of droplet microfluidics, we increase P91's activity by a factor of ≈360 (to a kcat/KM of ≈7 × 105 M-1 s-1) in only two rounds of evolution, rivaling the catalytic efficiencies of naturally evolved, metal-dependent phosphotriesterases. Unlike its homologue acetylcholinesterase, P91 does not suffer suicide inhibition; instead, fast dephosphorylation rates make the formation of the covalent adduct rather than its hydrolysis rate-limiting. This step is improved by directed evolution, with intermediate formation accelerated by 2 orders of magnitude. Combining focused, combinatorial libraries with the ultrahigh throughput of droplet microfluidics can be leveraged to identify and enhance mechanistic strategies that have not reached high efficiency in nature, resulting in alternative reagents with novel catalytic machineries.
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Affiliation(s)
- J David Schnettler
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Oskar James Klein
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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5
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Mali H, Shah C, Patel DH, Trivedi U, Subramanian RB. Bio-catalytic system of metallohydrolases for remediation of neurotoxin organophosphates and applications with a future vision. J Inorg Biochem 2022; 231:111771. [DOI: 10.1016/j.jinorgbio.2022.111771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 12/29/2022]
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6
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Fu Y, Zhang Y, Fan F, Wang B, Cao Z. Degradation of pesticides diazinon and diazoxon by phosphotriesterase: insight into divergent mechanisms from QM/MM and MD simulations. Phys Chem Chem Phys 2022; 24:687-696. [PMID: 34927643 DOI: 10.1039/d1cp05034f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymatic hydrolysis by phosphotriesterase (PTE) is one of the most effective ways of degrading organophosphorus pesticides, but the catalytic efficiency depends on the structural features of substrates. Here the enzymatic degradation of diazinon (DIN) and diazoxon (DON), characterized by PS and PO, respectively, have been investigated by QM/MM calculations and MM MD simulations. Our calculations demonstrate that the hydrolysis of DON (with PO) is inevitably initiated by the nucleophilic attack of the bridging-OH- on the phosphorus center, while for DIN (with PS), we proposed a new degradation mechanism, initiated by the nucleophilic attack of the Znα-bound water molecule, for its low-energy pathway. For both DIN and DON, the hydrolytic reaction is predicted to be the rate-limiting step, with energy barriers of 18.5 and 17.7 kcal mol-1, respectively. The transportation of substrates to the active site, the release of the leaving group and the degraded product are generally verified to be favorable by MD simulations via umbrella sampling, both thermodynamically and dynamically. The side-chain residues Phe132, Leu271 and Tyr309 play the gate-switching role to manipulate substrate delivery and product release. In comparison with the DON-enzyme system, the degraded product of DIN is more easily released from the active site. These new findings will contribute to the comprehensive understanding of the enzymatic degradation of toxic organophosphorus compounds by PTE.
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Affiliation(s)
- Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Yuwei Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Fangfang Fan
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, 310023, China.
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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7
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Abdou SN. Ultrasonic Assisted Nano-structures of Novel Organotin Supramolecular Coordination Polymers as Potent Antitumor Agents. J Inorg Organomet Polym Mater 2021. [DOI: 10.1007/s10904-021-02055-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Jain M, Yadav P, Joshi B, Joshi A, Kodgire P. Recombinant organophosphorus hydrolase (OPH) expression in E. coli for the effective detection of organophosphate pesticides. Protein Expr Purif 2021; 186:105929. [PMID: 34139322 DOI: 10.1016/j.pep.2021.105929] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 05/18/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022]
Abstract
Accumulation and exposure of organophosphate pesticides are of great concern today owing to their abundant usage and potential health hazards. Harmful effects of organophosphate pesticide exposure and limitations of the available treatment methods necessitate the development of reliable, selective, cost-effective, and sensitive methods of detection. We developed a novel biosensor based on the enzymatic action of recombinant organophosphorus hydrolase (OPH) expressed in E. coli. We report the development of colorimetric biosensors made of His-Nus-OPH as well as His-Nus-OPH loaded alginate microspheres. The colorimetric detection method developed using solution-phase and alginate-encapsulated His-Nus-OPH exhibited detection limits of 0.045 and 0.039 mM, respectively, for ethyl paraoxon, and 0.101 and 0.049 mM, respectively, for methyl parathion. Additionally, fluorescence measurement using pH-sensitive fluorescein isothiocyanate (FITC) was used to sense the quantity of organophosphorus pesticides. The fluorometric detection method using solution-phase His-Nus-OPH, with ethyl paraoxon and methyl parathion as the substrate, reveals the lower limit of detection as 0.014 mM and 0.044 mM, respectively. Our results demonstrate the viability of His-Nus-OPH for OP detection with good sensitivity, LOD, and linear range. We report the first use of N-terminal His-NusA-tagged OPH, which enhances solubility significantly and presents a significant advance for the scientific community.
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Affiliation(s)
- Monika Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Simrol, Khandwa Road, Indore, 453552, India
| | - Priyanka Yadav
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Simrol, Khandwa Road, Indore, 453552, India
| | - Bhavana Joshi
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Simrol, Khandwa Road, Indore, 453552, India
| | - Abhijeet Joshi
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Simrol, Khandwa Road, Indore, 453552, India.
| | - Prashant Kodgire
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Simrol, Khandwa Road, Indore, 453552, India.
