1
|
Morita Y, Kubo H, Matsumoto R, Fujieda N. A thiopyridine-bound mirror-image copper center in an artificial non-heme metalloenzyme. J Inorg Biochem 2024; 260:112694. [PMID: 39167879 DOI: 10.1016/j.jinorgbio.2024.112694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/31/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024]
Abstract
Artificial metalloenzymes, in which a metal complex and protein matrix are combined, have been synthesized to catalyze stereoselective reactions using the chiral environment provided by the protein cavity. Artificial metalloenzymes can be engineered by the chemical modification and mutagenesis of the protein matrix. We developed artificial non-heme metalloenzymes using a cupin superfamily protein (TM1459) with a 4-His tetrad-metal-binding motif. The Cu-bound H52A/C106D mutant with 3-His triad showed a S-enantioselective Michael addition of nitromethane to α,β-unsaturated ketone, 2-aza-chalcone 1. In this study, we demonstrated a chemical modification near the copper-binding site of this mutant to reverse its enantioselectivity. For chemical modification, the amino acid on the Si-face of the binding state of 1 to the copper center was replaced with Cys, followed by reaction with 4,4'-dithiopyridine (4-PDS) to form S-(pyridin-4-ylthio)cysteine (Cys-4py). Cu-bound I49C-4py/H52A/C106D showed reversal of the enantioselectivity from S-form to R-form (ee = 71%, (R)). The effect of steric hindrance of the amino acids at position 49 on enantioselectivity was investigated using I49X/H52A/C106D mutants (X = A, C, I, F, and W). Additionally, chemical modification with 2,2'-dithiopyridine (2-PDS) produced I49-2py/H52A/C106D, which showed lower R-enantioselectivity than I49-4py/H52A/C106D. Among the mutants, the 4py-modification on the Si-face was the most effective in reversing the enantioselectivity. By tuning the Re-face side, the H54A mutation introduced into the I49C-4py/H52A/C106D increased the R-enantioselectivity (ee = 88%, (R)). X-ray crystallography revealed a coordinated structure with ligation of thiopyridine in Cu-bound I49C-4py/H52A/H54A/C106D.
Collapse
Affiliation(s)
- Yoshitsugu Morita
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan.
| | - Hiroki Kubo
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan
| | - Ryusei Matsumoto
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan
| | - Nobutaka Fujieda
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan.
| |
Collapse
|
2
|
Albayati SH, Nezhad NG, Taki AG, Rahman RNZRA. Efficient and easible biocatalysts: Strategies for enzyme improvement. A review. Int J Biol Macromol 2024; 276:133978. [PMID: 39038570 DOI: 10.1016/j.ijbiomac.2024.133978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]
Abstract
Owing to the environmental friendliness and vast advantages that enzymes offer in the biotechnology and industry fields, biocatalysts are a prolific investigation field. However, the low catalytic activity, stability, and specific selectivity of the enzyme limit the range of the reaction enzymes involved in. A comprehensive understanding of the protein structure and dynamics in terms of molecular details enables us to tackle these limitations effectively and enhance the catalytic activity by enzyme engineering or modifying the supports and solvents. Along with different strategies including computational, enzyme engineering based on DNA recombination, enzyme immobilization, additives, chemical modification, and physicochemical modification approaches can be promising for the wide spread of industrial enzyme usage. This is attributed to the successful application of biocatalysts in industrial and synthetic processes requires a system that exhibits stability, activity, and reusability in a continuous flow process, thereby reducing the production cost. The main goal of this review is to display relevant approaches for improving enzyme characteristics to overcome their industrial application.
Collapse
Affiliation(s)
- Samah Hashim Albayati
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Anmar Ghanim Taki
- Department of Radiology Techniques, Health and Medical Techniques College, Alnoor University, Mosul, Iraq
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Institute Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| |
Collapse
|
3
|
Listov D, Goverde CA, Correia BE, Fleishman SJ. Opportunities and challenges in design and optimization of protein function. Nat Rev Mol Cell Biol 2024; 25:639-653. [PMID: 38565617 PMCID: PMC7616297 DOI: 10.1038/s41580-024-00718-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calculations, as well as machine learning tools, have dramatically improved protein engineering and design. In this Review, we discuss how these methods have enabled the design of increasingly complex structures and therapeutically relevant activities. Additionally, protein optimization methods have improved the stability and activity of complex eukaryotic proteins. Thanks to their increased reliability, computational design methods have been applied to improve therapeutics and enzymes for green chemistry and have generated vaccine antigens, antivirals and drug-delivery nano-vehicles. Moreover, the high success of design methods reflects an increased understanding of basic rules that govern the relationships among protein sequence, structure and function. However, de novo design is still limited mostly to α-helix bundles, restricting its potential to generate sophisticated enzymes and diverse protein and small-molecule binders. Designing complex protein structures is a challenging but necessary next step if we are to realize our objective of generating new-to-nature activities.
