1
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Behera S, Balasubramanian S. Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid. J Chem Inf Model 2023; 63:7545-7556. [PMID: 37989487 DOI: 10.1021/acs.jcim.3c01681] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Protein-ligand binding studies are crucial for understanding the molecular basis of biological processes and for further advancing industrial biocatalysis and drug discovery. Using computational modeling and molecular dynamics simulations, we investigated the binding of a butyrate ester substrate to the lipase A (LipA) enzyme of Bacillus subtilis. Besides obtaining a close agreement of the binding free energy with the experimental value, the study reveals a remarkable reorganization of the catalytic triad upon substrate binding, leading to increased essential hydrogen bond populations. The investigation shows the distortion of the oxyanion hole in both the substrate-bound and unbound states of LipA and highlights the strengthening of the same in the tetrahedral intermediate complex. Principal component analysis of the unbound ensemble reveals the dominant motion in LipA to be the movement of Loop-1 (Tyr129-Arg142) between two states that cover and uncover the active site, mirroring that of a lid prevalent in several lipases. This lid-like motion of Loop-1 is also supported by its tendency to spontaneously open up at an oil-water interface. Overall, this study provides valuable insights into the impact of substrate binding on the structure, flexibility, and conformational dynamics of the LipA enzyme.
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Affiliation(s)
- Sudarshan Behera
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
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2
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Schnettler JD, Klein OJ, Kaminski TS, Colin PY, Hollfelder F. Ultrahigh-Throughput Directed Evolution of a Metal-Free α/β-Hydrolase with a Cys-His-Asp Triad into an Efficient Phosphotriesterase. J Am Chem Soc 2023; 145:1083-1096. [PMID: 36583539 PMCID: PMC9853848 DOI: 10.1021/jacs.2c10673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Finding new mechanistic solutions for biocatalytic challenges is key in the evolutionary adaptation of enzymes, as well as in devising new catalysts. The recent release of man-made substances into the environment provides a dynamic testing ground for observing biocatalytic innovation at play. Phosphate triesters, used as pesticides, have only recently been introduced into the environment, where they have no natural counterpart. Enzymes have rapidly evolved to hydrolyze phosphate triesters in response to this challenge, converging onto the same mechanistic solution, which requires bivalent cations as a cofactor for catalysis. In contrast, the previously identified metagenomic promiscuous hydrolase P91, a homologue of acetylcholinesterase, achieves slow phosphotriester hydrolysis mediated by a metal-independent Cys-His-Asp triad. Here, we probe the evolvability of this new catalytic motif by subjecting P91 to directed evolution. By combining a focused library approach with the ultrahigh throughput of droplet microfluidics, we increase P91's activity by a factor of ≈360 (to a kcat/KM of ≈7 × 105 M-1 s-1) in only two rounds of evolution, rivaling the catalytic efficiencies of naturally evolved, metal-dependent phosphotriesterases. Unlike its homologue acetylcholinesterase, P91 does not suffer suicide inhibition; instead, fast dephosphorylation rates make the formation of the covalent adduct rather than its hydrolysis rate-limiting. This step is improved by directed evolution, with intermediate formation accelerated by 2 orders of magnitude. Combining focused, combinatorial libraries with the ultrahigh throughput of droplet microfluidics can be leveraged to identify and enhance mechanistic strategies that have not reached high efficiency in nature, resulting in alternative reagents with novel catalytic machineries.
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Affiliation(s)
- J David Schnettler
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Oskar James Klein
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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3
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Miton CM, Tokuriki N. Insertions and Deletions (Indels): A Missing Piece of the Protein Engineering Jigsaw. Biochemistry 2023; 62:148-157. [PMID: 35830609 DOI: 10.1021/acs.biochem.2c00188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the years, protein engineers have studied nature and borrowed its tricks to accelerate protein evolution in the test tube. While there have been considerable advances, our ability to generate new proteins in the laboratory is seemingly limited. One explanation for these shortcomings may be that insertions and deletions (indels), which frequently arise in nature, are largely overlooked during protein engineering campaigns. The profound effect of indels on protein structures, by way of drastic backbone alterations, could be perceived as "saltation" events that bring about significant phenotypic changes in a single mutational step. Should we leverage these effects to accelerate protein engineering and gain access to unexplored regions of adaptive landscapes? In this Perspective, we describe the role played by indels in the functional diversification of proteins in nature and discuss their untapped potential for protein engineering, despite their often-destabilizing nature. We hope to spark a renewed interest in indels, emphasizing that their wider study and use may prove insightful and shape the future of protein engineering by unlocking unique functional changes that substitutions alone could never achieve.