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9
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Xu W, Zhao S, Zhang W, Wu H, Guang C, Mu W. Recent advances and future prospective of organophosphorus-degrading enzymes: identification, modification, and application. Crit Rev Biotechnol 2021; 41:1096-1113. [PMID: 33906533 DOI: 10.1080/07388551.2021.1898331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The organophosphorus-based OPs) nerve agents and pesticides have been applied in the agriculture industry for a long time. However, they were found to have a persistent effect on the environment and threaten human health. Traditional methods, including incineration and landfilling, could not thoroughly remove these organophosphorus compounds (OPs). Meanwhile, chemical hydrolysis for decontamination was also inhibited due to the presence of corrosive materials and high costs. Biological remediation for OPs employing microorganisms and organophosphorus-degrading enzymes is promising due to a mild and controllable procedure, environmental-friendly reactions, and high efficacy. A wide variety of enzymes have shown latent ability in degrading OPs hazards like organophosphorus hydrolase (OPH), organophosphorus acid anhydrolase (OPAA), the diisopropylfluorophosphatase (DFPase), and mammalian paraoxonase 1 (PON 1). To this end, increasing efforts have been made on these intriguing enzymes to increase their expression level, enhance the catalytic activity, modify the optimal substrate, and expand the practical application. In this review, the enzyme resource, crystal structure, molecular modification, and industry application were compared and discussed in detail. Moreover, the proposed ideas and positive results could be useful for the other relevant OPs-degrading enzymes.
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Affiliation(s)
- Wei Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Sumao Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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10
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Wang L, Sun Y. Engineering organophosphate hydrolase for enhanced biocatalytic performance: A review. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107945] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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11
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Singh A, Saini S, Mayank, Kaur N, Singh A, Singh N, Jang DO. Paraoxonase Mimic by a Nanoreactor Aggregate Containing Benzimidazolium Calix and l-Histidine: Demonstration of the Acetylcholine Esterase Activity. Chemistry 2021; 27:5737-5744. [PMID: 33350530 DOI: 10.1002/chem.202004944] [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: 11/13/2020] [Indexed: 11/09/2022]
Abstract
An anion-mediated preorganization approach was used to design and synthesize the benzimidazolium-based calix compound R1⋅2 ClO4 - . X-ray crystallography analysis revealed that the hydrogen-bonding interactions between the benzimidazolium cations and N,N-dimethylformamide (DMF) helped R1⋅2 ClO4 - encapsulate DMF molecule(s). A nanoreactor, with R1⋅2 ClO4 - and l-histidine (l-His) as the components, was fabricated by using a neutralization method. The nanoreactor could detoxify paraoxon in 30 min. l-His played a vital role in this process. Paraoxonase is a well-known enzyme used for pesticide degradation. The Ellman's reagent was used to determine the percentage inhibition of the acetylcholinesterase (AChE) activity in the presence of the nanoreactor. The results indicated that the nanoreactor inhibited AChE inhibition.
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Affiliation(s)
- Amanpreet Singh
- Department of Chemistry, Indian Institute of Technology Ropar, Roopnagar, Punjab, 140001, India
| | - Sanjeev Saini
- Department of Chemistry, Indian Institute of Technology Ropar, Roopnagar, Punjab, 140001, India
| | - Mayank
- Department of Chemistry, Indian Institute of Technology Ropar, Roopnagar, Punjab, 140001, India
| | - Navneet Kaur
- Department of Chemistry, Panjab University, Chandigarh, 160014, India
| | - Ajnesh Singh
- Department of Applied Sciences & Humanities, Jawaharlal Nehru Govt. Eng. College, Sundernagar, 175018, India
| | - Narinder Singh
- Department of Chemistry, Indian Institute of Technology Ropar, Roopnagar, Punjab, 140001, India
| | - Doo Ok Jang
- Department of Chemistry, Yonsei University, Wonju, 26493, Republic of Korea
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12
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Saleh DI, Mahmoud SF, Etaiw SEH. Nanoscale supramolecular architectures assembly of copper cyanide, organotin, and 1,10‐phenanthroline coordination polymers: Design and biological applications. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dalia I. Saleh
- Department of Chemistry, College of Science Taif University Taif Saudi Arabia
| | - Samy F. Mahmoud
- Department of Biotechnology, College of Science Taif University Taif Saudi Arabia
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13
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Yang J, Xiao Y, Liu Y, Li R, Long L. Structure-based redesign of the bacterial prolidase active-site pocket for efficient enhancement of methyl-parathion hydrolysis. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00490e] [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
Mutagenesis at four residues surrounding the active-site pocket of an old bacterial prolidase scaffold led to a 10 000-fold increase in methyl-parathion hydrolysis and broadening substrate specificity against organophosphorus compounds.
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Affiliation(s)
- Jian Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
- Guangzhou 510301
| | - Yunzhu Xiao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
- Guangzhou 510301
| | - Yu Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
- Guangzhou 510301
| | - Ru Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
- Guangzhou 510301
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
- Guangzhou 510301
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14
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Abstract
Cold-active enzymes increase their catalytic efficiency at low-temperature, introducing structural flexibility at or near the active sites. Inevitably, this feat seems to be accompanied by lower thermal stability. These characteristics have made cold-active enzymes into attractive targets for the industrial applications, since they could reduce the energy cost in the reaction, attenuate side-reactions, and simply be inactivated. In addition, the increased structural flexibility could result in broad substrate specificity for various non-native substrates, which is called substrate promiscuity. In this perspective, we deal with a less addressed aspect of cold-active enzymes, substrate promiscuity, which has enormous potential for semi-synthesis or enzymatic modification of fine chemicals and drugs. Further structural and directed-evolutional studies on substrate promiscuity of cold-active enzymes will provide a new workhorse in white biotechnology.
