1
|
Zhou L, Tao C, Shen X, Sun X, Wang J, Yuan Q. Unlocking the potential of enzyme engineering via rational computational design strategies. Biotechnol Adv 2024; 73:108376. [PMID: 38740355 DOI: 10.1016/j.biotechadv.2024.108376] [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: 12/27/2023] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Enzymes play a pivotal role in various industries by enabling efficient, eco-friendly, and sustainable chemical processes. However, the low turnover rates and poor substrate selectivity of enzymes limit their large-scale applications. Rational computational enzyme design, facilitated by computational algorithms, offers a more targeted and less labor-intensive approach. There has been notable advancement in employing rational computational protein engineering strategies to overcome these issues, it has not been comprehensively reviewed so far. This article reviews recent developments in rational computational enzyme design, categorizing them into three types: structure-based, sequence-based, and data-driven machine learning computational design. Case studies are presented to demonstrate successful enhancements in catalytic activity, stability, and substrate selectivity. Lastly, the article provides a thorough analysis of these approaches, highlights existing challenges and potential solutions, and offers insights into future development directions.
Collapse
Affiliation(s)
- Lei Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chunmeng Tao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
2
|
Schreiber S, Gercke D, Lenz F, Jose J. Application of an alchemical free energy method for the prediction of thermostable DuraPETase variants. Appl Microbiol Biotechnol 2024; 108:305. [PMID: 38643427 PMCID: PMC11033240 DOI: 10.1007/s00253-024-13144-z] [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: 01/16/2024] [Revised: 03/25/2024] [Accepted: 04/09/2024] [Indexed: 04/22/2024]
Abstract
Non-equilibrium (NEQ) alchemical free energy calculations are an emerging tool for accurately predicting changes in protein folding free energy resulting from amino acid mutations. In this study, this method in combination with the Rosetta ddg monomer tool was applied to predict more thermostable variants of the polyethylene terephthalate (PET) degrading enzyme DuraPETase. The Rosetta ddg monomer tool efficiently enriched promising mutations prior to more accurate prediction by NEQ alchemical free energy calculations. The relative change in folding free energy of 96 single amino acid mutations was calculated by NEQ alchemical free energy calculation. Experimental validation of ten of the highest scoring variants identified two mutations (DuraPETaseS61M and DuraPETaseS223Y) that increased the melting temperature (Tm) of the enzyme by up to 1 °C. The calculated relative change in folding free energy showed an excellent correlation with experimentally determined Tm resulting in a Pearson's correlation coefficient of r = - 0.84. Limitations in the prediction of strongly stabilizing mutations were, however, encountered and are discussed. Despite these challenges, this study demonstrates the practical applicability of NEQ alchemical free energy calculations in prospective enzyme engineering projects. KEY POINTS: • Rosetta ddg monomer enriches stabilizing mutations in a library of DuraPETase variants • NEQ free energy calculations accurately predict changes in Tm of DuraPETase • The DuraPETase variants S223Y, S42M, and S61M have increased Tm.
Collapse
Affiliation(s)
- Sebastian Schreiber
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, PharmaCampus, Corrensstr. 48, 48149, Münster, Germany
| | - David Gercke
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, PharmaCampus, Corrensstr. 48, 48149, Münster, Germany
| | - Florian Lenz
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, PharmaCampus, Corrensstr. 48, 48149, Münster, Germany
| | - Joachim Jose
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, PharmaCampus, Corrensstr. 48, 48149, Münster, Germany.
| |
Collapse
|
3
|
Tripp A, Braun M, Wieser F, Oberdorfer G, Lechner H. Click, Compute, Create: A Review of Web-based Tools for Enzyme Engineering. Chembiochem 2024:e202400092. [PMID: 38634409 DOI: 10.1002/cbic.202400092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
Enzyme engineering, though pivotal across various biotechnological domains, is often plagued by its time-consuming and labor-intensive nature. This review aims to offer an overview of supportive in silico methodologies for this demanding endeavor. Starting from methods to predict protein structures, to classification of their activity and even the discovery of new enzymes we continue with describing tools used to increase thermostability and production yields of selected targets. Subsequently, we discuss computational methods to modulate both, the activity as well as selectivity of enzymes. Last, we present recent approaches based on cutting-edge machine learning methods to redesign enzymes. With exception of the last chapter, there is a strong focus on methods easily accessible via web-interfaces or simple Python-scripts, therefore readily useable for a diverse and broad community.
Collapse
Affiliation(s)
- Adrian Tripp
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Markus Braun
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Florian Wieser
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Gustav Oberdorfer
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
- BioTechMed, Graz, Austria
| | - Horst Lechner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
- BioTechMed, Graz, Austria
| |
Collapse
|
4
|
Wang X, Li A, Li X, Cui H. Empowering Protein Engineering through Recombination of Beneficial Substitutions. Chemistry 2024; 30:e202303889. [PMID: 38288640 DOI: 10.1002/chem.202303889] [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: 01/04/2024] [Indexed: 02/24/2024]
Abstract
Directed evolution stands as a seminal technology for generating novel protein functionalities, a cornerstone in biocatalysis, metabolic engineering, and synthetic biology. Today, with the development of various mutagenesis methods and advanced analytical machines, the challenge of diversity generation and high-throughput screening platforms is largely solved, and one of the remaining challenges is: how to empower the potential of single beneficial substitutions with recombination to achieve the epistatic effect. This review overviews experimental and computer-assisted recombination methods in protein engineering campaigns. In addition, integrated and machine learning-guided strategies were highlighted to discuss how these recombination approaches contribute to generating the screening library with better diversity, coverage, and size. A decision tree was finally summarized to guide the further selection of proper recombination strategies in practice, which was beneficial for accelerating protein engineering.
Collapse
Affiliation(s)
- Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Haiyang Cui
- School of Life Sciences, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| |
Collapse
|
5
|
Li L, Liu X, Bai Y, Yao B, Luo H, Tu T. High-Throughput Screening Techniques for the Selection of Thermostable Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3833-3845. [PMID: 38285533 DOI: 10.1021/acs.jafc.3c07554] [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: 01/31/2024]
Abstract
The acquisition of a thermostable enzyme is an indispensable prerequisite for its successful implementation in industrial applications and the development of novel functionalities. Various protein engineering approaches, including rational design, semirational design, and directed evolution, have been employed to enhance thermostability. However, all of these approaches require sensitive and reliable high-throughput screening (HTS) technologies to efficiently and rapidly identify variants with improved properties. While numerous reviews focus on modification strategies for enhancing enzyme thermostability, there is a dearth of literature reviewing HTS methods specifically aimed at this objective. Herein, we present a comprehensive overview of various HTS methods utilized for modifying enzyme thermostability across different screening platforms. Additionally, we highlight significant recent examples that demonstrate the successful application of these methods. Furthermore, we address the technical challenges associated with HTS technologies used for screening thermostable enzyme variants and discuss valuable perspectives to promote further advancements in this field. This review serves as an authoritative reference source offering theoretical support for selecting appropriate screening strategies tailored to specific enzymes with the aim of improving their thermostability.
Collapse
Affiliation(s)
- Lanxue Li
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| |
Collapse
|
6
|
Radley E, Davidson J, Foster J, Obexer R, Bell EL, Green AP. Engineering Enzymes for Environmental Sustainability. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202309305. [PMID: 38516574 PMCID: PMC10952289 DOI: 10.1002/ange.202309305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 03/23/2024]
Abstract
The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.
