1
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Tan DZJ, Fung V, Sun T, Tian K, Li Z, Zhou K. Developing a Nanopore Sequencing Workflow for Protein Engineering Applications. ACS Synth Biol 2023; 12:2041-2050. [PMID: 37403232 DOI: 10.1021/acssynbio.3c00087] [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] [Indexed: 07/06/2023]
Abstract
Sequencing plays a critical role in protein engineering, where the genetic information encoding for a desired mutation can be identified. We evaluated the performance of two commercially available NGS technologies (Illumina NGS and nanopore sequencing) on the available mutant libraries that were either previously constructed for other protein engineering projects or constructed in-house for this study. The sequencing results from Illumina sequencing indicated that a substantial proportion of the reads exhibited strand exchange, which mixed information of different mutants. When nanopore sequencing was used, the occurrence of strand exchange was substantially reduced compared with that of Illumina sequencing. We then developed a new library preparation workflow for nanopore sequencing and were successful in further reducing the incidence of strand exchange. The optimized workflow was successfully used to aid selection of improved alcohol dehydrogenase mutants in cells where their activities were coupled with the cell growth rate. The workflow quantified the enrichment fold change of most mutants in the library (size = 1728) in the growth-based selection passaging. A mutant that was >500% more active than its parent variant was identified based on the fold change data but not with the absolute abundance data (random sampling of the passaged cells), highlighting the usefulness of this rapid and affordable sequencing workflow in protein engineering.
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Affiliation(s)
- Daniel Zhi Jun Tan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Vincent Fung
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Tao Sun
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Kaiyuan Tian
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Kang Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
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2
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Yang Y, Liu S, Luo Y, Wang B, Wang J, Li J, Li J, Ye B, Wang Y, Xi JJ. High-throughput saturation mutagenesis generates a high-affinity antibody against SARS-CoV-2 variants using protein surface display assay on a human cell. PLoS Pathog 2023; 19:e1011119. [PMID: 36724179 PMCID: PMC9891525 DOI: 10.1371/journal.ppat.1011119] [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: 07/29/2022] [Accepted: 01/12/2023] [Indexed: 02/02/2023] Open
Abstract
As new mutations continue to emerge, the ability of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus to evade the human immune system and neutralizing antibodies remains a huge challenge for vaccine development and antibody research. The majority of neutralizing antibodies have reduced or lost activity against SARS-CoV-2 variants. In this study, we reported a novel protein surface display system on a mammalian cell for obtaining a higher-affinity antibody in high-throughput manner. Using a saturation mutagenesis strategy through integrating microarray-based oligonucleotide synthesis and single-cell screening assay, we generated a group of new antibodies against diverse prevalent SARS-CoV-2 variants through high-throughput screening the human antibody REGN10987 within 2 weeks. The affinity of those optimized antibodies to seven prevalent mutants was greatly improved, and the EC50 values were no higher than 5 ng/mL. These results demonstrate the robustness of our screening system in the rapid generation of an antibody with higher affinity against a new SARS-CoV-2 variant, and provides a potential application to other protein molecular interactions.
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Affiliation(s)
- Ye Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Shuo Liu
- Graduate School of Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Yufeng Luo
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Bolun Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Junyi Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Juan Li
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Jiaxin Li
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Buqing Ye
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Jianzhong Jeff Xi
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
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3
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Wang B, Zhao J, Liu S, Feng J, Luo Y, He X, Wang Y, Ge F, Wang J, Ye B, Huang W, Bo X, Wang Y, Xi JJ. ACE2 decoy receptor generated by high-throughput saturation mutagenesis efficiently neutralizes SARS-CoV-2 and its prevalent variants. Emerg Microbes Infect 2022; 11:1488-1499. [PMID: 35587428 PMCID: PMC9176695 DOI: 10.1080/22221751.2022.2079426] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The recent global pandemic was a spillover from the SARS-CoV-2 virus. Viral entry involves the receptor binding domain (RBD) of the viral spike protein interacting with the protease domain (PD) of the cellular receptor, ACE2. We hereby present a comprehensive mutational landscape of the effects of ACE2-PD point mutations on RBD-ACE2 binding using a saturation mutagenesis approach based on microarray-based oligo synthesis and a single-cell screening assay. We observed that changes in glycosylation sites and directly interacting sites of ACE2-PD significantly influenced ACE2-RBD binding. We further engineered an ACE2 decoy receptor with critical point mutations, D30I, L79W, T92N, N322V, and K475F, named C4-1. C4-1 shows a 200-fold increase in neutralization for the SARS-CoV-2 D614G pseudotyped virus compared to wild-type soluble ACE2 and a sevenfold increase in binding affinity to wild-type spike compared to the C-terminal Ig-Fc fused wild-type soluble ACE2. Moreover, C4-1 efficiently neutralized prevalent variants, especially the omicron variant (EC50=16 ng/mL), and rescued monoclonal antibodies, vaccine, and convalescent sera neutralization from viral immune-escaping. We hope to next investigate translating the therapeutic potential of C4-1 for the treatment of SARS-CoV-2.