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15
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Organophosphorus Nerve Agents: Types, Toxicity, and Treatments. J Toxicol 2020; 2020:3007984. [PMID: 33029136 PMCID: PMC7527902 DOI: 10.1155/2020/3007984] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/30/2020] [Accepted: 09/10/2020] [Indexed: 01/08/2023] Open
Abstract
Organophosphorus compounds are extensively used worldwide as pesticides which cause great hazards to human health. Nerve agents, a subcategory of the organophosphorus compounds, have been produced and used during wars, and they have also been used in terrorist activities. These compounds possess physiological threats by interacting and inhibiting acetylcholinesterase enzyme which leads to the cholinergic crisis. After a general introduction, this review elucidates the mechanisms underlying cholinergic and noncholinergic effects of organophosphorus compounds. The conceivable treatment strategies for organophosphate poisoning are different types of bioscavengers which include stoichiometric, catalytic, and pseudocatalytic. The current research on the promising treatments specifically the catalytic bioscavengers including several wild-type organophosphate hydrolases such as paraoxonase and phosphotriesterase, phosphotriesterase-like lactonase, methyl parathion hydrolase, organophosphate acid anhydrolase, diisopropyl fluorophosphatase, human triphosphate nucleotidohydrolase, and senescence marker protein has been widely discussed. Organophosphorus compounds are reported to be the nonphysiological substrate for many mammalian organophosphate hydrolysing enzymes; therefore, the efficiency of these enzymes toward these compounds is inadequate. Hence, studies have been conducted to create mutants with an enhanced rate of hydrolysis and high specificity. Several mutants have been created by applying directed molecular evolution and/or targeted mutagenesis, and catalytic efficiency has been characterized. Generally, organophosphorus compounds are chiral in nature. The development of mutant enzymes for providing superior stereoselective degradation of toxic organophosphorus compounds has also been widely accounted for in this review. Existing enzymes have shown limited efficiency; hence, more effective treatment strategies have also been critically analyzed.
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16
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Ali M, Ishqi HM, Husain Q. Enzyme engineering: Reshaping the biocatalytic functions. Biotechnol Bioeng 2020; 117:1877-1894. [DOI: 10.1002/bit.27329] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/13/2020] [Accepted: 03/09/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Misha Ali
- Department of Biochemistry, Faculty of Life SciencesAligarh Muslim University Aligarh Uttar Pradesh India
| | | | - Qayyum Husain
- Department of Biochemistry, Faculty of Life SciencesAligarh Muslim University Aligarh Uttar Pradesh India
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17
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Leveson-Gower RB, Mayer C, Roelfes G. The importance of catalytic promiscuity for enzyme design and evolution. Nat Rev Chem 2019. [DOI: 10.1038/s41570-019-0143-x] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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18
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Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset. Proc Natl Acad Sci U S A 2018; 115:E7293-E7302. [PMID: 30012610 DOI: 10.1073/pnas.1607817115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The recruitment and evolutionary optimization of promiscuous enzymes is key to the rapid adaptation of organisms to changing environments. Our understanding of the precise mechanisms underlying enzyme repurposing is, however, limited: What are the active-site features that enable the molecular recognition of multiple substrates with contrasting catalytic requirements? To gain insights into the molecular determinants of adaptation in promiscuous enzymes, we performed the laboratory evolution of an arylsulfatase to improve its initially weak phenylphosphonate hydrolase activity. The evolutionary trajectory led to a 100,000-fold enhancement of phenylphosphonate hydrolysis, while the native sulfate and promiscuous phosphate mono- and diester hydrolyses were only marginally affected (≤50-fold). Structural, kinetic, and in silico characterizations of the evolutionary intermediates revealed that two key mutations, T50A and M72V, locally reshaped the active site, improving access to the catalytic machinery for the phosphonate. Measured transition state (TS) charge changes along the trajectory suggest the creation of a new Michaelis complex (E•S, enzyme-substrate), with enhanced leaving group stabilization in the TS for the promiscuous phosphonate (βleavinggroup from -1.08 to -0.42). Rather than altering the catalytic machinery, evolutionary repurposing was achieved by fine-tuning the molecular recognition of the phosphonate in the Michaelis complex, and by extension, also in the TS. This molecular scenario constitutes a mechanistic alternative to adaptation solely based on enzyme flexibility and conformational selection. Instead, rapid functional transitions between distinct chemical reactions rely on the high reactivity of permissive active-site architectures that allow multiple substrate binding modes.
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19
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Abstract
Directed evolution is a powerful technique for generating tailor-made enzymes for a wide range of biocatalytic applications. Following the principles of natural evolution, iterative cycles of mutagenesis and screening or selection are applied to modify protein properties, enhance catalytic activities, or develop completely new protein catalysts for non-natural chemical transformations. This review briefly surveys the experimental methods used to generate genetic diversity and screen or select for improved enzyme variants. Emphasis is placed on a key challenge, namely how to generate novel catalytic activities that expand the scope of natural reactions. Two particularly effective strategies, exploiting catalytic promiscuity and rational design, are illustrated by representative examples of successfully evolved enzymes. Opportunities for extending these approaches to more complex biocatalytic systems are also considered.
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Affiliation(s)
- Cathleen Zeymer
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland;,
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland;,
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20
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Petrović D, Szeler K, Kamerlin SCL. Challenges and advances in the computational modeling of biological phosphate hydrolysis. Chem Commun (Camb) 2018; 54:3077-3089. [PMID: 29412205 DOI: 10.1039/c7cc09504j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well as insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer.
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Affiliation(s)
- Dušan Petrović
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
| | - Klaudia Szeler
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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21
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Jacquet P, Hiblot J, Daudé D, Bergonzi C, Gotthard G, Armstrong N, Chabrière E, Elias M. Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase. Sci Rep 2017; 7:16745. [PMID: 29196634 PMCID: PMC5711954 DOI: 10.1038/s41598-017-16841-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
The redesign of enzyme active sites to alter their function or specificity is a difficult yet appealing challenge. Here we used a structure-based design approach to engineer the lactonase SsoPox from Sulfolobus solfataricus into a phosphotriesterase. The five best variants were characterized and their structure was solved. The most active variant, αsD6 (V27A-Y97W-L228M-W263M) demonstrates a large increase in catalytic efficiencies over the wild-type enzyme, with increases of 2,210-fold, 163-fold, 58-fold, 16-fold against methyl-parathion, malathion, ethyl-paraoxon, and methyl-paraoxon, respectively. Interestingly, the best mutants are also capable of degrading fensulfothion, which is reported to be an inhibitor for the wild-type enzyme, as well as others that are not substrates of the starting template or previously reported W263 mutants. The broad specificity of these engineered variants makes them promising candidates for the bioremediation of organophosphorus compounds. Analysis of their structures reveals that the increase in activity mainly occurs through the destabilization of the active site loop involved in substrate binding, and it has been observed that the level of disorder correlates with the width of the enzyme specificity spectrum. This finding supports the idea that active site conformational flexibility is essential to the acquisition of broader substrate specificity.