Collapse
Affiliation(s)
- Dina Listov
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Casper A Goverde
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Sarel Jacob Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
4
|
Klemencic E, Brewster RC, Ali HS, Richardson JM, Jarvis AG. Using BpyAla to generate copper artificial metalloenzymes: a catalytic and structural study. Catal Sci Technol 2024; 14:1622-1632. [PMID: 38505507 PMCID: PMC10946309 DOI: 10.1039/d3cy01648j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/25/2024] [Indexed: 03/21/2024]
Abstract
Artificial metalloenzymes (ArMs) have emerged as a promising avenue in the field of biocatalysis, offering new reactivity. However, their design remains challenging due to the limited understanding of their protein dynamics and how the introduced cofactors alter the protein scaffold structure. Here we present the structures and catalytic activity of novel copper ArMs capable of (R)- or (S)-stereoselective control, utilizing a steroid carrier protein (SCP) scaffold. To incorporate 2,2'-bipyridine (Bpy) into SCP, two distinct strategies were employed: either Bpy was introduced as an unnatural amino acid (2,2'-bipyridin-5-yl)alanine (BpyAla) using amber stop codon expression or via bioconjugation of bromomethyl-Bpy to cysteine residues. The resulting ArMs proved to be effective at catalysing an enantioselective Friedel-Crafts reaction with SCP_Q111BpyAla achieving the best selectivity with an enantioselectivity of 72% ee (S). Interestingly, despite using the same protein scaffold, different attachment strategies for Bpy at the same residue (Q111) led to a switch in the enantiopreference of the ArM. X-ray crystal structures of SCP_Q111CBpy and SCP_Q111BpyAla ArMs with bound Cu(ii) ions unveiled crucial differences in the orientation of the catalytic centre. Combining structural information, alanine scanning studies, and computational analysis shed light on the distinct active sites of the ArMs, clarifying that these active sites stabilise the nucleophilic substrate on different sides of the electrophile leading to the observed switch in enantioselectivity. This work underscores the importance of integrating structural studies with catalytic screening to unravel the intricacies of ArM behaviour and facilitate their development for targeted applications in biocatalysis.
Collapse
Affiliation(s)
- E Klemencic
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road The King's Buildings Edinburgh EH9 3FJ UK
| | - R C Brewster
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road The King's Buildings Edinburgh EH9 3FJ UK
| | - H S Ali
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road The King's Buildings Edinburgh EH9 3FJ UK
| | - J M Richardson
- School of Biological Sciences, University of Edinburgh Swann Building Edinburgh EH9 3BF UK
| | - A G Jarvis
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road The King's Buildings Edinburgh EH9 3FJ UK
| |
Collapse
|
5
|
Sun J, He X, LE Y, Al-Tohamy R, Ali SS. Potential applications of extremophilic bacteria in the bioremediation of extreme environments contaminated with heavy metals. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 352:120081. [PMID: 38237330 DOI: 10.1016/j.jenvman.2024.120081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/31/2023] [Accepted: 01/07/2024] [Indexed: 02/04/2024]
Abstract
Protecting the environment from harmful pollutants has become increasingly difficult in recent decades. The presence of heavy metal (HM) pollution poses a serious environmental hazard that requires intricate attention on a worldwide scale. Even at low concentrations, HMs have the potential to induce deleterious health effects in both humans and other living organisms. Therefore, various strategies have been proposed to address this issue, with extremophiles being a promising solution. Bacteria that exhibit resistance to metals are preferred for applications involving metal removal due to their capacity for rapid multiplication and growth. Extremophiles are a special group of microorganisms that are capable of surviving under extreme conditions such as extreme temperatures, pH levels, and high salt concentrations where other organisms cannot. Due to their unique enzymes and adaptive capabilities, extremophiles are well suited as catalysts for environmental biotechnology applications, including the bioremediation of HMs through various strategies. The mechanisms of resistance to HMs by extremophilic bacteria encompass: (i) metal exclusion by permeability barrier; (ii) extracellular metal sequestration by protein/chelator binding; (iii) intracellular sequestration of the metal by protein/chelator binding; (iv) enzymatic detoxification of a metal to a less toxic form; (v) active transport of HMs; (vi) passive tolerance; (vii) reduced metal sensitivity of cellular targets to metal ions; and (viii) morphological change of cells. This review provides comprehensive information on extremophilic bacteria and their potential roles for bioremediation, particularly in environments contaminated with HMs, which pose a threat due to their stability and persistence. Genetic engineering of extremophilic bacteria in stressed environments could help in the bioremediation of contaminated sites. Due to their unique characteristics, these organisms and their enzymes are expected to bridge the gap between biological and chemical industrial processes. However, the structure and biochemical properties of extremophilic bacteria, along with any possible long-term effects of their applications, need to be investigated further.
