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Huang B, Yang K, Amanze C, Yan Z, Zhou H, Liu X, Qiu G, Zeng W. Sequence and structure-guided discovery of a novel NADH-dependent 7β-hydroxysteroid dehydrogenase for efficient biosynthesis of ursodeoxycholic acid. Bioorg Chem 2023; 131:106340. [PMID: 36586301 DOI: 10.1016/j.bioorg.2022.106340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/11/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022]
Abstract
7β-Hydroxysteroid dehydrogenases (7β-HSDHs) have attracted increasing attention due to their crucial roles in the biosynthesis of ursodeoxycholic acid (UDCA). However, most published 7β-HSDHs are strictly NADPH-dependent oxidoreductases with poor activity and low productivity. Compared with NADPH, NADH is more stable and cheaper, making it the more popular cofactor for industrial applications of dehydrogenases. Herein, by using a sequence and structure-guided genome mining approach based on the structural information of conserved cofactor-binding motifs, we uncovered a novel NADH-dependent 7β-HSDH (Cle7β-HSDH). The Cle7β-HSDH was overexpressed, purified, and characterized. It exhibited high specific activity (9.6 U/mg), good pH stability and thermostability, significant methanol tolerance, and showed excellent catalytic efficiencies (kcat/Km) towards 7-oxo-lithocholic acid (7-oxo-LCA) and NADH (70.8 mM-1s-1 and 31.8 mM-1s-1, respectively). Molecular docking and mutational analyses revealed that Asp42 could play a considerable role in NADH binding and recognition. Coupling with a glucose dehydrogenase for NADH regeneration, up to 20 mM 7-oxo-LCA could be completely transformed to UDCA within 90 min by Cle7β-HSDH. This study provides an efficient approach for mining promising enzymes from genomic databases for cost-effective biotechnological applications.
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Affiliation(s)
- Bin Huang
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Kai Yang
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Charles Amanze
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Zhen Yan
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Hunan 410083, China.
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2
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Yin W, Xu T, Altai M, Oroujeni M, Zhang J, Vorobyeva A, Vorontsova O, Vtorushin SV, Tolmachev V, Gräslund T, Orlova A. The Influence of Domain Permutations of an Albumin-Binding Domain-Fused HER2-Targeting Affibody-Based Drug Conjugate on Tumor Cell Proliferation and Therapy Efficacy. Pharmaceutics 2021; 13:1974. [PMID: 34834389 PMCID: PMC8617914 DOI: 10.3390/pharmaceutics13111974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/08/2021] [Accepted: 11/16/2021] [Indexed: 01/01/2023] Open
Abstract
Human epidermal growth factor receptor 2 (HER2) is a clinically validated target for breast cancer therapy. Previously, a drug-fused HER2-targeting affinity protein construct successfully extended the survival of mice bearing HER2-expressing xenografts. The aim of this study was to evaluate the influence of the number and positioning of the protein domains in the drug conjugate. Seven HER2-targeting affibody-based constructs, including one or two affibody molecules (Z) with or without an albumin-binding domain (ABD), namely Z, Z-ABD, ABD-Z, Z-Z, Z-Z-ABD, Z-ABD-Z, and ABD-Z-Z, were evaluated on their effects on cell growth, in vivo targeting, and biodistribution. The biodistribution study demonstrated that the monomeric constructs had longer blood retention and lower hepatic uptake than the dimeric ones. A dimeric construct, specifically ABD-Z-Z, could stimulate the proliferation of HER2 expressing SKOV-3 cells in vitro and the growth of tumors in vivo, whereas the monomeric construct Z-ABD could not. These two constructs demonstrated a therapeutic effect when coupled to mcDM1; however, the effect was more pronounced for the non-stimulating Z-ABD. The median survival of the mice treated with Z-ABD-mcDM1 was 63 days compared to the 37 days for those treated with ABD-Z-Z-mcDM1 or for the control animals. Domain permutation of an ABD-fused HER2-targeting affibody-based drug conjugate significantly influences tumor cell proliferation and therapy efficacy. The monomeric conjugate Z-ABD is the most promising format for targeted delivery of the cytotoxic drug DM1.
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Affiliation(s)
- Wen Yin
- Department of Protein Science, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden; (W.Y.); (J.Z.)
| | - Tianqi Xu
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 37 Uppsala, Sweden; (T.X.); (M.A.); (M.O.); (A.V.); (O.V.); (V.T.)
| | - Mohamed Altai
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 37 Uppsala, Sweden; (T.X.); (M.A.); (M.O.); (A.V.); (O.V.); (V.T.)