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Affiliation(s)
- Pauline Jacquet
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Julien Hiblot
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
- MPI for Medical Research, Chemical Biology department (EPFL), Heidelberg, Germany
| | - David Daudé
- Gene&GreenTK, IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Céline Bergonzi
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Guillaume Gotthard
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Nicholas Armstrong
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Eric Chabrière
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France.
| | - Mikael Elias
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA.
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22
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Hoque MA, Zhang Y, Chen L, Yang G, Khatun MA, Chen H, Hao L, Feng Y. Stepwise Loop Insertion Strategy for Active Site Remodeling to Generate Novel Enzyme Functions. ACS Chem Biol 2017; 12:1188-1193. [PMID: 28323400 DOI: 10.1021/acschembio.7b00018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The remodeling of active sites to generate novel biocatalysts is an attractive and challenging task. We developed a stepwise loop insertion strategy (StLois), in which randomized residue pairs are inserted into active site loops. The phosphotriesterase-like lactonase from Geobacillus kaustophilus (GkaP-PLL) was used to investigate StLois's potential for changing enzyme function. By inserting six residues into active site loop 7, the best variant ML7-B6 demonstrated a 16-fold further increase in catalytic efficiency toward ethyl-paraoxon compared with its initial template, that is a 609-fold higher, >107 fold substrate specificity shift relative to that of wild-type lactonase. The remodeled variants displayed 760-fold greater organophosphate hydrolysis activity toward the organophosphates parathion, diazinon, and chlorpyrifos. Structure and docking computations support the source of notably inverted enzyme specificity. Considering the fundamental importance of active site loops, the strategy has potential for the rapid generation of novel enzyme functions by loop remodeling.
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Affiliation(s)
- Md Anarul Hoque
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Zhang
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liuqing Chen
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guangyu Yang
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mst Afroza Khatun
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haifeng Chen
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liu Hao
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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23
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Iyengar ARS, Pande AH. Organophosphate-Hydrolyzing Enzymes as First-Line of Defence Against Nerve Agent-Poisoning: Perspectives and the Road Ahead. Protein J 2016; 35:424-439. [DOI: 10.1007/s10930-016-9686-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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24
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Kaltenbach M, Emond S, Hollfelder F, Tokuriki N. Functional Trade-Offs in Promiscuous Enzymes Cannot Be Explained by Intrinsic Mutational Robustness of the Native Activity. PLoS Genet 2016; 12:e1006305. [PMID: 27716796 PMCID: PMC5065130 DOI: 10.1371/journal.pgen.1006305] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/17/2016] [Indexed: 11/19/2022] Open
Abstract
The extent to which an emerging new function trades off with the original function is a key characteristic of the dynamics of enzyme evolution. Various cases of laboratory evolution have unveiled a characteristic trend; a large increase in a new, promiscuous activity is often accompanied by only a mild reduction of the native, original activity. A model that associates weak trade-offs with “evolvability” was put forward, which proposed that enzymes possess mutational robustness in the native activity and plasticity in promiscuous activities. This would enable the acquisition of a new function without compromising the original one, reducing the benefit of early gene duplication and therefore the selection pressure thereon. Yet, to date, no experimental study has examined this hypothesis directly. Here, we investigate the causes of weak trade-offs by systematically characterizing adaptive mutations that occurred in two cases of evolutionary transitions in enzyme function: (1) from phosphotriesterase to arylesterase, and (2) from atrazine chlorohydrolase to melamine deaminase. Mutational analyses in various genetic backgrounds revealed that, in contrast to the prevailing model, the native activity is less robust to mutations than the promiscuous activity. For example, in phosphotriesterase, the deleterious effect of individual mutations on the native phosphotriesterase activity is much larger than their positive effect on the promiscuous arylesterase activity. Our observations suggest a revision of the established model: weak trade-offs are not caused by an intrinsic robustness of the native activity and plasticity of the promiscuous activity. We propose that upon strong adaptive pressure for the new activity without selection against the original one, selected mutations will lead to the largest possible increases in the new function, but whether and to what extent they decrease the old function is irrelevant, creating a bias towards initially weak trade-offs and the emergence of generalist enzymes. Understanding how enzymes evolve is a fundamental question that can help us decipher not only the mechanisms of evolution on a higher level, i.e., whole organisms, but also advances our knowledge of sequence-structure-function relationships as a guide to artificial evolution in the test tube. An important yet unexplained phenomenon occurs during the evolution of a new enzymatic function; it has been observed that new and ancestral functions often trade-off only weakly, meaning the original native activity is initially maintained at a high level despite drastic improvement of the new promiscuous activity. It has previously been proposed that weak trade-offs occur because the native activity is robust to mutations while the promiscuous activity is not. However, the present work contradicts this hypothesis, based on the detailed characterization of mutational effects on both activities in two examples of enzyme evolution. We propose an alternative explanation: the weak activity trade-off is consistent with being a by-product of strong selection for the new activity rather than an intrinsic property of the native activity.