Collapse
Affiliation(s)
- Emily Radley
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - John Davidson
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Jake Foster
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Richard Obexer
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center National Renewable Energy Laboratory Golden CO USA
- BOTTLE Consortium Golden CO USA
| | - Anthony P Green
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| |
Collapse
|
7
|
Radley E, Davidson J, Foster J, Obexer R, Bell EL, Green AP. Engineering Enzymes for Environmental Sustainability. Angew Chem Int Ed Engl 2023; 62:e202309305. [PMID: 37651344 PMCID: PMC10952156 DOI: 10.1002/anie.202309305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023]
Abstract
The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2 ) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.
Collapse
Affiliation(s)
- Emily Radley
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - John Davidson
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Jake Foster
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Richard Obexer
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Elizabeth L. Bell
- Renewable Resources and Enabling Sciences CenterNational Renewable Energy LaboratoryGoldenCOUSA
- BOTTLE ConsortiumGoldenCOUSA
| | - Anthony P. Green
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| |
Collapse
|
8
|
Musil M, Jezik A, Horackova J, Borko S, Kabourek P, Damborsky J, Bednar D. FireProt 2.0: web-based platform for the fully automated design of thermostable proteins. Brief Bioinform 2023; 25:bbad425. [PMID: 38018911 PMCID: PMC10685400 DOI: 10.1093/bib/bbad425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023] Open
Abstract
Thermostable proteins find their use in numerous biomedical and biotechnological applications. However, the computational design of stable proteins often results in single-point mutations with a limited effect on protein stability. However, the construction of stable multiple-point mutants can prove difficult due to the possibility of antagonistic effects between individual mutations. FireProt protocol enables the automated computational design of highly stable multiple-point mutants. FireProt 2.0 builds on top of the previously published FireProt web, retaining the original functionality and expanding it with several new stabilization strategies. FireProt 2.0 integrates the AlphaFold database and the homology modeling for structure prediction, enabling calculations starting from a sequence. Multiple-point designs are constructed using the Bron-Kerbosch algorithm minimizing the antagonistic effect between the individual mutations. Users can newly limit the FireProt calculation to a set of user-defined mutations, run a saturation mutagenesis of the whole protein or select rigidifying mutations based on B-factors. Evolution-based back-to-consensus strategy is complemented by ancestral sequence reconstruction. FireProt 2.0 is significantly faster and a reworked graphical user interface broadens the tool's availability even to users with older hardware. FireProt 2.0 is freely available at http://loschmidt.chemi.muni.cz/fireprotweb.
Collapse
Affiliation(s)
- Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - Andrej Jezik
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - Jana Horackova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
| | - Simeon Borko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - Petr Kabourek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| |
Collapse
|
9
|
Milčić N, Švaco P, Sudar M, Tang L, Findrik Blažević Z, Majerić Elenkov M. Impact of organic solvents on the catalytic performance of halohydrin dehalogenase. Appl Microbiol Biotechnol 2023; 107:2351-2361. [PMID: 36881116 DOI: 10.1007/s00253-023-12450-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 03/08/2023]
Abstract
Biocatalytic transformations in organic synthesis often require the use of organic solvents to improve substrate solubility and promote the product formation. Halohydrin dehalogenases (HHDHs) are enzymes that catalyze the formation and conversion of epoxides, important synthetic class of compounds that are often sparingly soluble in water and prone to hydrolysis. In this study, the activity, stability, and enantioselectivity of HHDH from Agrobacterium radiobacter AD1 (HheC) in form of cell-free extract were evaluated in various aqueous-organic media. A correlation was discovered between the enzyme activity in the ring-closure reaction and logP of the solvent. Knowledge of such a relationship makes biocatalysis with organic solvents more predictable, which may reduce the need to experiment with a variety of solvents in the future. The results revealed a high enzyme compatibility with hydrophobic solvents (e.g., n-heptane) in terms of activity and stability. Regarding the HHDH applicability in an organic medium, inhibitions by a number of solvents (e.g., THF, toluene, chloroform) proved to be a more challenging problem than the protein stability, especially in the ring-opening reaction, thus suggesting which solvents should be avoided. In addition, solvent tolerance of the thermostable variant ISM-4 was also evaluated, revealing increased stability and to a lesser extent enantioselectivity compared to the wild-type. This is the first time such a systematic analysis has been reported, giving insight into the behavior of HHDHs in nonconventional media and opening new opportunities for the future biocatalytic applications. KEY POINTS: • HheC performs better in the presence of hydrophobic than hydrophilic solvents. • Enzyme activity in the PNSHH ring-closure reaction is a function of the logP. • Thermostability of ISM-4 variant is accompanied by superior solvent tolerance.
Collapse
Affiliation(s)
- Nevena Milčić
- Faculty of Chemical Engineering and Technology, University of Zagreb, Savska c, 16, Zagreb, Croatia
| | - Petra Švaco
- Ruđer Bošković Institute, Bijenička c, 54, Zagreb, Croatia
| | - Martina Sudar
- Faculty of Chemical Engineering and Technology, University of Zagreb, Savska c, 16, Zagreb, Croatia
| | - Lixia Tang
- University of Electronic Science and Technology, No. 4, Section 2, North Jianshe Road, Chengdu, China
| | | | | |
Collapse
|
10
|
Raczyńska A, Kapica P, Papaj K, Stańczak A, Shyntum D, Spychalska P, Byczek-Wyrostek A, Góra A. Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity. PLoS One 2023; 18:e0280776. [PMID: 36827335 PMCID: PMC9956002 DOI: 10.1371/journal.pone.0280776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 01/09/2023] [Indexed: 02/25/2023] Open
Abstract
The haloalkane dehalogenase LinB is a well-known enzyme that contains buried active site and is used for many modelling studies. Using classical molecular dynamics simulations of enzymes and substrates, we searched for transient binding sites on the surface of the LinB protein by calculating maps of enzyme-ligand interactions that were then transformed into sparse matrices. All residues considered as functionally important for enzyme performance (e.g., tunnel entrances) were excluded from the analysis to concentrate rather on non-obvious surface residues. From a set of 130 surface residues, twenty-six were proposed as a promising improvement of enzyme performance. Eventually, based on rational selection and filtering out the potentially unstable mutants, a small library of ten mutants was proposed to validate the possibility of fine-tuning the LinB protein. Nearly half of the predicted mutant structures showed improved activity towards the selected substrates, which demonstrates that the proposed approach could be applied to identify non-obvious yet beneficial mutations for enzyme performance especially when obvious locations have already been explored.