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, 221 84 Lund, Sweden
| | - Maryam Oroujeni
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 37 Uppsala, Sweden; (T.X.); (M.A.); (M.O.); (A.V.); (O.V.); (V.T.)
| | - Jie Zhang
- Department of Protein Science, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden; (W.Y.); (J.Z.)
| | - Anzhelika Vorobyeva
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 37 Uppsala, Sweden; (T.X.); (M.A.); (M.O.); (A.V.); (O.V.); (V.T.)
| | - Olga Vorontsova
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 37 Uppsala, Sweden; (T.X.); (M.A.); (M.O.); (A.V.); (O.V.); (V.T.)
| | - Sergey V. Vtorushin
- Pathology Department, Siberian State Medical University, 634050 Tomsk, Russia;
- General and Molecular Pathology Department, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Vladimir Tolmachev
- Department of Immunology, Genetics and Pathology, Uppsala University, 752 37 Uppsala, Sweden; (T.X.); (M.A.); (M.O.); (A.V.); (O.V.); (V.T.)
- Research Centrum for Oncotheranostics, Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, 634050 Tomsk, Russia
| | - Torbjörn Gräslund
- Department of Protein Science, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden; (W.Y.); (J.Z.)
| | - Anna Orlova
- Pathology Department, Siberian State Medical University, 634050 Tomsk, Russia;
- Research Centrum for Oncotheranostics, Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, 634050 Tomsk, Russia
- Department of Medicinal Chemistry, Uppsala University, 751 23 Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, 752 37 Uppsala, Sweden
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3
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Kong XD, Carle V, Díaz-Perlas C, Butler K, Heinis C. Generation of a Large Peptide Phage Display Library by Self-Ligation of Whole-Plasmid PCR Product. ACS Chem Biol 2020; 15:2907-2915. [PMID: 33125222 DOI: 10.1021/acschembio.0c00497] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The success of phage display, used for developing target-specific binders based on peptides and proteins, depends on the size and diversity of the library screened, but generating large libraries of phage-encoded polypeptides remains challenging. New peptide phage display libraries developed in recent years rarely contained more than 1 billion clones, which appears to have become the upper size limit for libraries generated with reasonable effort. Here, we established a strategy based on whole-plasmid PCR and self-ligation to clone a library with more than 2 × 1010 members. The enormous library size could be obtained through amplifying the entire vector DNA by PCR, which omitted the step of vector isolation from bacterial cells, and through appending DNA coding for the peptide library via a PCR primer, which enabled efficient DNA circularization by end-ligation to facilitate the difficult step of vector-insertion of DNA fragments. Panning the peptide repertoires against a target yielded high-affinity ligands and validated the quality of the library and thus the new library cloning strategy. This simple and efficient strategy places larger libraries within reach for nonspecialist researchers to hopefully expand the possible targets of phage display applications.
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Affiliation(s)
- Xu-Dong Kong
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Vanessa Carle
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Cristina Díaz-Perlas
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Kaycie Butler
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
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4
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Tang L, Su M, Yan J, Xie S, Zhang W. Lid hinge region of Penicillium expansum lipase affects enzyme activity and interfacial activation. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.04.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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5
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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6
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Ruff AJ, Dennig A, Schwaneberg U. To get what we aim for - progress in diversity generation methods. FEBS J 2013; 280:2961-78. [DOI: 10.1111/febs.12325] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Anna J. Ruff
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Germany
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7
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Le Y, Chen H, Zagursky R, Wu JHD, Shao W. Thermostable DNA ligase-mediated PCR production of circular plasmid (PPCP) and its application in directed evolution via in situ error-prone PCR. DNA Res 2013; 20:375-82. [PMID: 23633530 PMCID: PMC3738163 DOI: 10.1093/dnares/dst016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Polymerase chain reaction (PCR) is a powerful method to produce linear DNA fragments. Here we describe the Tma thermostable DNA ligase-mediated PCR production of circular plasmid (PPCP) and its application in directed evolution via in situ error-prone PCR. In this thermostable DNA ligase-mediated whole-plasmid amplification method, the resultant DNA nick between the 5′ end of the PCR primer and the extended newly synthesized DNA 3′ end of each PCR cycle is ligated by Tma DNA ligase, resulting in circular plasmid DNA product that can be directly transformed. The template plasmid DNA is eliminated by ‘selection marker swapping’ upon transformation. When performed under an error-prone condition with Taq DNA polymerase, PPCP allows one-step construction of mutagenesis libraries based on in situ error-prone PCR so that random mutations are introduced into the target gene without altering the expression vector plasmid. A significant difference between PPCP and previously published methods is that PPCP allows exponential amplification of circular DNA. We used this method to create random mutagenesis libraries of a xylanase gene and two cellulase genes. Screening of these libraries resulted in mutant proteins with desired properties, demonstrating the usefulness of in situ error-prone PPCP for creating random mutagenesis libraries for directed evolution.