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Affiliation(s)
- Charlotte M Miton
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 BC, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 BC, Canada
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4
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Savino S, Desmet T, Franceus J. Insertions and deletions in protein evolution and engineering. Biotechnol Adv 2022; 60:108010. [PMID: 35738511 DOI: 10.1016/j.biotechadv.2022.108010] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022]
Abstract
Protein evolution or engineering studies are traditionally focused on amino acid substitutions and the way these contribute to fitness. Meanwhile, the insertion and deletion of amino acids is often overlooked, despite being one of the most common sources of genetic variation. Recent methodological advances and successful engineering stories have demonstrated that the time is ripe for greater emphasis on these mutations and their understudied effects. This review highlights the evolutionary importance and biotechnological relevance of insertions and deletions (indels). We provide a comprehensive overview of approaches that can be employed to include indels in random, (semi)-rational or computational protein engineering pipelines. Furthermore, we discuss the tolerance to indels at the structural level, address how domain indels can link the function of unrelated proteins, and feature studies that illustrate the surprising and intriguing potential of frameshift mutations.
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Affiliation(s)
- Simone Savino
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium..
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5
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Bhattacharyya M, Basu S, Dhar R, Dutta TK. Phthalate hydrolase: distribution, diversity and molecular evolution. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:333-346. [PMID: 34816599 DOI: 10.1111/1758-2229.13028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 05/12/2023]
Abstract
The alpha/beta-fold superfamily of hydrolases is rapidly becoming one of the largest groups of structurally related enzymes with diverse catalytic functions. In this superfamily of enzymes, esterase deserves special attention because of their wide distribution in biological systems and importance towards environmental and industrial applications. Among various esterases, phthalate hydrolases are the key alpha/beta enzymes involved in the metabolism of structurally diverse estrogenic phthalic acid esters, ubiquitously distributed synthetic chemicals, used as plasticizer in plastic manufacturing processes. Although they vary both at the sequence and functional levels, these hydrolases use a similar acid-base-nucleophile catalytic mechanism to catalyse reactions on structurally different substrates. The current review attempts to present insights on phthalate hydrolases, describing their sources, structural diversities, phylogenetic affiliations and catalytically different types or classes of enzymes, categorized as diesterase, monoesterase and diesterase-monoesterase, capable of hydrolysing phthalate diester, phthalate monoester and both respectively. Furthermore, available information on in silico analyses and site-directed mutagenesis studies revealing structure-function integrity and altered enzyme kinetics have been highlighted along with the possible scenario of their evolution at the molecular level.