Collapse
Affiliation(s)
- Agata Raczyńska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Patryk Kapica
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Katarzyna Papaj
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Agnieszka Stańczak
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Divine Shyntum
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Patrycja Spychalska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | | | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
- * E-mail:
| |
Collapse
|
11
|
Improving Both the Thermostability and Catalytic Efficiency of Phospholipase D from Moritella sp. JT01 through Disulfide Bond Engineering Strategy. Int J Mol Sci 2022; 23:ijms231911319. [PMID: 36232620 PMCID: PMC9570233 DOI: 10.3390/ijms231911319] [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] [Received: 08/13/2022] [Revised: 09/11/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Mining of Phospholipase D (PLD) with high activity and stability has attracted strong interest for investigation. A novel PLD from marine Moritella sp. JT01 (MsPLD) was biochemically and structurally characterized in our previous study; however, the short half-life time (t1/2) under its optimum reaction temperature seriously hampered its further applications. Herein, the disulfide bond engineering strategy was applied to improve its thermostability. Compared with wild-type MsPLD, mutant S148C-T206C/D225C-A328C with the addition of two disulfide bonds exhibited a 3.1-fold t1/2 at 35 °C and a 5.7 °C increase in melting temperature (Tm). Unexpectedly, its specific activity and catalytic efficiency (kcat/Km) also increased by 22.7% and 36.5%, respectively. The enhanced activity might be attributed to an increase in the activation entropy by displacing more water molecules by the transition state. The results of molecular dynamics simulations (MD) revealed that the introduction of double disulfide bonds rigidified the global structure of the mutant, which might cause the enhanced thermostability. Finally, the synthesis capacity of the mutant to synthesize phosphatidic acid (PA) was evaluated. The conversion rate of PA reached about 80% after 6 h reaction with wild-type MsPLD but reached 78% after 2 h with mutant S148C-T206C/D225C-A328C, which significantly reduced the time needed for the reaction to reach equilibrium. The present results pave the way for further application of MsPLD in the food and pharmaceutical industries.
Collapse
|
12
|
Li L, Wu W, Deng Z, Zhang S, Guan W. Improved thermostability of lipase Lip2 from Yarrowia lipolytica through disulfide bond design for preparation of medium-long-medium structured lipids. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
13
|
Tatta ER, Imchen M, Moopantakath J, Kumavath R. Bioprospecting of microbial enzymes: current trends in industry and healthcare. Appl Microbiol Biotechnol 2022; 106:1813-1835. [PMID: 35254498 DOI: 10.1007/s00253-022-11859-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/15/2022] [Accepted: 02/26/2022] [Indexed: 12/13/2022]
Abstract
Microbial enzymes have an indispensable role in producing foods, pharmaceuticals, and other commercial goods. Many novel enzymes have been reported from all domains of life, such as plants, microbes, and animals. Nonetheless, industrially desirable enzymes of microbial origin are limited. This review article discusses the classifications, applications, sources, and challenges of most demanded industrial enzymes such as pectinases, cellulase, lipase, and protease. In addition, the production of novel enzymes through protein engineering technologies such as directed evolution, rational, and de novo design, for the improvement of existing industrial enzymes is also explored. We have also explored the role of metagenomics, nanotechnology, OMICs, and machine learning approaches in the bioprospecting of novel enzymes. Overall, this review covers the basics of biocatalysts in industrial and healthcare applications and provides an overview of existing microbial enzyme optimization tools. KEY POINTS: • Microbial bioactive molecules are vital for therapeutic and industrial applications. • High-throughput OMIC is the most proficient approach for novel enzyme discovery. • Comprehensive databases and efficient machine learning models are the need of the hour to fast forward de novo enzyme design and discovery.
Collapse
Affiliation(s)
- Eswar Rao Tatta
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India.
| |
Collapse
|
14
|
Computational enzyme redesign: large jumps in function. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
15
|
Roda S, Robles-Martín A, Xiang R, Kazemi M, Guallar V. Structural-Based Modeling in Protein Engineering. A Must Do. J Phys Chem B 2021; 125:6491-6500. [PMID: 34106727 DOI: 10.1021/acs.jpcb.1c02545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biotechnological solutions will be a key aspect in our immediate future society, where optimized enzymatic processes through enzyme engineering might be an important solution for waste transformation, clean energy production, biodegradable materials, and green chemistry, for example. Here we advocate the importance of structural-based bioinformatics and molecular modeling tools in such developments. We summarize our recent experiences indicating a great prediction/success ratio, and we suggest that an early in silico phase should be performed in enzyme engineering studies. Moreover, we demonstrate the potential of a new technique combining Rosetta and PELE, which could provide a faster and more automated procedure, an essential aspect for a broader use.
Collapse
Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | | | - Ruite Xiang
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Masoud Kazemi
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| |
Collapse
|
16
|
Wullich SC, Wijma HJ, Janssen DB, Fetzner S. Stabilizing AqdC, a Pseudomonas Quinolone Signal-Cleaving Dioxygenase from Mycobacteria, by FRESCO-Based Protein Engineering. Chembiochem 2021; 22:733-742. [PMID: 33058333 PMCID: PMC7894191 DOI: 10.1002/cbic.202000641] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/13/2020] [Indexed: 12/11/2022]
Abstract
The mycobacterial PQS dioxygenase AqdC, a cofactor-less protein with an α/β-hydrolase fold, inactivates the virulence-associated quorum-sensing signal molecule 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS) produced by the opportunistic pathogen Pseudomonas aeruginosa and is therefore a potential anti-virulence tool. We have used computational library design to predict stabilizing amino acid replacements in AqdC. While 57 out of 91 tested single substitutions throughout the protein led to stabilization, as judged by increases in T app m of >2 °C, they all impaired catalytic activity. Combining substitutions, the proteins AqdC-G40K-A134L-G220D-Y238W and AqdC-G40K-G220D-Y238W showed extended half-lives and the best trade-off between stability and activity, with increases in T app m of 11.8 and 6.1 °C and relative activities of 22 and 72 %, respectively, compared to AqdC. Molecular dynamics simulations and principal component analysis suggested that stabilized proteins are less flexible than AqdC, and the loss of catalytic activity likely correlates with an inability to effectively open the entrance to the active site.
Collapse
Affiliation(s)
- Sandra C. Wullich
- Institut für Molekulare Mikrobiologie und BiotechnologieWWU MünsterCorrensstraße 348149 MünsterGermany
| | - Hein J. Wijma
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningen (TheNetherlands
| | - Dick B. Janssen
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningen (TheNetherlands
| | - Susanne Fetzner
- Institut für Molekulare Mikrobiologie und BiotechnologieWWU MünsterCorrensstraße 348149 MünsterGermany
| |
Collapse
|
17
|
Enhancement of hydrogen peroxide tolerance of lipase LipA from Bacillus subtilis using semi-rational design. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
18
|
Broom A, Trainor K, Jacobi Z, Meiering EM. Computational Modeling of Protein Stability: Quantitative Analysis Reveals Solutions to Pervasive Problems. Structure 2020; 28:717-726.e3. [DOI: 10.1016/j.str.2020.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/26/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022]
|
19
|
Aalbers FS, Fürst MJ, Rovida S, Trajkovic M, Gómez Castellanos JR, Bartsch S, Vogel A, Mattevi A, Fraaije MW. Approaching boiling point stability of an alcohol dehydrogenase through computationally-guided enzyme engineering. eLife 2020; 9:e54639. [PMID: 32228861 PMCID: PMC7164962 DOI: 10.7554/elife.54639] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
Enzyme instability is an important limitation for the investigation and application of enzymes. Therefore, methods to rapidly and effectively improve enzyme stability are highly appealing. In this study we applied a computational method (FRESCO) to guide the engineering of an alcohol dehydrogenase. Of the 177 selected mutations, 25 mutations brought about a significant increase in apparent melting temperature (ΔTm ≥ +3 °C). By combining mutations, a 10-fold mutant was generated with a Tm of 94 °C (+51 °C relative to wild type), almost reaching water's boiling point, and the highest increase with FRESCO to date. The 10-fold mutant's structure was elucidated, which enabled the identification of an activity-impairing mutation. After reverting this mutation, the enzyme showed no loss in activity compared to wild type, while displaying a Tm of 88 °C (+45 °C relative to wild type). This work demonstrates the value of enzyme stabilization through computational library design.