Collapse
Affiliation(s)
- Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Xing He
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yilin LE
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Rania Al-Tohamy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Sameh S Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| |
Collapse
|
6
|
Xu SY, Zhou L, Xu Y, Hong HY, Dai C, Wang YJ, Zheng YG. Recent advances in structure-based enzyme engineering for functional reconstruction. Biotechnol Bioeng 2023; 120:3427-3445. [PMID: 37638646 DOI: 10.1002/bit.28540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/27/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023]
Abstract
Structural information can help engineer enzymes. Usually, specific amino acids in particular regions are targeted for functional reconstruction to enhance the catalytic performance, including activity, stereoselectivity, and thermostability. Appropriate selection of target sites is the key to structure-based design, which requires elucidation of the structure-function relationships. Here, we summarize the mutations of residues in different specific regions, including active center, access tunnels, and flexible loops, on fine-tuning the catalytic performance of enzymes, and discuss the effects of altering the local structural environment on the functions. In addition, we keep up with the recent progress of structure-based approaches for enzyme engineering, aiming to provide some guidance on how to take advantage of the structural information.
Collapse
Affiliation(s)
- Shen-Yuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Lei Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Han-Yue Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Chen Dai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| |
Collapse
|
7
|
Luo J, Song C, Cui W, Han L, Zhou Z. Counteraction of stability-activity trade-off of Nattokinase through flexible region shifting. Food Chem 2023; 423:136241. [PMID: 37178594 DOI: 10.1016/j.foodchem.2023.136241] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 04/16/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
The widespread trade-off between stability and activity severely limits enzyme evolution. Although some progresses have been made to overcome this limitation, the counteraction mechanism for enzyme stability-activity trade-off remains obscure. Here, we clarified the counteraction mechanism of the Nattokinase stability-activity trade-off. A combinatorial mutant M4 was obtained by multi-strategy engineering, exhibiting a 20.7-fold improved half-life; meanwhile, the catalytic efficiency was doubled. Molecular dynamics simulation revealed that an obvious flexible region shifting in the structure of mutant M4 was occurred. The flexible region shifting which contributed to maintain the global structural flexibility, was considered to be the key factor for counteracting the stability-activity trade-off. Further analysis illustrated that the flexible region shifting was driven by region dynamical networks reshaping. This work provided deep insight into the counteraction mechanism of enzyme stability-activity trade-off, suggesting that flexible region shifting would be an effective strategy for enzyme evolution through computational protein engineering.
Collapse
Affiliation(s)
- Jie Luo
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Chenshuo Song
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.
| |
Collapse
|
8
|
Cai Y, Zhou J, Huang J, Zhou W, Wan Y, Cohen Stuart MA, Wang J. Rational design of polymeric nanozymes with robust catalytic performance via copper-ligand coordination. J Colloid Interface Sci 2023; 645:458-465. [PMID: 37156154 DOI: 10.1016/j.jcis.2023.04.142] [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: 02/27/2023] [Revised: 04/18/2023] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
Incorporating copper (Cu) ions into polymeric particles can be a straightforward strategy for mimicking copper enzymes, but it is challenging to simultaneously control the structure of the nanozyme and of the active sites. In this report, we present a novel bis-ligand (L2) containing bipyridine groups connected by a tetra-ethylene oxide (4EO) spacer. In phosphate buffer the Cu-L2 mixture forms coordination complexes that (at proper composition) can bind polyacrylic acid (PAA) to produce catalytically active polymeric nanoparticles with well-defined structure and size, which we refer to as 'nanozymes'. Manipulating the L2/Cu mixing ratio and using phosphate as a co-binding motif, cooperative copper centres are realized that exhibit promoted oxidation activity. The structure and activity of the so-designed nanozymes remain stable upon increasing temperature and over multiple cycles of application. Increasing ionic strength causes enhanced activity, a response also seen for natural tyrosinase. By means of our rational design we obtain nanozymes with optimized structure and active sites that in several respects outperform natural enzymes. This approach therefore demonstrates a novel strategy for developing functional nanozymes, which may well stimulate the application of this class of catalysts.