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Affiliation(s)
- Miriam Kaltenbach
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Stephane Emond
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- * E-mail:
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25
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Yang G, Hong N, Baier F, Jackson CJ, Tokuriki N. Conformational Tinkering Drives Evolution of a Promiscuous Activity through Indirect Mutational Effects. Biochemistry 2016; 55:4583-93. [PMID: 27444875 DOI: 10.1021/acs.biochem.6b00561] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
How remote mutations can lead to changes in enzyme function at a molecular level is a central question in evolutionary biochemistry and biophysics. Here, we combine laboratory evolution with biochemical, structural, genetic, and computational analysis to dissect the molecular basis for the functional optimization of phosphotriesterase activity in a bacterial lactonase (AiiA) from the metallo-β-lactamase (MBL) superfamily. We show that a 1000-fold increase in phosphotriesterase activity is caused by a more favorable catalytic binding position of the paraoxon substrate in the evolved enzyme that resulted from conformational tinkering of the active site through peripheral mutations. A nonmutated active site residue, Phe68, was displaced by ∼3 Å through the indirect effects of two second-shell trajectory mutations, allowing molecular interactions between the residue and paraoxon. Comparative mutational scanning, i.e., examining the effects of alanine mutagenesis on different genetic backgrounds, revealed significant changes in the functional roles of Phe68 and other nonmutated active site residues caused by the indirect effects of trajectory mutations. Our work provides a quantitative measurement of the impact of second-shell mutations on the catalytic contributions of nonmutated residues and unveils the underlying intramolecular network of strong epistatic mutational relationships between active site residues and more remote residues. Defining these long-range conformational and functional epistatic relationships has allowed us to better understand the subtle, but cumulatively significant, role of second- and third-shell mutations in evolution.
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Affiliation(s)
- Gloria Yang
- Michael Smith Laboratories, University of British Columbia , Vancouver, BC V6T 1Z4, Canada
| | - Nansook Hong
- Research School of Chemistry, Australian National University , Canberra, ACT 0200, Australia
| | - Florian Baier
- Michael Smith Laboratories, University of British Columbia , Vancouver, BC V6T 1Z4, Canada
| | - Colin J Jackson
- Research School of Chemistry, Australian National University , Canberra, ACT 0200, Australia
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia , Vancouver, BC V6T 1Z4, Canada
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26
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Luo XJ, Zhao J, Li CX, Bai YP, Reetz MT, Yu HL, Xu JH. Combinatorial evolution of phosphotriesterase toward a robust malathion degrader by hierarchical iteration mutagenesis. Biotechnol Bioeng 2016; 113:2350-7. [DOI: 10.1002/bit.26012] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 05/12/2016] [Accepted: 05/15/2016] [Indexed: 01/24/2023]
Affiliation(s)
- Xiao-Jing Luo
- State Key Laboratory of Bioreactor Engineering; Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 China
| | - Jian Zhao
- State Key Laboratory of Bioreactor Engineering; Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 China
| | - Chun-Xiu Li
- State Key Laboratory of Bioreactor Engineering; Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 China
| | - Yun-Peng Bai
- State Key Laboratory of Bioreactor Engineering; Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung; Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Marburg Germany
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering; Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering; Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 China
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27
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Molina-Espeja P, Viña-Gonzalez J, Gomez-Fernandez BJ, Martin-Diaz J, Garcia-Ruiz E, Alcalde M. Beyond the outer limits of nature by directed evolution. Biotechnol Adv 2016; 34:754-767. [PMID: 27064127 DOI: 10.1016/j.biotechadv.2016.03.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/22/2016] [Accepted: 03/27/2016] [Indexed: 01/19/2023]
Abstract
For more than thirty years, biotechnology has borne witness to the power of directed evolution in designing molecules of industrial relevance. While scientists all over the world discuss the future of molecular evolution, dozens of laboratory-designed products are being released with improved characteristics in terms of turnover rates, substrate scope, catalytic promiscuity or stability. In this review we aim to present the most recent advances in this fascinating research field that are allowing us to surpass the limits of nature and apply newly gained attributes to a range of applications, from gene therapy to novel green processes. The use of directed evolution in non-natural environments, the generation of catalytic promiscuity for non-natural reactions, the insertion of unnatural amino acids into proteins or the creation of unnatural DNA, is described comprehensively, together with the potential applications in bioremediation, biomedicine and in the generation of new bionanomaterials. These successful case studies show us that the limits of directed evolution will be defined by our own imagination, and in some cases, stretching beyond that.
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Affiliation(s)
- Patricia Molina-Espeja
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Javier Viña-Gonzalez
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | | | - Javier Martin-Diaz
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61801, USA
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain.
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28
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Guan S, Zhao L, Jin H, Shan N, Han W, Wang S, Shan Y. Binding modes of phosphotriesterase-like lactonase complexed with δ-nonanoic lactone and paraoxon using molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:273-286. [DOI: 10.1080/07391102.2016.1142899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Shanshan Guan
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Li Zhao
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Hanyong Jin
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Ning Shan
- Editorial Department of Journal of Jilin University (Science Edition), Changchun, China
| | - Weiwei Han
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Song Wang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Yaming Shan
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
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29
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30
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Miton CM, Tokuriki N. How mutational epistasis impairs predictability in protein evolution and design. Protein Sci 2016; 25:1260-72. [PMID: 26757214 DOI: 10.1002/pro.2876] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/06/2016] [Accepted: 01/06/2016] [Indexed: 01/05/2023]
Abstract
There has been much debate about the extent to which mutational epistasis, that is, the dependence of the outcome of a mutation on the genetic background, constrains evolutionary trajectories. The degree of unpredictability introduced by epistasis, due to the non-additivity of functional effects, strongly hinders the strategies developed in protein design and engineering. While many studies have addressed this issue through systematic characterization of evolutionary trajectories within individual enzymes, the field lacks a consensus view on this matter. In this work, we performed a comprehensive analysis of epistasis by analyzing the mutational effects from nine adaptive trajectories toward new enzymatic functions. We quantified epistasis by comparing the effect of mutations occurring between two genetic backgrounds: the starting enzyme (for example, wild type) and the intermediate variant on which the mutation occurred during the trajectory. We found that most trajectories exhibit positive epistasis, in which the mutational effect is more beneficial when it occurs later in the evolutionary trajectory. Approximately half (49%) of functional mutations were neutral or negative on the wild-type background, but became beneficial at a later stage in the trajectory, indicating that these functional mutations were not predictable from the initial starting point. While some cases of strong epistasis were associated with direct interaction between residues, many others were caused by long-range indirect interactions between mutations. Our work highlights the prevalence of epistasis in enzyme adaptive evolution, in particular positive epistasis, and suggests the necessity of incorporating mutational epistasis in protein engineering and design to create highly efficient catalysts.