Collapse
Affiliation(s)
- Friso S Aalbers
- Molecular Enzymology Group, University of Groningen, Groningen, Netherlands
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Maximilian Jlj Fürst
- Molecular Enzymology Group, University of Groningen, Groningen, Netherlands
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Stefano Rovida
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Milos Trajkovic
- Molecular Enzymology Group, University of Groningen, Groningen, Netherlands
| | | | | | | | - Andrea Mattevi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, Netherlands
| |
Collapse
|
20
|
Meng Q, Capra N, Palacio CM, Lanfranchi E, Otzen M, van Schie LZ, Rozeboom HJ, Thunnissen AMWH, Wijma HJ, Janssen DB. Robust ω-Transaminases by Computational Stabilization of the Subunit Interface. ACS Catal 2020; 10:2915-2928. [PMID: 32953233 PMCID: PMC7493286 DOI: 10.1021/acscatal.9b05223] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/31/2020] [Indexed: 12/25/2022]
Abstract
Transaminases are attractive catalysts for the production of enantiopure amines. However, the poor stability of these enzymes often limits their application in biocatalysis. Here, we used a framework for enzyme stability engineering by computational library design (FRESCO) to stabilize the homodimeric PLP fold type I ω-transaminase from Pseudomonas jessenii. A large number of surface-located point mutations and mutations predicted to stabilize the subunit interface were examined. Experimental screening revealed that 10 surface mutations out of 172 tested were indeed stabilizing (6% success), whereas testing 34 interface mutations gave 19 hits (56% success). Both the extent of stabilization and the spatial distribution of stabilizing mutations showed that the subunit interface was critical for stability. After mutations were combined, 2 very stable variants with 4 and 6 mutations were obtained, which in comparison to wild type (T m app = 62 °C) displayed T m app values of 80 and 85 °C, respectively. These two variants were also 5-fold more active at their optimum temperatures and tolerated high concentrations of isopropylamine and cosolvents. This allowed conversion of 100 mM acetophenone to (S)-1-phenylethylamine (>99% enantiomeric excess) with high yield (92%, in comparison to 24% with the wild-type transaminase). Crystal structures mostly confirmed the expected structural changes and revealed that the most stabilizing mutation, I154V, featured a rarely described stabilization mechanism: namely, removal of steric strain. The results show that computational interface redesign can be a rapid and powerful strategy for transaminase stabilization.
Collapse
Affiliation(s)
- Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nikolas Capra
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Cyntia M. Palacio
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Elisa Lanfranchi
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Luc Z. van Schie
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Henriëtte J. Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hein J. Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
21
|
Arabnejad H, Bombino E, Colpa DI, Jekel PA, Trajkovic M, Wijma HJ, Janssen DB. Computational Design of Enantiocomplementary Epoxide Hydrolases for Asymmetric Synthesis of Aliphatic and Aromatic Diols. Chembiochem 2020; 21:1893-1904. [PMID: 31961471 PMCID: PMC7383614 DOI: 10.1002/cbic.201900726] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/16/2020] [Indexed: 12/13/2022]
Abstract
The use of enzymes in preparative biocatalysis often requires tailoring enzyme selectivity by protein engineering. Herein we explore the use of computational library design and molecular dynamics simulations to create variants of limonene epoxide hydrolase that produce enantiomeric diols from meso‐epoxides. Three substrates of different sizes were targeted: cis‐2,3‐butene oxide, cyclopentene oxide, and cis‐stilbene oxide. Most of the 28 designs tested were active and showed the predicted enantioselectivity. Excellent enantioselectivities were obtained for the bulky substrate cis‐stilbene oxide, and enantiocomplementary mutants produced (S,S)‐ and (R,R)‐stilbene diol with >97 % enantiomeric excess. An (R,R)‐selective mutant was used to prepare (R,R)‐stilbene diol with high enantiopurity (98 % conversion into diol, >99 % ee). Some variants displayed higher catalytic rates (kcat) than the original enzyme, but in most cases KM values increased as well. The results demonstrate the feasibility of computational design and screening to engineer enantioselective epoxide hydrolase variants with very limited laboratory screening.
Collapse
Affiliation(s)
- Hesam Arabnejad
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Elvira Bombino
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Dana I. Colpa
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Peter A. Jekel
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Milos Trajkovic
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Hein J. Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| |
Collapse
|
22
|
Jones BJ, Kan CNE, Luo C, Kazlauskas RJ. Consensus Finder web tool to predict stabilizing substitutions in proteins. Methods Enzymol 2020; 643:129-148. [DOI: 10.1016/bs.mie.2020.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
23
|
Pongpamorn P, Watthaisong P, Pimviriyakul P, Jaruwat A, Lawan N, Chitnumsub P, Chaiyen P. Identification of a Hotspot Residue for Improving the Thermostability of a Flavin‐Dependent Monooxygenase. Chembiochem 2019; 20:3020-3031. [DOI: 10.1002/cbic.201900413] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Pornkanok Pongpamorn
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Pratchaya Watthaisong
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Panu Pimviriyakul
- Department of BiotechnologyFaculty of Engineering and Industrial TechnologySilpakorn University 6 Rajamankha Nai Road Nakornpathom 73000 Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Paholyothin Road Klong 1 Klong Luang Pathumthani 12120 Thailand
| | - Narin Lawan
- Department of ChemistryFaculty of ScienceChiang Mai University Chiang Mai 50200 Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Paholyothin Road Klong 1 Klong Luang Pathumthani 12120 Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| |
Collapse
|
24
|
Interference with Pseudomonas aeruginosa Quorum Sensing and Virulence by the Mycobacterial Pseudomonas Quinolone Signal Dioxygenase AqdC in Combination with the N-Acylhomoserine Lactone Lactonase QsdA. Infect Immun 2019; 87:IAI.00278-19. [PMID: 31308081 DOI: 10.1128/iai.00278-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/26/2019] [Indexed: 11/20/2022] Open
Abstract
The nosocomial pathogen Pseudomonas aeruginosa regulates its virulence via a complex quorum sensing network, which, besides N-acylhomoserine lactones, includes the alkylquinolone signal molecules 2-heptyl-3-hydroxy-4(1H)-quinolone (Pseudomonas quinolone signal [PQS]) and 2-heptyl-4(1H)-quinolone (HHQ). Mycobacteroides abscessus subsp. abscessus, an emerging pathogen, is capable of degrading the PQS and also HHQ. Here, we show that although M. abscessus subsp. abscessus reduced PQS levels in coculture with P. aeruginosa PAO1, this did not suffice for quenching the production of the virulence factors pyocyanin, pyoverdine, and rhamnolipids. However, the levels of these virulence factors were reduced in cocultures of P. aeruginosa PAO1 with recombinant M. abscessus subsp. massiliense overexpressing the PQS dioxygenase gene aqdC of M. abscessus subsp. abscessus, corroborating the potential of AqdC as a quorum quenching enzyme. When added extracellularly to P. aeruginosa cultures, AqdC quenched alkylquinolone and pyocyanin production but induced an increase in elastase levels. When supplementing P. aeruginosa cultures with QsdA, an enzyme from Rhodococcus erythropolis which inactivates N-acylhomoserine lactone signals, rhamnolipid and elastase levels were quenched, but HHQ and pyocyanin synthesis was promoted. Thus, single quorum quenching enzymes, targeting individual circuits within a complex quorum sensing network, may also elicit undesirable regulatory effects. Supernatants of P. aeruginosa cultures grown in the presence of AqdC, QsdA, or both enzymes were less cytotoxic to human epithelial lung cells than supernatants of untreated cultures. Furthermore, the combination of both aqdC and qsdA in P. aeruginosa resulted in a decline of Caenorhabditis elegans mortality under P. aeruginosa exposure.