Collapse
Affiliation(s)
- Ying Cai
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130, Meilong Road, 200237 Shanghai, People's Republic of China
| | - Jin Zhou
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130, Meilong Road, 200237 Shanghai, People's Republic of China
| | - Jianan Huang
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130, Meilong Road, 200237 Shanghai, People's Republic of China
| | - Wenjuan Zhou
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130, Meilong Road, 200237 Shanghai, People's Republic of China
| | - Yuting Wan
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130, Meilong Road, 200237 Shanghai, People's Republic of China
| | - Martien A Cohen Stuart
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130, Meilong Road, 200237 Shanghai, People's Republic of China
| | - Junyou Wang
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130, Meilong Road, 200237 Shanghai, People's Republic of China.
| |
Collapse
|
9
|
Zhang Z, Long M, Zheng N, Lü X, Zhu C, Osire T, Xia X. Inside Out Computational Redesign of Cavities for Improving Thermostability and Catalytic Activity of Rhizomucor Miehei Lipase. Appl Environ Microbiol 2023; 89:e0217222. [PMID: 36912632 PMCID: PMC10057959 DOI: 10.1128/aem.02172-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
Cavities are created by hydrophobic interactions between residue side chain atoms during the folding of enzymes. Redesigning cavities can improve the thermostability and catalytic activity of the enzyme; however, the synergistic effect of cavities remains unclear. In this study, Rhizomucor miehei lipase (RML) was used as a model to explore volume fluctuation and spatial distribution changes of the internal cavities, which could reveal the roles of internal cavities in the thermostability and catalytic activity. We present an inside out cavity engineering (CE) strategy based on computational techniques to explore how changes in the volumes and spatial distribution of cavities affect the thermostability and catalytic activity of the enzyme. We obtained 12 single-point mutants, among which the melting temperatures (Tm) of 8 mutants showed an increase of more than 2°C. Sixteen multipoint mutations were further designed by spatial distribution rearrangement of internal cavities. The Tm of the most stable triple variant, with mutations including T21V (a change of T to V at position 21), S27A, and T198L (T21V/S27A/T198L), was elevated by 11.0°C, together with a 28.7-fold increase in the half-life at 65°C and a specific activity increase of 9.9-fold (up to 5,828 U mg-1), one of the highest lipase activities reported. The possible mechanism of decreased volumes and spatial rearrangement of the internal cavities improved the stability of the enzyme, optimizing the outer substrate tunnel to improve the catalytic efficiency. Overall, the inside out computational redesign of cavities method could help to deeply understand the effect of cavities on enzymatic stability and activity, which would be beneficial for protein engineering efforts to optimize natural enzymes. IMPORTANCE In the present study, R. miehei lipase, which is widely used in various industries, provides an opportunity to explore the effects of internal cavities on the thermostability and catalytic activity of enzymes. Here, we execute high hydrostatic pressure molecular dynamics (HP-MD) simulations to screen the critical internal cavity and reshape the internal cavities through site-directed mutation. We show that as the global internal cavity volume decreases, cavity rearrangement can improve the stability of the protein while optimizing the substrate channel to improve the catalytic efficiency. Our results provide significant insights into understanding the mechanism of action of the internal cavity. Our strategy is expected to be applied to other enzymes to promote increases in thermostability and catalytic activity.