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Affiliation(s)
- Charlotte M Miton
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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31
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Sugrue E, Hartley CJ, Scott C, Jackson CJ. The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes. Aust J Chem 2016. [DOI: 10.1071/ch16426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An increasing number of bacterial metalloenzymes have been shown to catalyse the breakdown of xenobiotics in the environment, while others exhibit a variety of promiscuous xenobiotic-degrading activities. Several different evolutionary processes have allowed these enzymes to gain or enhance xenobiotic-degrading activity. In this review, we have surveyed the range of xenobiotic-degrading metalloenzymes, and discuss the molecular and catalytic basis for the development of new activities. We also highlight how our increased understanding of the natural evolution of xenobiotic-degrading metalloenzymes can be been applied to laboratory enzyme design.
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32
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Abstract
AbstractI describe how we direct the evolution of non-natural enzyme activities, using chemical intuition and information on structure and mechanism to guide us to the most promising reaction/enzyme systems. With synthetic reagents to generate new reactive intermediates and just a few amino acid substitutions to tune the active site, a cytochrome P450 can catalyze a variety of carbene and nitrene transfer reactions. The cyclopropanation, N–H insertion, C–H amination, sulfimidation, and aziridination reactions now demonstrated are all well known in chemical catalysis but have no counterparts in nature. The new enzymes are fully genetically encoded, assemble and function inside of cells, and can be optimized for different substrates, activities, and selectivities. We are learning how to use nature's innovation mechanisms to marry some of the synthetic chemists’ favorite transformations with the exquisite selectivity and tunability of enzymes.
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33
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Zhan D, Guan S, Jin H, Han W, Wang S. Stereoselectivity of phosphotriesterase with paraoxon derivatives: a computational study. J Biomol Struct Dyn 2015; 34:600-11. [PMID: 25929154 DOI: 10.1080/07391102.2015.1046937] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The bacterial enzyme phosphotriesterase (PTE) exhibits stereoselectivity toward hydrolysis of chiral substrates with a preference for the Sp enantiomer. In this work, docking analysis and two explicit-solvent molecular dynamics (MD) simulations were performed to characterize and differentiate the structural dynamics of PTE bound to the Sp and Rp paraoxon derivative enantiomers (Rp-1 and Sp-1) hydrolyzed with distinct catalytic efficiencies. Comparative analysis of the molecular trajectories for PTE bound to Rp-1 and Sp-1 suggested that substrate binding induced conformational changes in the loops near the active site. After 100 ns of MD simulation, the Zn β(2+) metal ion formed hexacoordinated- and tetracoordinated geometries in the Sp-1-PTE and Rp-1-PTE ensembles, respectively. Simulation results further showed that the hydrogen bond between Asp301 and His254 occurred with a higher probability after Sp-1 binding to PTE (47.5%) than that after Rp-1 binding (22.2%). These results provide a qualitative and molecular-level explanation for the 10 orders of magnitude increase in the catalytic efficiency of PTE toward the Sp enantiomer of paraoxon.
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Affiliation(s)
- Dongling Zhan
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science , Jilin University , Changchun 130023 , China.,b College of Food Science and Engineering , Jilin Agricultural University , Changchun 130118 , China
| | - Shanshan Guan
- c State Key Laboratory of Theoretical and Computational Chemistry , Institute of Theoretical Chemistry, Jilin University , Changchun 130023 , China
| | - Hanyong Jin
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science , Jilin University , Changchun 130023 , China
| | - Weiwei Han
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science , Jilin University , Changchun 130023 , China
| | - Song Wang
- c State Key Laboratory of Theoretical and Computational Chemistry , Institute of Theoretical Chemistry, Jilin University , Changchun 130023 , China
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Xiang DF, Patskovsky Y, Nemmara VV, Toro R, Almo SC, Raushel FM. Function discovery and structural characterization of a methylphosphonate esterase. Biochemistry 2015; 54:2919-30. [PMID: 25873441 PMCID: PMC4477287 DOI: 10.1021/acs.biochem.5b00199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pmi1525, an enzyme of unknown function from Proteus mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG ). The structure was also determined with manganese and butyrate in the active site (PDB id: 4QSF ). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. The substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization, and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat/Km values of 580 s(-1) and 1.2 × 10(5) M(-1) s(-1), respectively) and 4-nitrophenyl butyrate (kcat and kcat/Km values of 140 s(-1) and 1.4 × 10(5) M(-1) s(-1), respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents.