Collapse
|
25
|
Mu Q, Cui Y, Tian Y, Hu M, Tao Y, Wu B. Thermostability improvement of the glucose oxidase from Aspergillus niger for efficient gluconic acid production via computational design. Int J Biol Macromol 2019; 136:1060-1068. [DOI: 10.1016/j.ijbiomac.2019.06.094] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/15/2022]
|
26
|
Fürst MJLJ, Boonstra M, Bandstra S, Fraaije MW. Stabilization of cyclohexanone monooxygenase by computational and experimental library design. Biotechnol Bioeng 2019; 116:2167-2177. [PMID: 31124128 PMCID: PMC6836875 DOI: 10.1002/bit.27022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/14/2019] [Accepted: 05/18/2019] [Indexed: 12/23/2022]
Abstract
Enzymes often by far exceed the activity, selectivity, and sustainability achieved with chemical catalysts. One of the main reasons for the lack of biocatalysis in the chemical industry is the poor stability exhibited by many enzymes when exposed to process conditions. This dilemma is exemplified in the usually very temperature‐sensitive enzymes catalyzing the Baeyer–Villiger reaction, which display excellent stereo‐ and regioselectivity and offer a green alternative to the commonly used, explosive peracids. Here we describe a protein engineering approach applied to cyclohexanone monooxygenase from Rhodococcus sp. HI‐31, a substrate‐promiscuous enzyme that efficiently catalyzes the production of the nylon‐6 precursor ε‐caprolactone. We used a framework for rapid enzyme stabilization by computational libraries (FRESCO), which predicts protein‐stabilizing mutations. From 128 screened point mutants, approximately half had a stabilizing effect, albeit mostly to a small degree. To overcome incompatibility effects observed upon combining the best hits, an easy shuffled library design strategy was devised. The most stable and highly active mutant displayed an increase in unfolding temperature of 13°C and an approximately 33x increase in half‐life at 30°C. In contrast to the wild‐type enzyme, this thermostable 8x mutant is an attractive biocatalyst for biotechnological applications.
Collapse
Affiliation(s)
| | - Marjon Boonstra
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Selle Bandstra
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| |
Collapse
|
27
|
Musil M, Stourac J, Bendl J, Brezovsky J, Prokop Z, Zendulka J, Martinek T, Bednar D, Damborsky J. FireProt: web server for automated design of thermostable proteins. Nucleic Acids Res 2019; 45:W393-W399. [PMID: 28449074 PMCID: PMC5570187 DOI: 10.1093/nar/gkx285] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 04/11/2017] [Indexed: 01/07/2023] Open
Abstract
There is a continuous interest in increasing proteins stability to enhance their usability in numerous biomedical and biotechnological applications. A number of in silico tools for the prediction of the effect of mutations on protein stability have been developed recently. However, only single-point mutations with a small effect on protein stability are typically predicted with the existing tools and have to be followed by laborious protein expression, purification, and characterization. Here, we present FireProt, a web server for the automated design of multiple-point thermostable mutant proteins that combines structural and evolutionary information in its calculation core. FireProt utilizes sixteen tools and three protein engineering strategies for making reliable protein designs. The server is complemented with interactive, easy-to-use interface that allows users to directly analyze and optionally modify designed thermostable mutants. FireProt is freely available at http://loschmidt.chemi.muni.cz/fireprot.
Collapse
Affiliation(s)
- Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, Brno, Czech Republic.,Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jaroslav Bendl
- Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, Brno, Czech Republic.,Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jaroslav Zendulka
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic.,Centre of Excellence IT4Innovations, Technical University Ostrava, Ostrava
| | - Tomas Martinek
- Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, Brno, Czech Republic.,Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic.,Centre of Excellence IT4Innovations, Technical University Ostrava, Ostrava
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| |
Collapse
|
28
|
Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 280] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| |
Collapse
|
29
|
Computational design of thermostable mutants for cephalosporin C acylase from Pseudomonas strain SE83. Comput Chem Eng 2018. [DOI: 10.1016/j.compchemeng.2018.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
30
|
Fürst MJLJ, Martin C, Lončar N, Fraaije MW. Experimental Protocols for Generating Focused Mutant Libraries and Screening for Thermostable Proteins. Methods Enzymol 2018; 608:151-187. [PMID: 30173762 DOI: 10.1016/bs.mie.2018.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Many proteins are rapidly deactivated when exposed to high or even ambient temperatures. This cannot only impede the study of a particular protein, but also is one of the major reasons why enzyme catalysis is still widely unable to compete with established chemical processes. Furthermore, differences in protein stability are a challenge in synthetic biology, when individual modules prove to be incompatible. The targeted stabilization of proteins can overcome these hurdles, and protein engineering techniques are more and more reliably supported by computational chemistry tools. Accordingly, algorithms to predict the differences in folding energy of a mutant compared to the wild-type, ΔΔGfold, are used in the highly successful FRESCO workflow. The resulting single mutant prediction library consists typically of a few hundred amino acid exchanges, and after combining the most successful hits we so far obtained stabilized mutants which exhibited increases in apparent melting temperature of 20-35°C and showed vastly increased half-lives, as well as resistance to cosolvents. Here, we report a detailed protocol to generate these mutant libraries experimentally, covering the entire workflow from primer design, through mutagenesis, protein production and screening, to mutation combination strategies. The individual parts of the method are furthermore applicable to many other scenarios besides protein stabilization, and these protocols are valuable for any project requiring individual or semi high-throughput site-directed mutagenesis, protein expression and purification, or generation of mutant combination libraries.