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Affiliation(s)
- Yilin Le
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
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8
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Parravicini F, Natalello A, Papaleo E, De Gioia L, Doglia SM, Lotti M, Brocca S. Reciprocal influence of protein domains in the cold-adapted acyl aminoacyl peptidase from Sporosarcina psychrophila. PLoS One 2013; 8:e56254. [PMID: 23457536 PMCID: PMC3574126 DOI: 10.1371/journal.pone.0056254] [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: 10/22/2012] [Accepted: 01/07/2013] [Indexed: 11/24/2022] Open
Abstract
Acyl aminoacyl peptidases are two-domain proteins composed by a C-terminal catalytic α/β-hydrolase domain and by an N-terminal β-propeller domain connected through a structural element that is at the N-terminus in sequence but participates in the 3D structure of the C-domain. We investigated about the structural and functional interplay between the two domains and the bridge structure (in this case a single helix named α1-helix) in the cold-adapted enzyme from Sporosarcina psychrophila (SpAAP) using both protein variants in which entire domains were deleted and proteins carrying substitutions in the α1-helix. We found that in this enzyme the inter-domain connection dramatically affects the stability of both the whole enzyme and the β-propeller. The α1-helix is required for the stability of the intact protein, as in other enzymes of the same family; however in this psychrophilic enzyme only, it destabilizes the isolated β-propeller. A single charged residue (E10) in the α1-helix plays a major role for the stability of the whole structure. Overall, a strict interaction of the SpAAP domains seems to be mandatory for the preservation of their reciprocal structural integrity and may witness their co-evolution.
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Affiliation(s)
- Federica Parravicini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Elena Papaleo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Silvia Maria Doglia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- * E-mail: (SB); (ML)
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- * E-mail: (SB); (ML)
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9
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Siloto RM, Weselake RJ. Site saturation mutagenesis: Methods and applications in protein engineering. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2012. [DOI: 10.1016/j.bcab.2012.03.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Dennig A, Shivange AV, Marienhagen J, Schwaneberg U. OmniChange: the sequence independent method for simultaneous site-saturation of five codons. PLoS One 2011; 6:e26222. [PMID: 22039444 PMCID: PMC3198389 DOI: 10.1371/journal.pone.0026222] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 09/22/2011] [Indexed: 12/20/2022] Open
Abstract
Focused mutant library generation methods have been developed to improve mainly "localizable" enzyme properties such as activity and selectivity. Current multi-site saturation methods are restricted by the gene sequence, require subsequent PCR steps and/or additional enzymatic modifications. Here we report, a multiple site saturation mutagenesis method, OmniChange, which simultaneously and efficiently saturates five independent codons. As proof of principle, five chemically cleaved DNA fragments, each carrying one NNK-degenerated codon, were generated and assembled to full gene length in a one-pot-reaction without additional PCR-amplification or use of restriction enzymes or ligases. Sequencing revealed the presence of up to 27 different codons at individual positions, corresponding to 84.4% of the theoretical diversity offered by NNK-degeneration. OmniChange is absolutely sequence independent, does not require a minimal distance between mutated codons and can be accomplished within a day.
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Affiliation(s)
- Alexander Dennig
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Amol V. Shivange
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Jan Marienhagen
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- * E-mail:
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11
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Reetz MT, Zheng H. Manipulating the Expression Rate and Enantioselectivity of an Epoxide Hydrolase by Using Directed Evolution. Chembiochem 2011; 12:1529-35. [DOI: 10.1002/cbic.201100078] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Indexed: 11/06/2022]
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12
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Defining Structural Domains of an Intrinsically Disordered Protein: Sic1, the Cyclin-Dependent Kinase Inhibitor of Saccharomyces cerevisiae. Mol Biotechnol 2010; 47:34-42. [DOI: 10.1007/s12033-010-9309-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Stone EM, Glazer ES, Chantranupong L, Cherukuri P, Breece RM, Tierney DL, Curley SA, Iverson BL, Georgiou G. Replacing Mn(2+) with Co(2+) in human arginase i enhances cytotoxicity toward l-arginine auxotrophic cancer cell lines. ACS Chem Biol 2010; 5:333-42. [PMID: 20050660 DOI: 10.1021/cb900267j] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Replacing the two Mn(2+) ions normally present in human Arginase I with Co(2+) resulted in a significantly lowered K(M) value without a concomitant reduction in k(cat). In addition, the pH dependence of the reaction was shifted from a pK(a) of 8.5 to a pK(a) of 7.5. The combination of these effects led to a 10-fold increase in overall catalytic activity (k(cat)/K(M)) at pH 7.4, close to the pH of human serum. Just as important for therapeutic applications, Co(2+) substitution lead to significantly increased serum stability of the enzyme. Our data can be explained by direct coordination of l-Arg to one of the Co(2+) ions during reaction, consistent with previously reported model studies. In vitro cytotoxicity experiments verified that the Co(2+)-substituted human Arg I displays an approximately 12- to 15-fold lower IC(50) value for the killing of human hepatocellular carcinoma and melanoma cell lines and thus constitutes a promising new candidate for the treatment of l-Arg auxotrophic tumors.