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Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Yury Patskovsky
- Department of Biochemistry, Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Venkatesh V. Nemmara
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Rafael Toro
- Department of Biochemistry, Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Steven C. Almo
- Department of Biochemistry, Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461,To whom correspondence may be sent: (FMR) Telephone: 979-845-3373; , (SCA) Telephone: 718-430-2746;
| | - Frank M. Raushel
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012,To whom correspondence may be sent: (FMR) Telephone: 979-845-3373; , (SCA) Telephone: 718-430-2746;
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Renata H, Wang ZJ, Arnold FH. Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution. Angew Chem Int Ed Engl 2015; 54:3351-67. [PMID: 25649694 PMCID: PMC4404643 DOI: 10.1002/anie.201409470] [Citation(s) in RCA: 375] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Indexed: 11/10/2022]
Abstract
High selectivity and exquisite control over the outcome of reactions entice chemists to use biocatalysts in organic synthesis. However, many useful reactions are not accessible because they are not in nature's known repertoire. In this Review, we outline an evolutionary approach to engineering enzymes to catalyze reactions not found in nature. We begin with examples of how nature has discovered new catalytic functions and how such evolutionary progression has been recapitulated in the laboratory starting from extant enzymes. We then examine non-native enzyme activities that have been exploited for chemical synthesis, with an emphasis on reactions that do not have natural counterparts. Non-natural activities can be improved by directed evolution, thus mimicking the process used by nature to create new catalysts. Finally, we describe the discovery of non-native catalytic functions that may provide future opportunities for the expansion of the enzyme universe.
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Affiliation(s)
- Hans Renata
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA 91125 (USA)
| | - Z. Jane Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA 91125 (USA)
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd. MC 210-41, Pasadena, CA 91125 (USA)
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Zhang Y, An J, Yang GY, Bai A, Zheng B, Lou Z, Wu G, Ye W, Chen HF, Feng Y, Manco G. Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426. PLoS One 2015; 10:e0115130. [PMID: 25706379 PMCID: PMC4338136 DOI: 10.1371/journal.pone.0115130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/19/2014] [Indexed: 02/02/2023] Open
Abstract
Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, People’s Republic of China
- Environmental Science Research and Design Institute of Zhejiang Province, Hangzhou, People’s Republic of China
| | - Jiao An
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, People’s Republic of China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Aixi Bai
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, People’s Republic of China
| | - Baisong Zheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, People’s Republic of China
| | - Zhiyong Lou
- Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Wei Ye
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, People’s Republic of China
- * E-mail: (YF); (GM)
| | - Giuseppe Manco
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
- * E-mail: (YF); (GM)
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Park JT, Gómez Ramos LM, Bommarius AS. Engineering towards Nitroreductase Functionality in Ene-Reductase Scaffolds. Chembiochem 2015; 16:811-8. [DOI: 10.1002/cbic.201402667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Indexed: 11/10/2022]
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Renata H, Wang ZJ, Arnold FH. Ausdehnung des Enzym-Universums: Zugang zu nicht-natürlichen Reaktionen durch mechanismusgeleitete, gerichtete Evolution. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409470] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Iyer R, Iken B. Protein engineering of representative hydrolytic enzymes for remediation of organophosphates. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.11.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Etaiw SEDH, Abdou SN, Faheim AA. Self-assembly and antitumor activity of an organotin coordination polymer containing a helical structure based on copper cyanide and phenanthroline ligand. J COORD CHEM 2015. [DOI: 10.1080/00958972.2014.996559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Safaa N. Abdou
- Faculty of Education and Science (Khourma), Chemistry Department, Taif University, Taif, Saudi Arabia
| | - Abeer A. Faheim
- Faculty of Education and Science (Khourma), Chemistry Department, Taif University, Taif, Saudi Arabia
- Faculty of Science (Girl’s), Chemistry Department, Al-Azhar University, Cairo, Egypt
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Arora B, Mukherjee J, Gupta MN. Enzyme promiscuity: using the dark side of enzyme specificity in white biotechnology. ACTA ACUST UNITED AC 2014. [DOI: 10.1186/s40508-014-0025-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abstract
Enzyme promiscuity can be classified into substrate promiscuity, condition promiscuity and catalytic promiscuity. Enzyme promiscuity results in far larger ranges of organic compounds which can be obtained by biocatalysis. While early examples mostly involved use of lipases, more recent literature shows that catalytic promiscuity occurs more widely and many other classes of enzymes can be used to obtain diverse kinds of molecules. This is of immense relevance in the context of white biotechnology as enzyme catalysed reactions use greener conditions.
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Luo XJ, Kong XD, Zhao J, Chen Q, Zhou J, Xu JH. Switching a newly discovered lactonase into an efficient and thermostable phosphotriesterase by simple double mutations His250Ile/Ile263Trp. Biotechnol Bioeng 2014; 111:1920-30. [PMID: 24771278 DOI: 10.1002/bit.25272] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/17/2014] [Accepted: 04/21/2014] [Indexed: 12/12/2022]
Abstract
OPHC2 is a thermostable organophosphate (OP) hydrolase in the β-lactamase superfamily. OPs are highly toxic synthetic chemicals with no natural analogs. How did OPHC2 acquire phosphotriesterase (PTE) activity remained unclear. In this study, an OPHC2 analogue, PoOPH was discovered from Pseudomonas oleovorans exhibiting high lactonase and esterase activities and latent PTE activity. Sequence analysis revealed conserved His250 and Ile263 and site-directed mutagenesis at these crucial residues enhanced PTE activity. The best variant PoOPHM2 carrying H250I/I263W mutations displayed 6,962- and 106-fold improvements in catalytic efficiency for methyl-parathion and ethyl-paraoxon degradation, whereas the original lactonase and esterase activities decreased dramatically. A 1.4 × 10(7) -fold of specificity inversion was achieved by only two residue substitutions. Significantly, thermostability of the variants was not compromised. Crystal structure of PoOPHM2 was determined at 2.25 Å resolution and docking studies suggested that the two residues in the binding pocket determine substrate recognition. Lastly, new organophosphorus hydrolases (OPHs) were discovered using simple double mutations. Among them, PpOPHM2 from Pseudomonas putida emerged as a new promising OPH with very high activity (41.0 U mg(-1) ) toward methyl-parathion. Our results offer a first scrutiny to PTE activity evolution of OPHs in β-lactamase superfamily and provide efficient and robust enzymes for OP detoxification.