Collapse
Affiliation(s)
- Max J L J Fürst
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Caterina Martin
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Nikola Lončar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Marco W Fraaije
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
31
|
Engineering improved thermostability of the GH11 xylanase from Neocallimastix patriciarum via computational library design. Appl Microbiol Biotechnol 2018; 102:3675-3685. [DOI: 10.1007/s00253-018-8872-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/12/2018] [Accepted: 02/13/2018] [Indexed: 12/26/2022]
|
32
|
Martin C, Ovalle Maqueo A, Wijma HJ, Fraaije MW. Creating a more robust 5-hydroxymethylfurfural oxidase by combining computational predictions with a novel effective library design. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:56. [PMID: 29507608 PMCID: PMC5831843 DOI: 10.1186/s13068-018-1051-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND HMF oxidase (HMFO) from Methylovorus sp. is a recently characterized flavoprotein oxidase. HMFO is a remarkable enzyme as it is able to oxidize 5-hydroxymethylfurfural (HMF) into 2,5-furandicarboxylic acid (FDCA): a catalytic cascade of three oxidation steps. Because HMF can be formed from fructose or other sugars and FDCA is a polymer building block, this enzyme has gained interest as an industrially relevant biocatalyst. RESULTS To increase the robustness of HMFO, a requirement for biotechnological applications, we decided to enhance its thermostability using the recently developed FRESCO method: a computational approach to identify thermostabilizing mutations in a protein structure. To make this approach even more effective, we now developed a new and facile gene shuffling approach to rapidly combine stabilizing mutations in a one-pot reaction. This allowed the identification of the optimal combination of seven beneficial mutations. The created thermostable HMFO mutant was further studied as a biocatalyst for the production of FDCA from HMF and was shown to perform significantly better than the original HMFO. CONCLUSIONS The described new gene shuffling approach quickly discriminates stable and active multi-site variants. This makes it a very useful addition to FRESCO. The resulting thermostable HMFO variant tolerates the presence of cosolvents and also remained thermotolerant after introduction of additional mutations aimed at improving the catalytic activity. Due to its stability and catalytic efficiency, the final HMFO variant appears to be a promising candidate for industrial scale production of FDCA from HMF.
Collapse
Affiliation(s)
- Caterina Martin
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Amaury Ovalle Maqueo
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hein J. Wijma
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
33
|
Buß O, Rudat J, Ochsenreither K. FoldX as Protein Engineering Tool: Better Than Random Based Approaches? Comput Struct Biotechnol J 2018; 16:25-33. [PMID: 30275935 PMCID: PMC6158775 DOI: 10.1016/j.csbj.2018.01.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/21/2017] [Accepted: 01/20/2018] [Indexed: 02/04/2023] Open
Abstract
Improving protein stability is an important goal for basic research as well as for clinical and industrial applications but no commonly accepted and widely used strategy for efficient engineering is known. Beside random approaches like error prone PCR or physical techniques to stabilize proteins, e.g. by immobilization, in silico approaches are gaining more attention to apply target-oriented mutagenesis. In this review different algorithms for the prediction of beneficial mutation sites to enhance protein stability are summarized and the advantages and disadvantages of FoldX are highlighted. The question whether the prediction of mutation sites by the algorithm FoldX is more accurate than random based approaches is addressed.
Collapse
Affiliation(s)
- Oliver Buß
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | | |
Collapse
|
34
|
A Computational Library Design Protocol for Rapid Improvement of Protein Stability: FRESCO. Methods Mol Biol 2018; 1685:69-85. [PMID: 29086304 DOI: 10.1007/978-1-4939-7366-8_5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The ability to stabilize enzymes and other proteins has wide-ranging applications. Most protocols for enhancing enzyme stability require multiple rounds of high-throughput screening of mutant libraries and provide only modest improvements of stability. Here, we describe a computational library design protocol that can increase enzyme stability by 20-35 °C with little experimental screening, typically fewer than 200 variants. This protocol, termed FRESCO, scans the entire protein structure to identify stabilizing disulfide bonds and point mutations, explores their effect by molecular dynamics simulations, and provides mutant libraries with variants that have a good chance (>10%) to exhibit enhanced stability. After experimental verification, the most effective mutations are combined to produce highly robust enzymes.
Collapse
|
35
|
Abstract
The dynamic native, functional folded forms of proteins are unstable mainly because they readily unfold into flexible unstructured forms.
Collapse
Affiliation(s)
- Romas Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics
- University of Minnesota
- St Paul
- USA
| |
Collapse
|
36
|
Abstract
The last decade has seen a dramatic increase in the utilization of enzymes as green and sustainable (bio)catalysts in pharmaceutical and industrial applications. This trend has to a significant degree been fueled by advances in scientists' and engineers' ability to customize native enzymes by protein engineering. A review of the literature quickly reveals the tremendous success of this approach; protein engineering has generated enzyme variants with improved catalytic activity, broadened or altered substrate specificity, as well as raised or reversed stereoselectivity. Enzymes have been tailored to retain activity at elevated temperatures and to function in the presence of organic solvents, salts and pH values far from physiological conditions. However, readers unfamiliar with the field will soon encounter the confusingly large number of experimental techniques that have been employed to accomplish these engineering feats. Herein, we use history to guide a brief overview of the major strategies for protein engineering-past, present, and future.
Collapse
Affiliation(s)
- Stefan Lutz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, 30322, USA.
| | - Samantha M Iamurri
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, 30322, USA
| |
Collapse
|
37
|
Jones BJ, Lim HY, Huang J, Kazlauskas RJ. Comparison of Five Protein Engineering Strategies for Stabilizing an α/β-Hydrolase. Biochemistry 2017; 56:6521-6532. [PMID: 29087185 DOI: 10.1021/acs.biochem.7b00571] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A review of the previous stabilization of α/β-hydrolase fold enzymes revealed many different strategies, but no comparison of strategies on the same enzyme. For this reason, we compared five strategies to identify stabilizing mutations in a model α/β-hydrolase fold enzyme, salicylic acid binding protein 2, to reversible denaturation by urea and to irreversible denaturation by heat. The five strategies included one location agnostic approach (random mutagenesis using error-prone polymerase chain reaction), two structure-based approaches [computational design (Rosetta, FoldX) and mutation of flexible regions], and two sequence-based approaches (addition of proline at locations where a more stable homologue has proline and mutation to consensus). All strategies identified stabilizing mutations, but the best balance of success rate, degree of stabilization, and ease of implementation was mutation to consensus. A web-based automated program that predicts substitutions needed to mutate to consensus is available at http://kazlab.umn.edu .
Collapse
Affiliation(s)
- Bryan J Jones
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - Huey Yee Lim
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - Jun Huang
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States.,School of Biological and Chemical Engineering, Zhejiang University of Science and Technology , Hangzhou 310023, People's Republic of China
| | - Romas J Kazlauskas
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| |
Collapse
|
38
|
Broom A, Jacobi Z, Trainor K, Meiering EM. Computational tools help improve protein stability but with a solubility tradeoff. J Biol Chem 2017; 292:14349-14361. [PMID: 28710274 DOI: 10.1074/jbc.m117.784165] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 07/11/2017] [Indexed: 01/18/2023] Open
Abstract
Accurately predicting changes in protein stability upon amino acid substitution is a much sought after goal. Destabilizing mutations are often implicated in disease, whereas stabilizing mutations are of great value for industrial and therapeutic biotechnology. Increasing protein stability is an especially challenging task, with random substitution yielding stabilizing mutations in only ∼2% of cases. To overcome this bottleneck, computational tools that aim to predict the effect of mutations have been developed; however, achieving accuracy and consistency remains challenging. Here, we combined 11 freely available tools into a meta-predictor (meieringlab.uwaterloo.ca/stabilitypredict/). Validation against ∼600 experimental mutations indicated that our meta-predictor has improved performance over any of the individual tools. The meta-predictor was then used to recommend 10 mutations in a previously designed protein of moderate thermodynamic stability, ThreeFoil. Experimental characterization showed that four mutations increased protein stability and could be amplified through ThreeFoil's structural symmetry to yield several multiple mutants with >2-kcal/mol stabilization. By avoiding residues within functional ties, we could maintain ThreeFoil's glycan-binding capacity. Despite successfully achieving substantial stabilization, however, almost all mutations decreased protein solubility, the most common cause of protein design failure. Examination of the 600-mutation data set revealed that stabilizing mutations on the protein surface tend to increase hydrophobicity and that the individual tools favor this approach to gain stability. Thus, whereas currently available tools can increase protein stability and combining them into a meta-predictor yields enhanced reliability, improvements to the potentials/force fields underlying these tools are needed to avoid gaining protein stability at the cost of solubility.