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Affiliation(s)
| | - Suman Basu
- Department of Microbiology, Bose Institute, Kolkata, West Bengal, India
| | - Rinita Dhar
- Department of Microbiology, Bose Institute, Kolkata, West Bengal, India
| | - Tapan K Dutta
- Department of Microbiology, Bose Institute, Kolkata, West Bengal, India
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6
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Li D, Chen X, Chen Z, Lin X, Xu J, Wu Q. Directed evolution of lipase A from Bacillus subtilis for the preparation of enantiocomplementary sec-alcohols. GREEN SYNTHESIS AND CATALYSIS 2021. [DOI: 10.1016/j.gresc.2021.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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7
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Plaks JG, Brewer JA, Jacobsen NK, McKenna M, Uzarski JR, Lawton TJ, Filocamo SF, Kaar JL. Rosetta-Enabled Structural Prediction of Permissive Loop Insertion Sites in Proteins. Biochemistry 2020; 59:3993-4002. [PMID: 32970423 DOI: 10.1021/acs.biochem.0c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While loop motifs frequently play a major role in protein function, our understanding of how to rationally engineer proteins with novel loop domains remains limited. In the absence of rational approaches, the incorporation of loop domains often destabilizes proteins, thereby requiring massive screening and selection to identify sites that can accommodate loop insertion. We developed a computational strategy for rapidly scanning the entire structure of a scaffold protein to determine the impact of loop insertion at all possible amino acid positions. This approach is based on the Rosetta kinematic loop modeling protocol and was demonstrated by identifying sites in lipase that were permissive to insertion of the LAP peptide. Interestingly, the identification of permissive sites was dependent on the contribution of the residues in the near-loop environment on the Rosetta score and did not correlate with conventional structural features (e.g., B-factors). As evidence of this, several insertion sites (e.g., following residues 17, 47-49, and 108), which were predicted and confirmed to be permissive, interrupted helices, while others (e.g., following residues 43, 67, 116, 119, and 121), which are situated in loop regions, were nonpermissive. This approach was further shown to be predictive for β-glucosidase and human phosphatase and tensin homologue (PTEN), and to facilitate the engineering of insertion sites through in silico mutagenesis. By enabling the design of loop-containing protein libraries with high probabilities of soluble expression, this approach has broad implications in many areas of protein engineering, including antibody design, improving enzyme activity, and protein modification.
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Affiliation(s)
- Joseph G Plaks
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Jeff A Brewer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Nicole K Jacobsen
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Michael McKenna
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Joshua R Uzarski
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Timothy J Lawton
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Shaun F Filocamo
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
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8
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Hoque MA, Zhang Y, Li Z, Cui L, Feng Y. Remodeling enzyme active sites by stepwise loop insertion. Methods Enzymol 2020; 643:111-127. [PMID: 32896277 DOI: 10.1016/bs.mie.2020.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The remolding active site loops via residue insertion/deletion as well as substitution is thought to play a key role in enzyme divergent evolution. However, enzyme engineering by residue insertion in active site loops often severely perturbs the protein structural integrity and causes protein misfolding and activity loss. We have designed a stepwise loop insertion strategy (StLois), in which a pair of randomized residues is introduced in a stepwise manner, efficiently collating mutational fitness effects. The strategy of StLois constitutes three key steps. First, the target regions should be identified through structural and functional analysis on the counterpart enzymes. Second, pair residues can be introduced in loop regions through insertion with NNK codon degeneracy. Third, the best hit used as a template for the next round mutagenesis. The residue insertion process can repeat as many times as necessary. By using the StLois method, we have evolved the substrate preference of a lactonase to phosphotriesterase. In this chapter, we describe the detailed StLois technique, which efficiently expands the residue in the loop region and remolds the architecture of enzyme active site for novel catalytic properties.
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Affiliation(s)
- Md Anarul Hoque
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Li Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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9
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Wójcik M, Szala K, van Merkerk R, Quax WJ, Boersma YL. Engineering the specificity of Streptococcus pyogenes sortase A by loop grafting. Proteins 2020; 88:1394-1400. [PMID: 32501594 PMCID: PMC7586933 DOI: 10.1002/prot.25958] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/30/2020] [Accepted: 05/27/2020] [Indexed: 11/24/2022]
Abstract
Sortases are a group of enzymes displayed on the cell‐wall of Gram‐positive bacteria. They are responsible for the attachment of virulence factors onto the peptidoglycan in a transpeptidation reaction through recognition of a pentapeptide substrate. Most housekeeping sortases recognize one specific pentapeptide motif; however, Streptococcus pyogenes sortase A (SpSrtA WT) recognizes LPETG, LPETA and LPKLG motifs. Here, we examined SpSrtA's flexible substrate specificity by investigating the role of the β7/β8 loop in determining substrate specificity. We exchanged the β7/β8 loop in SpSrtA with corresponding β7/β8 loops from Staphylococcus aureus (SaSrtA WT) and Bacillus anthracis (BaSrtA WT). While the BaSrtA‐derived variant showed no enzymatic activity toward either LPETG or LPETA substrates, the activity of the SaSrtA‐derived mutant toward the LPETA substrate was completely abolished. Instead, the mutant had an improved activity toward LPETG, the preferred substrate of SaSrtA WT.