Collapse
Affiliation(s)
- Zehua Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Mengfei Long
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Nan Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiang Lü
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Cailin Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Tolbert Osire
- Faculty of Biology, Shenzhen MSU-BIT University, Guangdong, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| |
Collapse
|
10
|
Hanreich S, Bonandi E, Drienovská I. Design of Artificial Enzymes: Insights into Protein Scaffolds. Chembiochem 2023; 24:e202200566. [PMID: 36418221 DOI: 10.1002/cbic.202200566] [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: 09/27/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
The design of artificial enzymes has emerged as a promising tool for the generation of potent biocatalysts able to promote new-to-nature reactions with improved catalytic performances, providing a powerful platform for wide-ranging applications and a better understanding of protein functions and structures. The selection of an appropriate protein scaffold plays a key role in the design process. This review aims to give a general overview of the most common protein scaffolds that can be exploited for the generation of artificial enzymes. Several examples are discussed and categorized according to the strategy used for the design of the artificial biocatalyst, namely the functionalization of natural enzymes, the creation of a new catalytic site in a protein scaffold bearing a wide hydrophobic pocket and de novo protein design. The review is concluded by a comparison of these different methods and by our perspective on the topic.
Collapse
Affiliation(s)
- Stefanie Hanreich
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Elisa Bonandi
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Ivana Drienovská
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| |
Collapse
|
11
|
Hu J, Chen X, Zhang L, Zhou J, Xu G, Ni Y. Engineering the Thermostability of a d-Carbamoylase Based on Ancestral Sequence Reconstruction for the Efficient Synthesis of d-Tryptophan. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:660-670. [PMID: 36541894 DOI: 10.1021/acs.jafc.2c07781] [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: 06/17/2023]
Abstract
Employing ancestral sequence reconstruction and consensus sequence analysis, the thermostability of a novel d-carbamoylase derived from Nitratireductor indicus (NiHyuC) was engineered through greedy-oriented iterative combinatorial mutagenesis. A mutant S202P/E208D/R277L (M4Th3) was obtained with significantly elevated thermostability. M4Th3 has a half-life of 36.5 h at 40 °C, about 28.5 times of 1.3 h of its parent M4. For the reaction at 40 °C, M4Th3 can catalyze 10 mM N-carbamoyl-d-tryptophan to produce d-tryptophan with a conversion ratio of 96.4% after 12 h, which is significantly higher than 64.1% of M4. MD simulation reveals that new hydrogen bonds emerging from E208D on the surface can increase the hydrophobicity of the protein, leading to improved stability. More importantly, R277L could contribute to enhanced interface stability of homodimeric M4. This study provides a thermostable d-carbamoylase for the "hydantoinase process", which has potential in the industrial synthesis of optically pure natural and non-natural amino acids.
Collapse
Affiliation(s)
- Jiamin Hu
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, Jiangsu, China
| | - Xiaoyu Chen
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, Jiangsu, China
| | - Lu Zhang
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, Jiangsu, China
| | - Jieyu Zhou
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, Jiangsu, China
| | - Guochao Xu
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, Jiangsu, China
| | - Ye Ni
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi214122, Jiangsu, China
| |
Collapse
|
12
|
Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
Collapse
Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| |
Collapse
|
13
|
Hueting DA, Vanga SR, Syrén PO. Thermoadaptation in an Ancestral Diterpene Cyclase by Altered Loop Stability. J Phys Chem B 2022; 126:3809-3821. [PMID: 35583961 PMCID: PMC9169049 DOI: 10.1021/acs.jpcb.1c10605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Thermostability is
the key to maintain the structural integrity
and catalytic activity of enzymes in industrial biotechnological processes,
such as terpene cyclase-mediated generation of medicines, chiral synthons,
and fine chemicals. However, affording a large increase in the thermostability
of enzymes through site-directed protein engineering techniques can
constitute a challenge. In this paper, we used ancestral sequence
reconstruction to create a hyperstable variant of the ent-copalyl diphosphate synthase PtmT2, a terpene cyclase involved in
the assembly of antibiotics. Molecular dynamics simulations on the
μs timescale were performed to shed light on possible molecular
mechanisms contributing to activity at an elevated temperature and
the large 40 °C increase in melting temperature observed for
an ancestral variant of PtmT2. In silico analysis
revealed key differences in the flexibility of a loop capping the
active site, between extant and ancestral proteins. For the modern
enzyme, the loop collapses into the active site at elevated temperatures,
thus preventing biocatalysis, whereas the loop remains in a productive
conformation both at ambient and high temperatures in the ancestral
variant. Restoring a Pro loop residue introduced in the ancestral
variant to the corresponding Gly observed in the extant protein led
to reduced catalytic activity at high temperatures, with only moderate
effects on the melting temperature, supporting the importance of the
flexibility of the capping loop in thermoadaptation. Conversely, the
inverse Gly to Pro loop mutation in the modern enzyme resulted in
a 3-fold increase in the catalytic rate. Despite an overall decrease
in maximal activity of ancestor compared to wild type, its increased
thermostability provides a robust backbone amenable for further enzyme
engineering. Our work cements the importance of loops in enzyme catalysis
and provides a molecular mechanism contributing to thermoadaptation
in an ancestral enzyme.