Collapse
Affiliation(s)
- Aron Broom
- From the Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Zachary Jacobi
- From the Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Kyle Trainor
- From the Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | | |
Collapse
|
39
|
Babkova P, Sebestova E, Brezovsky J, Chaloupkova R, Damborsky J. Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity. Chembiochem 2017; 18:1448-1456. [PMID: 28419658 DOI: 10.1002/cbic.201700197] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Indexed: 11/08/2022]
Abstract
Ancestral sequence reconstruction (ASR) represents a powerful approach for empirical testing structure-function relationships of diverse proteins. We employed ASR to predict sequences of five ancestral haloalkane dehalogenases (HLDs) from the HLD-II subfamily. Genes encoding the inferred ancestral sequences were synthesized and expressed in Escherichia coli, and the resurrected ancestral enzymes (AncHLD1-5) were experimentally characterized. Strikingly, the ancestral HLDs exhibited significantly enhanced thermodynamic stability compared to extant enzymes (ΔTm up to 24 °C), as well as higher specific activities with preference for short multi-substituted halogenated substrates. Moreover, multivariate statistical analysis revealed a shift in the substrate specificity profiles of AncHLD1 and AncHLD2. This is extremely difficult to achieve by rational protein engineering. The study highlights that ASR is an efficient approach for the development of novel biocatalysts and robust templates for directed evolution.
Collapse
Affiliation(s)
- Petra Babkova
- Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Eva Sebestova
- Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| |
Collapse
|
40
|
Arabnejad H, Dal Lago M, Jekel PA, Floor RJ, Thunnissen AMWH, Terwisscha van Scheltinga AC, Wijma HJ, Janssen DB. A robust cosolvent-compatible halohydrin dehalogenase by computational library design. Protein Eng Des Sel 2017; 30:173-187. [PMID: 27999093 DOI: 10.1093/protein/gzw068] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/02/2016] [Indexed: 01/05/2023] Open
Abstract
To improve the applicability of halohydrin dehalogenase as a catalyst for reactions in the presence of organic cosolvents, we explored a computational library design strategy (Framework for Rapid Enzyme Stabilization by Computational libraries) that involves discovery and in silico evaluation of stabilizing mutations. Energy calculations, disulfide bond predictions and molecular dynamics simulations identified 218 point mutations and 35 disulfide bonds with predicted stabilizing effects. Experiments confirmed 29 stabilizing point mutations, most of which were located in two distinct regions, whereas introduction of disulfide bonds was not effective. Combining the best mutations resulted in a 12-fold mutant (HheC-H12) with a 28°C higher apparent melting temperature and a remarkable increase in resistance to cosolvents. This variant also showed a higher optimum temperature for catalysis while activity at low temperature was preserved. Mutant H12 was used as a template for the introduction of mutations that enhance enantioselectivity or activity. Crystal structures showed that the structural changes in the H12 mutant mostly agreed with the computational predictions and that the enhanced stability was mainly due to mutations that redistributed surface charges and improved interactions between subunits, the latter including better interactions of water molecules at the subunit interfaces.
Collapse
Affiliation(s)
- Hesam Arabnejad
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco Dal Lago
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Peter A Jekel
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Robert J Floor
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W H Thunnissen
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anke C Terwisscha van Scheltinga
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
41
|
Brezovsky J, Babkova P, Degtjarik O, Fortova A, Gora A, Iermak I, Rezacova P, Dvorak P, Smatanova IK, Prokop Z, Chaloupkova R, Damborsky J. Engineering a de Novo Transport Tunnel. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02081] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jan Brezovsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Petra Babkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Oksana Degtjarik
- Faculty
of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic
- Center for Nanobiology and Structural Biology ASCR, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Andrea Fortova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Artur Gora
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Iuliia Iermak
- Faculty
of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic
- Center for Nanobiology and Structural Biology ASCR, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Pavlina Rezacova
- Institute of Organic Chemistry and Biochemistry ASCR, v.v.i. Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics of the ASCR, v.v.i. Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Pavel Dvorak
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Ivana Kuta Smatanova
- Faculty
of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic
- Center for Nanobiology and Structural Biology ASCR, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| |
Collapse
|
42
|
Wu B, Wijma HJ, Song L, Rozeboom HJ, Poloni C, Tian Y, Arif MI, Nuijens T, Quaedflieg PJLM, Szymanski W, Feringa BL, Janssen DB. Versatile Peptide C-Terminal Functionalization via a Computationally Engineered Peptide Amidase. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01062] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Bian Wu
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, 9747 AG Groningen, The Netherlands
- CAS
Key Laboratory of Microbial Physiological and Metabolic Engineering,
Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
- State
Key Laboratory of Transducer Technology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Hein J. Wijma
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Lu Song
- CAS
Key Laboratory of Microbial Physiological and Metabolic Engineering,
Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
- State
Key Laboratory of Transducer Technology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Henriëtte J. Rozeboom
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Claudia Poloni
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, Faculty
of Mathematics and Natural Sciences, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Yue Tian
- CAS
Key Laboratory of Microbial Physiological and Metabolic Engineering,
Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
- State
Key Laboratory of Transducer Technology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Muhammad I. Arif
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Timo Nuijens
- Enzypep B.V., Urmonderbaan 22,
Chemelot Campus, 6167 RD Geleen, The Netherlands
| | | | - Wiktor Szymanski
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, Faculty
of Mathematics and Natural Sciences, University of Groningen, 9747 AG Groningen, The Netherlands
- Department
of Radiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Ben L. Feringa
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, Faculty
of Mathematics and Natural Sciences, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Dick B. Janssen
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| |
Collapse
|
43
|
Tavakoli Y, Esmaeili A, Saber H. Increasing thermal stability and catalytic activity of glutamate decarboxylase in E. coli: An in silico study. Comput Biol Chem 2016; 64:74-81. [PMID: 27294557 DOI: 10.1016/j.compbiolchem.2016.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 04/12/2016] [Accepted: 05/19/2016] [Indexed: 11/15/2022]
Abstract
Glutamate decarboxylase (GAD) is an enzyme that converts l-glutamate to gamma amino butyric acid (GABA) that is a widely used drug to treat mental disorders like Alzheimer's disease. In this study for the first time point mutation was performed virtually in the active site of the E. coli GAD in order to increase thermal stability and catalytic activity of the enzyme. Energy minimization and addition of water box were performed using GROMACS 5.4.6 package. PoPMuSiC 2.1 web server was used to predict potential spots for point mutation and Modeller software was used to perform point mutation on three dimensional model. Molegro virtual docker software was used for cavity detection and stimulated docking study. Results indicate that performing mutation separately at positions 164, 302, 304, 393, 396, 398 and 410 increase binding affinity to substrate. The enzyme is predicted to be more thermo- stable in all 7 mutants based on ΔΔG value.