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Affiliation(s)
- Magdalena Wójcik
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Kamil Szala
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Ykelien L Boersma
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
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10
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Abstract
The question of how to distinguish between lipases and esterases is about as old as the definition of the subclassification is. Many different criteria have been proposed to this end, all indicative but not decisive. Here, the activity of lipases in dry organic solvents as a criterion is probed on a minimal α/β hydrolase fold enzyme, the Bacillus subtilis lipase A (BSLA), and compared to Candida antarctica lipase B (CALB), a proven lipase. Both hydrolases show activity in dry solvents and this proves BSLA to be a lipase. Overall, this demonstrates the value of this additional parameter to distinguish between lipases and esterases. Lipases tend to be active in dry organic solvents, while esterases are not active under these circumstances.
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11
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Dulcey CE, López de Los Santos Y, Létourneau M, Déziel E, Doucet N. Semi-rational evolution of the 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA to improve rhamnolipid production in Pseudomonas aeruginosa and Burkholderia glumae. FEBS J 2019; 286:4036-4059. [PMID: 31177633 DOI: 10.1111/febs.14954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/12/2019] [Accepted: 06/06/2019] [Indexed: 12/15/2022]
Abstract
The 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA is an essential enzyme involved in the biosynthesis of HAAs in Pseudomonas and Burkholderia species. RhlA modulates the aliphatic chain length in rhamnolipids, conferring distinct physicochemical properties to these biosurfactants exhibiting promising industrial and pharmaceutical value. A detailed molecular understanding of substrate specificity and catalytic performance in RhlA could offer protein engineering tools to develop designer variants involved in the synthesis of novel rhamnolipid mixtures for tailored eco-friendly products. However, current directed evolution progress remains limited due to the absence of high-throughput screening methodologies and lack of an experimentally resolved RhlA structure. In the present work, we used comparative modeling and chimeric-based approaches to perform a comprehensive semi-rational mutagenesis of RhlA from Pseudomonas aeruginosa. Our extensive RhlA mutational variants and chimeric hybrids between the Pseudomonas and Burkholderia homologs illustrate selective modulation of rhamnolipid alkyl chain length in both Pseudomonas aeruginosa and Burkholderia glumae. Our results also demonstrate the implication of a putative cap-domain motif that covers the catalytic site of the enzyme and provides substrate specificity to RhlA. This semi-rational mutant-based survey reveals promising 'hot-spots' for the modulation of RL congener patterns and potential control of enzyme activity, in addition to uncovering residue positions that modulate substrate selectivity between the Pseudomonas and Burkholderia functional homologs. DATABASE: Model data are available in the PMDB database under the accession number PM0081867.
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Affiliation(s)
- Carlos Eduardo Dulcey
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Yossef López de Los Santos
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Canada
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12
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Liu C, Zhao J, Liu J, Guo X, Rao D, Liu H, Zheng P, Sun J, Ma Y. Simultaneously improving the activity and thermostability of a new proline 4-hydroxylase by loop grafting and site-directed mutagenesis. Appl Microbiol Biotechnol 2018; 103:265-277. [DOI: 10.1007/s00253-018-9410-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 02/03/2023]
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13
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Sankar K, Achary A, Mehala N, Rajendran L. Empirical and Analytical Correlation of the Reaction Kinetics Parameters of Cuttle Bone Powder Immobilized Lipase Catalyzed Ethyl Ferulate Synthesis. Catal Letters 2017. [DOI: 10.1007/s10562-017-2108-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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14
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Hoque MA, Zhang Y, Chen L, Yang G, Khatun MA, Chen H, Hao L, Feng Y. Stepwise Loop Insertion Strategy for Active Site Remodeling to Generate Novel Enzyme Functions. ACS Chem Biol 2017; 12:1188-1193. [PMID: 28323400 DOI: 10.1021/acschembio.7b00018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The remodeling of active sites to generate novel biocatalysts is an attractive and challenging task. We developed a stepwise loop insertion strategy (StLois), in which randomized residue pairs are inserted into active site loops. The phosphotriesterase-like lactonase from Geobacillus kaustophilus (GkaP-PLL) was used to investigate StLois's potential for changing enzyme function. By inserting six residues into active site loop 7, the best variant ML7-B6 demonstrated a 16-fold further increase in catalytic efficiency toward ethyl-paraoxon compared with its initial template, that is a 609-fold higher, >107 fold substrate specificity shift relative to that of wild-type lactonase. The remodeled variants displayed 760-fold greater organophosphate hydrolysis activity toward the organophosphates parathion, diazinon, and chlorpyrifos. Structure and docking computations support the source of notably inverted enzyme specificity. Considering the fundamental importance of active site loops, the strategy has potential for the rapid generation of novel enzyme functions by loop remodeling.