Collapse
Affiliation(s)
- David A Hueting
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Sudarsana R Vanga
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
| |
Collapse
|
14
|
Lemay-St-Denis C, Doucet N, Pelletier JN. Integrating dynamics into enzyme engineering. Protein Eng Des Sel 2022; 35:6842866. [PMID: 36416215 DOI: 10.1093/protein/gzac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/02/2022] [Accepted: 11/06/2022] [Indexed: 11/24/2022] Open
Abstract
Enzyme engineering has become a widely adopted practice in research labs and industry. In parallel, the past decades have seen tremendous strides in characterizing the dynamics of proteins, using a growing array of methodologies. Importantly, links have been established between the dynamics of proteins and their function. Characterizing the dynamics of an enzyme prior to, and following, its engineering is beginning to inform on the potential of 'dynamic engineering', i.e. the rational modification of protein dynamics to alter enzyme function. Here we examine the state of knowledge at the intersection of enzyme engineering and protein dynamics, describe current challenges and highlight pioneering work in the nascent area of dynamic engineering.
Collapse
Affiliation(s)
- Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Nicolas Doucet
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, QC, Canada
| | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
- Chemistry Department, Université de Montréal, Montreal, QC, Canada
| |
Collapse
|
15
|
Hot spots-making directed evolution easier. Biotechnol Adv 2022; 56:107926. [DOI: 10.1016/j.biotechadv.2022.107926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 01/20/2023]
|
16
|
Stein A, Chen D, Igareta NV, Cotelle Y, Rebelein JG, Ward TR. A Dual Anchoring Strategy for the Directed Evolution of Improved Artificial Transfer Hydrogenases Based on Carbonic Anhydrase. ACS CENTRAL SCIENCE 2021; 7:1874-1884. [PMID: 34849402 PMCID: PMC8620556 DOI: 10.1021/acscentsci.1c00825] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Artificial metalloenzymes result from anchoring a metal cofactor within a host protein. Such hybrid catalysts combine the selectivity and specificity of enzymes with the versatility of (abiotic) transition metals to catalyze new-to-nature reactions in an evolvable scaffold. With the aim of improving the localization of an arylsulfonamide-bearing iridium-pianostool catalyst within human carbonic anhydrase II (hCAII) for the enantioselective reduction of prochiral imines, we introduced a covalent linkage between the host and the guest. Herein, we show that a judiciously positioned cysteine residue reacts with a p-nitropicolinamide ligand bound to iridium to afford an additional sulfonamide covalent linkage. Three rounds of directed evolution, performed on the dually anchored cofactor, led to improved activity and selectivity for the enantioselective reduction of harmaline (up to 97% ee (R) and >350 turnovers on a preparative scale). To evaluate the substrate scope, the best hits of each generation were tested with eight substrates. X-ray analysis, carried out at various stages of the evolutionary trajectory, was used to scrutinize (i) the nature of the covalent linkage between the cofactor and the host as well as (ii) the remodeling of the substrate-binding pocket.
Collapse
Affiliation(s)
- Alina Stein
- Department
of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
- National
Center of Competence in Research “Molecular Systems Engineering”, 4058 Basel, Switzerland
| | - Dongping Chen
- Department
of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
- National
Center of Competence in Research “Molecular Systems Engineering”, 4058 Basel, Switzerland
| | - Nico V. Igareta
- Department
of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
- National
Center of Competence in Research “Molecular Systems Engineering”, 4058 Basel, Switzerland
| | - Yoann Cotelle
- Aix-Marseille
Université, CNRS, Centrale Marseille, iSm2, 13284 Marseille, France
| | - Johannes G. Rebelein
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
| | - Thomas R. Ward
- Department
of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland
- National
Center of Competence in Research “Molecular Systems Engineering”, 4058 Basel, Switzerland
| |
Collapse
|
17
|
Chakrabortty S, Almasalma AA, de Vries JG. Recent developments in asymmetric hydroformylation. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00737h] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review describes the recent developments in the field of asymmetric hydroformylation. A large variety of ligands is now available, some of which are extremely effective in inducing high enantio- and regioselectivity.
Collapse
|