Collapse
Affiliation(s)
- Yasaman Tavakoli
- Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Abolghasem Esmaeili
- Cell, Molecular and Developmental Biology Division, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
| | - Hossein Saber
- Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
| |
Collapse
|
44
|
Dörr M, Fibinger MP, Last D, Schmidt S, Santos-Aberturas J, Böttcher D, Hummel A, Vickers C, Voss M, Bornscheuer UT. Fully automatized high-throughput enzyme library screening using a robotic platform. Biotechnol Bioeng 2016; 113:1421-32. [DOI: 10.1002/bit.25925] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 12/15/2015] [Accepted: 12/28/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Mark Dörr
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Michael P.C. Fibinger
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Daniel Last
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Sandy Schmidt
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Javier Santos-Aberturas
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Dominique Böttcher
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Anke Hummel
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Clare Vickers
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Moritz Voss
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| |
Collapse
|
45
|
Shirke AN, Basore D, Butterfoss GL, Bonneau R, Bystroff C, Gross RA. Toward rational thermostabilization of Aspergillus oryzae cutinase: Insights into catalytic and structural stability. Proteins 2015; 84:60-72. [PMID: 26522152 DOI: 10.1002/prot.24955] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/11/2015] [Accepted: 10/12/2015] [Indexed: 11/10/2022]
Abstract
Cutinases are powerful hydrolases that can cleave ester bonds of polyesters such as poly(ethylene terephthalate) (PET), opening up new options for enzymatic routes for polymer recycling and surface modification reactions. Cutinase from Aspergillus oryzae (AoC) is promising owing to the presence of an extended groove near the catalytic triad which is important for the orientation of polymeric chains. However, the catalytic efficiency of AoC on rigid polymers like PET is limited by its low thermostability; as it is essential to work at or over the glass transition temperature (Tg) of PET, that is, 70 °C. Consequently, in this study we worked toward the thermostabilization of AoC. Use of Rosetta computational protein design software in conjunction with rational design led to a 6 °C improvement in the thermal unfolding temperature (Tm) and a 10-fold increase in the half-life of the enzyme activity at 60 °C. Surprisingly, thermostabilization did not improve the rate or temperature optimum of enzyme activity. Three notable findings are presented as steps toward designing more thermophilic cutinase: (a) surface salt bridge optimization produced enthalpic stabilization, (b) mutations to proline reduced the entropy loss upon folding, and (c) the lack of a correlative increase in the temperature optimum of catalytic activity with thermodynamic stability suggests that the active site is locally denatured at a temperature below the Tm of the global structure.
Collapse
Affiliation(s)
- Abhijit N Shirke
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Danielle Basore
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York.,Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Richard Bonneau
- Center for Genomics and Systems Biology, New York University, New York
| | - Christopher Bystroff
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York.,Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York.,Department of Computer Science, Rensselaer Polytechnic Institute, Troy, New York
| | - Richard A Gross
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| |
Collapse
|
46
|
Bednar D, Beerens K, Sebestova E, Bendl J, Khare S, Chaloupkova R, Prokop Z, Brezovsky J, Baker D, Damborsky J. FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PLoS Comput Biol 2015; 11:e1004556. [PMID: 26529612 PMCID: PMC4631455 DOI: 10.1371/journal.pcbi.1004556] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 09/14/2015] [Indexed: 01/01/2023] Open
Abstract
There is great interest in increasing proteins' stability to enhance their utility as biocatalysts, therapeutics, diagnostics and nanomaterials. Directed evolution is a powerful, but experimentally strenuous approach. Computational methods offer attractive alternatives. However, due to the limited reliability of predictions and potentially antagonistic effects of substitutions, only single-point mutations are usually predicted in silico, experimentally verified and then recombined in multiple-point mutants. Thus, substantial screening is still required. Here we present FireProt, a robust computational strategy for predicting highly stable multiple-point mutants that combines energy- and evolution-based approaches with smart filtering to identify additive stabilizing mutations. FireProt's reliability and applicability was demonstrated by validating its predictions against 656 mutations from the ProTherm database. We demonstrate that thermostability of the model enzymes haloalkane dehalogenase DhaA and γ-hexachlorocyclohexane dehydrochlorinase LinA can be substantially increased (ΔTm = 24°C and 21°C) by constructing and characterizing only a handful of multiple-point mutants. FireProt can be applied to any protein for which a tertiary structure and homologous sequences are available, and will facilitate the rapid development of robust proteins for biomedical and biotechnological applications.
Collapse
Affiliation(s)
- David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Koen Beerens
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic
| | - Eva Sebestova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic
| | - Jaroslav Bendl
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - Sagar Khare
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Enantis, Ltd., Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Enantis, Ltd., Brno, Czech Republic
- * E-mail:
| |
Collapse
|
47
|
Properties and biotechnological applications of natural and engineered haloalkane dehalogenases. Appl Microbiol Biotechnol 2015; 99:9865-81. [DOI: 10.1007/s00253-015-6954-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/19/2015] [Accepted: 08/22/2015] [Indexed: 01/01/2023]
|
48
|
Toplak A, Nuijens T, Quaedflieg PJ, Wu B, Janssen DB. Peptide synthesis in neat organic solvents with novel thermostable proteases. Enzyme Microb Technol 2015; 73-74:20-8. [DOI: 10.1016/j.enzmictec.2015.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/24/2015] [Accepted: 03/03/2015] [Indexed: 11/30/2022]
|
49
|
Floor RJ, Wijma HJ, Jekel PA, Terwisscha van Scheltinga AC, Dijkstra BW, Janssen DB. X-ray crystallographic validation of structure predictions used in computational design for protein stabilization. Proteins 2015; 83:940-51. [PMID: 25739581 DOI: 10.1002/prot.24791] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/11/2015] [Accepted: 02/14/2015] [Indexed: 11/10/2022]
Abstract
Protein engineering aimed at enhancing enzyme stability is increasingly supported by computational methods for calculation of mutant folding energies and for the design of disulfide bonds. To examine the accuracy of mutant structure predictions underlying these computational methods, crystal structures of thermostable limonene epoxide hydrolase variants obtained by computational library design were determined. Four different predicted effects indeed contributed to the obtained stabilization: (i) enhanced interactions between a flexible loop close to the N-terminus and the rest of the protein; (ii) improved interactions at the dimer interface; (iii) removal of unsatisfied hydrogen bonding groups; and (iv) introduction of additional positively charged groups at the surface. The structures of an eightfold and an elevenfold mutant showed that most mutations introduced the intended stabilizing interactions, and side-chain conformations were correctly predicted for 72-88% of the point mutations. However, mutations that introduced a disulfide bond in a flexible region had a larger influence on the backbone conformation than predicted. The enzyme active sites were unaltered, in agreement with the observed preservation of catalytic activities. The structures also revealed how a c-Myc tag, which was introduced for facile detection and purification, can reduce access to the active site and thereby lower the catalytic activity. Finally, sequence analysis showed that comprehensive mutant energy calculations discovered stabilizing mutations that are not proposed by the consensus or B-FIT methods.
Collapse
Affiliation(s)
- Robert J Floor
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
50
|
Yang H, Liu L, Li J, Chen J, Du G. Rational Design to Improve Protein Thermostability: Recent Advances and Prospects. CHEMBIOENG REVIEWS 2015. [DOI: 10.1002/cben.201400032] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|