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Affiliation(s)
- Md Anarul Hoque
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Zhang
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liuqing Chen
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guangyu Yang
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mst Afroza Khatun
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haifeng Chen
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liu Hao
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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15
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16
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Hwang HT, Qi F, Yuan C, Zhao X, Ramkrishna D, Liu D, Varma A. Lipase-catalyzed process for biodiesel production: Protein engineering and lipase production. Biotechnol Bioeng 2013; 111:639-53. [PMID: 24284881 DOI: 10.1002/bit.25162] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/16/2013] [Accepted: 11/20/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Hyun Tae Hwang
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Feng Qi
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Chongli Yuan
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Xuebing Zhao
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Doraiswami Ramkrishna
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Dehua Liu
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Arvind Varma
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
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17
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Yun HS, Park HJ, Joo JC, Yoo YJ. Thermostabilization of Bacillus subtilis lipase A by minimizing the structural deformation caused by packing enhancement. ACTA ACUST UNITED AC 2013; 40:1223-9. [DOI: 10.1007/s10295-013-1330-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 08/06/2013] [Indexed: 11/24/2022]
Abstract
Abstract
Enzyme thermostabilization is a critical research topic due to potential industrial benefits. Among the various reasons to increase enzyme thermostability, enhancement of residual packing at the core of the enzyme structure has been commonly accepted as a successful strategy. However, structural changes that occur with residual packing enhancement may decrease enzyme activity. In this study, a strategy to minimize structural deformation by calculating the overlapping packing volume of a single-point mutation followed by applying a double-point mutation was suggested. Four double mutants, A38V_K23A, A75V_T83A, G80A_N106A, and G172A_V100A, were selected for the in vitro experiment; three of the four showed enhancements in both thermostability and catalytic activity. In particular, G80A_N106A showed 2.78 times higher catalytic activity compared with wild type.
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Affiliation(s)
- Hong Seung Yun
- grid.31501.36 0000000404705905 School of Chemical and Biological Engineering Seoul National University 151-742 Seoul Korea
| | - Hyun June Park
- grid.31501.36 0000000404705905 Graduate Program of Bioengineering Seoul National University 151-742 Seoul Korea
| | - Jeong Chan Joo
- grid.31501.36 0000000404705905 School of Chemical and Biological Engineering Seoul National University 151-742 Seoul Korea
| | - Young Je Yoo
- grid.31501.36 0000000404705905 School of Chemical and Biological Engineering Seoul National University 151-742 Seoul Korea
- grid.31501.36 0000000404705905 Graduate Program of Bioengineering Seoul National University 151-742 Seoul Korea
- grid.31501.36 0000000404705905 Bio-Max Institute Seoul National University 151-742 Seoul Korea
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18
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Nov Y. Fitness loss and library size determination in saturation mutagenesis. PLoS One 2013; 8:e68069. [PMID: 23844158 PMCID: PMC3700877 DOI: 10.1371/journal.pone.0068069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/24/2013] [Indexed: 01/31/2023] Open
Abstract
Saturation mutagenesis is a widely used directed evolution technique, in which a large number of protein variants, each having random amino acids in certain predetermined positions, are screened in order to discover high-fitness variants among them. Several metrics for determining the library size (the number of variants screened) have been suggested in the literature, but none of them incorporates the actual fitness of the variants discovered in the experiment. We present the results of an extensive simulation study, which is based on probabilistic models for protein fitness landscape, and which investigates how the result of a saturation mutagenesis experiment – the fitness of the best variant discovered – varies as a function of the library size. In particular, we study the loss of fitness in the experiment: the difference between the fitness of the best variant discovered, and the fitness of the best variant in variant space. Our results are that the existing criteria for determining the library size are conservative, so smaller libraries are often satisfactory. Reducing the library size can save labor, time, and expenses in the laboratory.