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Affiliation(s)
- Xiao-Jing Luo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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Bzdrenga J, Hiblot J, Gotthard G, Champion C, Elias M, Chabriere E. SacPox from the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius is a proficient lactonase. BMC Res Notes 2014; 7:333. [PMID: 24894602 PMCID: PMC4068969 DOI: 10.1186/1756-0500-7-333] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/27/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND SacPox, an enzyme from the extremophilic crenarchaeal Sulfolobus acidocaldarius (Sac), was isolated by virtue of its phosphotriesterase (or paraoxonase; Pox) activity, i.e. its ability to hydrolyze the neurotoxic organophosphorus insecticides. Later on, SacPox was shown to belong to the Phosphotriesterase-Like Lactonase family that comprises natural lactonases, possibly involved in quorum sensing, and endowed with promiscuous, phosphotriesterase activity. RESULTS Here, we present a comprehensive and broad enzymatic characterization of the natural lactonase and promiscuous organophosphorus hydrolase activities of SacPox, as well as a structural analysis using a model. CONCLUSION Kinetic experiments show that SacPox is a proficient lactonase, including at room temperature. Moreover, we discuss the observed differences in substrate specificity between SacPox and its closest homologues SsoPox and SisLac together with the possible structural causes for these observations.
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Affiliation(s)
- Janek Bzdrenga
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Julien Hiblot
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Guillaume Gotthard
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Charlotte Champion
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Mikael Elias
- Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel
| | - Eric Chabriere
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
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Xiang DF, Kumaran D, Swaminathan S, Raushel FM. Structural characterization and function determination of a nonspecific carboxylate esterase from the amidohydrolase superfamily with a promiscuous ability to hydrolyze methylphosphonate esters. Biochemistry 2014; 53:3476-85. [PMID: 24832101 PMCID: PMC4045322 DOI: 10.1021/bi5004266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The uncharacterized protein Rsp3690 from Rhodobacter sphaeroides is a member of the amidohydrolase superfamily of enzymes. In this investigation the gene for Rsp3690 was expressed in Escherichia coli and purified to homogeneity, and the three-dimensional structure was determined to a resolution of 1.8 Å. The protein folds as a distorted (β/α)8-barrel, and the subunits associate as a homotetramer. The active site is localized to the C-terminal end of the β-barrel and is highlighted by the formation of a binuclear metal center with two manganese ions that are bridged by Glu-175 and hydroxide. The remaining ligands to the metal center include His-32, His-34, His-207, His-236, and Asp-302. Rsp3690 was shown to catalyze the hydrolysis of a wide variety of carboxylate esters, in addition to organophosphate and organophosphonate esters. The best carboxylate ester substrates identified for Rsp3690 included 2-naphthyl acetate (kcat/Km = 1.0 × 10(5) M(-1) s(-1)), 2-naphthyl propionate (kcat/Km = 1.5 × 10(5) M(-1) s(-1)), 1-naphthyl acetate (kcat/Km = 7.5 × 10(3) M(-1) s(-1)), 4-methylumbelliferyl acetate (kcat/Km = 2.7 × 10(3) M(-1) s(-1)), 4-nitrophenyl acetate (kcat/Km = 2.3 × 10(5) M(-1) s(-1)), and 4-nitrophenyl butyrate (kcat/Km = 8.8 × 10(5) M(-1) s(-1)). The best organophosphonate ester substrates included ethyl 4-nitrophenyl methylphosphonate (kcat/Km = 3.8 × 10(5) M(-1) s(-1)) and isobutyl 4-nitrophenyl methylphosphonate (kcat/Km = 1.1 × 10(4) M(-1) s(-1)). The (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate was hydrolyzed 10 times faster than the less toxic (RP)-enantiomer. The high inherent catalytic activity of Rsp3690 for the hydrolysis of the toxic enantiomer of methylphosphonate esters make this enzyme an attractive target for directed evolution investigations.
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Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, Texas A&M University , P.O. Box 30012, College Station, Texas 77842-3012, United States
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Baier F, Tokuriki N. Connectivity between catalytic landscapes of the metallo-β-lactamase superfamily. J Mol Biol 2014; 426:2442-56. [PMID: 24769192 DOI: 10.1016/j.jmb.2014.04.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
Abstract
The expansion of functions in an enzyme superfamily is thought to occur through recruitment of latent promiscuous functions within existing enzymes. Thus, the promiscuous activities of enzymes represent connections between different catalytic landscapes and provide an additional layer of evolutionary connectivity between functional families alongside their sequence and structural relationships. Functional connectivity has been observed between individual functional families; however, little is known about how catalytic landscapes are connected throughout a highly diverged superfamily. Here, we describe a superfamily-wide analysis of evolutionary and functional connectivity in the metallo-β-lactamase (MBL) superfamily. We investigated evolutionary connections between functional families and related evolutionary to functional connectivity; 24 enzymes from 15 distinct functional families were challenged against 10 catalytically distinct reactions. We revealed that enzymes of this superfamily are generally promiscuous, as each enzyme catalyzes on average 1.5 reactions in addition to its native one. Catalytic landscapes in the MBL superfamily overlap substantially; each reaction is connected on average to 3.7 other reactions whereas some connections appear to be unrelated to recent evolutionary events and occur between chemically distinct reactions. These findings support the idea that the highly distinct reactions in the MBL superfamily could have evolved from a common ancestor traversing a continuous network via promiscuous enzymes. Several functional connections (e.g., the lactonase/phosphotriesterase and phosphonatase/phosphodiesterase/arylsulfatase reactions) are also observed in structurally and evolutionary distinct superfamilies, suggesting that these catalytic landscapes are substantially connected. Our results show that new enzymatic functions could evolve rapidly from the current diversity of enzymes and range of promiscuous activities.
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Affiliation(s)
- Florian Baier
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.
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Kaltenbach M, Tokuriki N. Dynamics and constraints of enzyme evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:468-87. [DOI: 10.1002/jez.b.22562] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Miriam Kaltenbach
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
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