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Affiliation(s)
- Everett M. Stone
- Departments of Chemical Engineering, Biomedical Engineering, Molecular Genetics and Microbiology
| | - Evan S. Glazer
- Department of Surgical Oncology, University of Texas, M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Lynne Chantranupong
- Departments of Chemical Engineering, Biomedical Engineering, Molecular Genetics and Microbiology
| | - Paul Cherukuri
- Department of Surgical Oncology, University of Texas, M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Robert M. Breece
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - David L. Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Steven A. Curley
- Department of Surgical Oncology, University of Texas, M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Brent L. Iverson
- Institute for Cell and Institute for Molecular and Cell Biology
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712
| | - George Georgiou
- Departments of Chemical Engineering, Biomedical Engineering, Molecular Genetics and Microbiology
- Institute for Cell and Institute for Molecular and Cell Biology
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14
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Brocca S, Samalíková M, Uversky VN, Lotti M, Vanoni M, Alberghina L, Grandori R. Order propensity of an intrinsically disordered protein, the cyclin-dependent-kinase inhibitor Sic1. Proteins 2009; 76:731-46. [PMID: 19280601 DOI: 10.1002/prot.22385] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Intrinsically disordered proteins (IDPs) carry out important biological functions and offer an instructive model system for folding and binding studies. However, their structural characterization in the absence of interactors is hindered by their highly dynamic conformation. The cyclin-dependent-kinase inhibitor (Cki) Sic1 from Saccharomyces cerevisiae is a key regulator of the yeast cell cycle, which controls entrance into S phase and coordination between cell growth and proliferation. Its last 70 out of 284 residues display functional and structural homology to the inhibitory domain of mammalian p21 and p27. Sic1 has escaped systematic structural characterization until now. Here, complementary biophysical methods are applied to the study of conformational properties of pure Sic1 in solution. Based on sequence analysis, gel filtration, circular dichroism (CD), electrospray-ionization mass spectrometry (ESI-MS), and limited proteolysis, it can be concluded that the whole molecule exists in a highly disordered state and can, therefore, be classified as an IDP. However, the results of these experiments indicate, at the same time, that the protein displays some content in secondary and tertiary structure, having properties similar to those of molten globules or premolten globules. Proteolysis-hypersensitive sites cluster at the N-terminus and in the middle of the molecule, whereas the most structured region resides at the C-terminus, including part of the inhibitory domain and the casein-kinase-2 (CK2) phosphorylation target S201. The mutations S201A and S201E, which are known to affect Sic1 function, do not have significant effects on the conformational properties of the pure protein.
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Affiliation(s)
- Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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15
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Parikh MR, Matsumura I. Site-saturation mutagenesis is more efficient than DNA shuffling for the directed evolution of beta-fucosidase from beta-galactosidase. J Mol Biol 2005; 352:621-8. [PMID: 16095606 PMCID: PMC2014722 DOI: 10.1016/j.jmb.2005.07.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2005] [Revised: 06/30/2005] [Accepted: 07/11/2005] [Indexed: 11/29/2022]
Abstract
Protein engineers use a variety of mutagenic strategies to adapt enzymes to novel substrates. Directed evolution techniques (random mutagenesis and high-throughput screening) offer a systematic approach to the management of protein complexity. This sub-discipline was galvanized by the invention of DNA shuffling, a procedure that randomly recombines point mutations in vitro. In one influential study, Escherichia coli beta-galactosidase (BGAL) variants with enhanced beta-fucosidase activity (tenfold increase in k(cat)/K(M) in reactions with the novel para-nitrophenyl-beta-d-fucopyranoside substrate; 39-fold decrease in reactivity with the "native"para-nitrophenyl-beta-d-galactopyranoside substrate) were evolved in seven rounds of DNA shuffling and screening. Here, we show that a single round of site-saturation mutagenesis and screening enabled the identification of beta-fucosidases that are significantly more active (180-fold increase in k(cat)/K(M) in reactions with the novel substrate) and specific (700,000-fold inversion of specificity) than the best variants in the previous study. Site-saturation mutagenesis thus proved faster, less resource-intensive and more effective than DNA shuffling for this particular evolutionary pathway.
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Affiliation(s)
| | - Ichiro Matsumura
- *Corresponding author. E-mail address of the corresponding author:
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Directed enzyme evolution: Bridging the gap between natural enzymes and commercial applications. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.bioeng.2005.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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