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Affiliation(s)
- Yuval Nov
- Department of Statistics, University of Haifa, Haifa, Israel.
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19
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Akbulut N, Tuzlakoğlu Öztürk M, Pijning T, İşsever Öztürk S, Gümüşel F. Improved activity and thermostability of Bacillus pumilus lipase by directed evolution. J Biotechnol 2013; 164:123-9. [DOI: 10.1016/j.jbiotec.2012.12.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/20/2012] [Accepted: 12/21/2012] [Indexed: 11/27/2022]
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20
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Bassegoda A, Cesarini S, Diaz P. Lipase improvement: goals and strategies. Comput Struct Biotechnol J 2012; 2:e201209005. [PMID: 24688646 PMCID: PMC3962121 DOI: 10.5936/csbj.201209005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/20/2012] [Accepted: 09/23/2012] [Indexed: 12/22/2022] Open
Affiliation(s)
- Arnau Bassegoda
- Department of Microbiology, University of Barcelona. Av. Diagonal 643, 08028-Barcelona. Spain
| | - Silvia Cesarini
- Department of Microbiology, University of Barcelona. Av. Diagonal 643, 08028-Barcelona. Spain
| | - Pilar Diaz
- Department of Microbiology, University of Barcelona. Av. Diagonal 643, 08028-Barcelona. Spain
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21
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Goldsmith M, Ashani Y, Simo Y, Ben-David M, Leader H, Silman I, Sussman JL, Tawfik DS. Evolved stereoselective hydrolases for broad-spectrum G-type nerve agent detoxification. ACTA ACUST UNITED AC 2012; 19:456-66. [PMID: 22520752 DOI: 10.1016/j.chembiol.2012.01.017] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 01/16/2012] [Accepted: 01/18/2012] [Indexed: 11/17/2022]
Abstract
A preferred strategy for preventing nerve agents intoxication is catalytic scavenging by enzymes that hydrolyze them before they reach their targets. Using directed evolution, we simultaneously enhanced the activity of a previously described serum paraoxonase 1 (PON1) variant for hydrolysis of the toxic S(P) isomers of the most threatening G-type nerve agents. The evolved variants show ≤340-fold increased rates and catalytic efficiencies of 0.2-5 × 10(7) M(-1) min(-1). Our selection for prevention of acetylcholinesterase inhibition also resulted in the complete reversion of PON1's stereospecificity, from an enantiomeric ratio (E) < 6.3 × 10(-4) in favor of the R(P) isomer of a cyclosarin analog in wild-type PON1, to E > 2,500 for the S(P) isomer in an evolved variant. Given their ability to hydrolyze G-agents, these evolved variants may serve as broad-range G-agent prophylactics.
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Affiliation(s)
- Moshe Goldsmith
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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22
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Flores H, Lin S, Contreras-Ferrat G, Cronan JE, Morett E. Evolution of a new function in an esterase: simple amino acid substitutions enable the activity present in the larger paralog, BioH. Protein Eng Des Sel 2012; 25:387-95. [PMID: 22691705 DOI: 10.1093/protein/gzs035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Gene duplication and divergence are essential processes for the evolution of new activities. Divergence may be gradual, involving simple amino acid residue substitutions, or drastic, such that larger structural elements are inserted, deleted or rearranged. Vast protein sequence comparisons, supported by some experimental evidence, argue that large structural modifications have been necessary for certain catalytic activities to evolve. However, it is not clear whether these activities could not have been attained by gradual changes. Interestingly, catalytic promiscuity could play a fundamental evolutionary role: a preexistent secondary activity could be increased by simple amino acid residue substitutions that do not affect the enzyme's primary activity. The promiscuous profile of the enzyme may be modified gradually by genetic drift, making a pool of potentially useful activities that can be selected before duplication. In this work, we used random mutagenesis and in vivo selection to evolve the Pseudomonas aeruginosa PAO1 carboxylesterase PA3859, a small protein, to attain the function of BioH, a much larger paralog involved in biotin biosynthesis. BioH was chosen as a target activity because it provides a highly sensitive selection for evolved enzymatic activities by auxotrophy complementation. After only two cycles of directed evolution, mutants with the ability to efficiently complement biotin auxotrophy were selected. The in vivo and in vitro characterization showed that the activity of one of our mutant proteins was similar to that of the wild-type BioH enzyme. Our results demonstrate that it is possible to evolve enzymatic activities present in larger proteins by discrete amino acid substitutions.
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Affiliation(s)
- Humberto Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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23
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van Leeuwen JGE, Wijma HJ, Floor RJ, van der Laan JM, Janssen DB. Directed Evolution Strategies for Enantiocomplementary Haloalkane Dehalogenases: From Chemical Waste to Enantiopure Building Blocks. Chembiochem 2011; 13:137-48. [DOI: 10.1002/cbic.201100579] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Indexed: 01/06/2023]
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24
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Discovery of an Escherichia coli esterase with high activity and enantioselectivity toward 1,2-O-isopropylideneglycerol esters. Appl Environ Microbiol 2011; 77:6094-9. [PMID: 21764964 DOI: 10.1128/aem.05122-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli has been widely used as an expression host for the identification of desired biocatalysts through screening or selection assays. We have previously used E. coli in growth selection and screening assays for identification of Bacillus subtilis lipase variants (located in the periplasm) with improved activity and enantioselectivity toward 1,2-O-isopropylideneglycerol (IPG) esters. In the course of these studies, we discovered that E. coli itself exhibits significant cytoplasmic esterase activity toward IPG esters. In order to identify the enzyme (or enzymes) responsible for this esterase activity, we analyzed eight E. coli knockout strains, in which single esterase genes were deleted, for their ability to hydrolyze IPG butyrate. This approach led to the identification of esterase YbfF as the major E. coli enzyme responsible for the hydrolytic activity toward IPG esters. The gene coding for YbfF was cloned and overexpressed in E. coli, and the corresponding protein was purified and characterized for its biocatalytic performance. YbfF displays a high level of activity toward IPG butyrate and IPG caprylate and prefers the R-enantiomer of these substrates, producing the S-enantiomer of the IPG product with high enantiomeric excess (72 to 94% ee). The enantioselectivity of YbfF for IPG caprylate (E = 40) could be significantly enhanced when using dimethylformamide (DMF) or dimethyl sulfoxide (DMSO) as cosolvents in kinetic resolution experiments. The enzyme also shows high enantioselectivity toward 1-phenylethyl acetate (E ≥ 200), giving the chiral product (R)-1-phenylethanol with >99% ee. The high activity and enantioselectivity of YbfF make it an attractive enzyme for organic synthesis.
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Ni Z, Jin X, Zhou P, Wu Q, Lin XF. A Combination of Computational and Experimental Approaches to Investigate the Binding Behavior of B.sub Lipase A Mutants with Substrate pNPP. Mol Inform 2011; 30:359-67. [PMID: 27466952 DOI: 10.1002/minf.201000110] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 01/29/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Zhong Ni
- Department of Chemistry, Zhejiang University, Hangzhou 31002, P. R. China tel: +86 571 87952618, fax: +86 571 87951588
| | - Xin Jin
- Department of Chemistry, Zhejiang University, Hangzhou 31002, P. R. China tel: +86 571 87952618, fax: +86 571 87951588
| | - Peng Zhou
- Department of Chemistry, Zhejiang University, Hangzhou 31002, P. R. China tel: +86 571 87952618, fax: +86 571 87951588
| | - Qi Wu
- Department of Chemistry, Zhejiang University, Hangzhou 31002, P. R. China tel: +86 571 87952618, fax: +86 571 87951588
| | - Xian-Fu Lin
- Department of Chemistry, Zhejiang University, Hangzhou 31002, P. R. China tel: +86 571 87952618, fax: +86 571 87951588.
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26
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Jez JM. Toward protein engineering for phytoremediation: possibilities and challenges. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2011; 13 Suppl 1:77-89. [PMID: 22046752 DOI: 10.1080/15226514.2011.568537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The combination of rational protein engineering and directed evolution techniques allow for the redesign of enzymes with tailored properties for use in environmental remediation. This review summarizes current molecular methods for either altering or improving protein function and highlights examples of how these methods can address bioremediation problems. Although much of the protein engineering applied to environmental clean-up employs microbial systems, there is great potential for and significant challenges to translating these approaches to plant systems for phytoremediation purposes. Protein engineering technologies combined with genomic information and metabolic engineering strategies hold promise for the design of plants and microbes to remediate organic and inorganic pollutants.
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Affiliation(s)
- Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
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Kourist R, Jochens H, Bartsch S, Kuipers R, Padhi SK, Gall M, Böttcher D, Joosten HJ, Bornscheuer UT. The alpha/beta-hydrolase fold 3DM database (ABHDB) as a tool for protein engineering. Chembiochem 2010; 11:1635-43. [PMID: 20593436 DOI: 10.1002/cbic.201000213] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Robert Kourist
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
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28
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Prokop Z, Sato Y, Brezovsky J, Mozga T, Chaloupkova R, Koudelakova T, Jerabek P, Stepankova V, Natsume R, van Leeuwen J, Janssen D, Florian J, Nagata Y, Senda T, Damborsky J. Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering. Angew Chem Int Ed Engl 2010; 49:6111-5. [DOI: 10.1002/anie.201001753] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Prokop Z, Sato Y, Brezovsky J, Mozga T, Chaloupkova R, Koudelakova T, Jerabek P, Stepankova V, Natsume R, van Leeuwen J, Janssen D, Florian J, Nagata Y, Senda T, Damborsky J. Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001753] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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30
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Wieczorek B, Lemcke B, Dijkstra HP, Egmond MR, Klein Gebbink RJM, van Koten G. Site-Selective Ser-Hydrolase Labelling with a Luminescent Organometallic NCN-Platinum Complex. Eur J Inorg Chem 2010. [DOI: 10.1002/ejic.200900980] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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31
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Kourist R, Brundiek H, Bornscheuer UT. Protein engineering and discovery of lipases. EUR J LIPID SCI TECH 2010. [DOI: 10.1002/ejlt.200900143] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Chen B, Cai Z, Wu W, Huang Y, Pleiss J, Lin Z. Morphing activity between structurally similar enzymes: from heme-free bromoperoxidase to lipase. Biochemistry 2009; 48:11496-504. [PMID: 19883129 DOI: 10.1021/bi9014727] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, to explore the plasticity of the alpha/beta-hydrolase fold family, we converted bromoperoxidase A2 (BPO-A2) from Streptomyces aureofaciens to a lipase by structure comparison with lipase A (LipA) from Bacillus subtilis. These two enzymes have similar structures (2.1 A rmsd) and a very low level of sequence identity ( approximately 18%). A variant BL1 was constructed by deleting the caplike domain of BPO-A2 and further fine-tuning the newly formed substrate binding site. The lipase activity was successfully transplanted on BL1, while the halogenation activity was totally lost. BL1 also showed higher hydrolytic activities toward long chain p-nitrophenyl esters, such as p-nitrophenyl caprylate (3.7-fold) and p-nitrophenyl palmitate (7.0-fold), while its activity toward a short chain ester (p-nitrophenyl acetate) decreased dramatically, to only 1.2% of that of BPO-A2. After two rounds of directed evolution and site-directed mutagenesis on selected residues, several mutants with both improved hydrolytic activities and substrate preferences toward long chain substrates were obtained. The highest hydrolytic activity toward p-nitrophenyl palmitate of the best mutant BL1-2-E8-plusI was improved by 40-fold compared with that of BL1. These results demonstrate the possibility of manipulating the caplike domain of alpha/beta-hydrolase fold enzymes and provide further understanding of the structure-function relationship of the alpha/beta-hydrolase fold enzymes. The design strategy used in this study could serve as a useful approach for constructing variants with targeted catalytic properties using the alpha/beta-hydrolase fold.
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Affiliation(s)
- Bo Chen
- Department of Chemical Engineering, Tsinghua University, Tsinghua Garden Road 1, 100084 Beijing, China
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