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Affiliation(s)
- Bolun Wang
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Junxuan Zhao
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Shuo Liu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Jingyuan Feng
- College of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Yufeng Luo
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Xinyu He
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Yanmin Wang
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Feixiang Ge
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Junyi Wang
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Buqing Ye
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing, People's Republic of China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Jianzhong Jeff Xi
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
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4
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Gisdon FJ, Kynast JP, Ayyildiz M, Hine AV, Plückthun A, Höcker B. Modular peptide binders - development of a predictive technology as alternative for reagent antibodies. Biol Chem 2022; 403:535-543. [PMID: 35089661 DOI: 10.1515/hsz-2021-0384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/11/2022] [Indexed: 11/15/2022]
Abstract
Current biomedical research and diagnostics critically depend on detection agents for specific recognition and quantification of protein molecules. Monoclonal antibodies have been used for this purpose over decades and facilitated numerous biological and biomedical investigations. Recently, however, it has become apparent that many commercial reagent antibodies lack specificity or do not recognize their target at all. Thus, synthetic alternatives are needed whose complex designs are facilitated by multidisciplinary approaches incorporating experimental protein engineering with computational modeling. Here, we review the status of such an engineering endeavor based on the modular armadillo repeat protein scaffold and discuss challenges in its implementation.
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Affiliation(s)
- Florian J Gisdon
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
| | - Josef P Kynast
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
| | - Merve Ayyildiz
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
| | - Anna V Hine
- College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
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5
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Chembath A, Wagstaffe BPG, Ashraf M, Amaral MMF, Frigotto L, Hine AV. Nondegenerate Saturation Mutagenesis: Library Construction and Analysis via MAX and ProxiMAX Randomization. Methods Mol Biol 2022; 2461:19-41. [PMID: 35727442 DOI: 10.1007/978-1-0716-2152-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Protein engineering can enhance desirable features and improve performance outside of the natural context. Several strategies have been adopted over the years for gene diversification, and engineering of modular proteins in particular is most effective when a high-throughput, library-based approach is employed. Nondegenerate saturation mutagenesis plays a dynamic role in engineering proteins by targeting multiple codons to generate massively diverse gene libraries. Herein, we describe the nondegenerate saturation mutagenesis techniques that we have developed for contiguous (ProxiMAX) and noncontiguous (MAX) randomized codon generation to create precisely defined, diverse gene libraries, in the context of other fully nondegenerate strategies. ProxiMAX randomization comprises saturation cycling with repeated cycles of blunt-ended ligation, type IIS restriction, and PCR amplification, and is now a commercially automated process predominantly used for antibody library generation. MAX randomization encompasses a manual process of selective hybridisation between individual custom oligonucleotide mixes and a conventionally randomized template and is principally employed in the research laboratory setting, to engineer alpha helical proteins and active sites of enzymes. DNA libraries generated using either technology create high-throughput amino acid substitutions via codon randomization, to generate genetically diverse clones.
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Affiliation(s)
- Anupama Chembath
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham, UK
| | | | - Mohammed Ashraf
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham, UK
| | - Marta M Ferreira Amaral
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham, UK
- Bicycle Therapeutics, Cambridge, UK
| | | | - Anna V Hine
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham, UK.
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6
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Currin A, Parker S, Robinson CJ, Takano E, Scrutton NS, Breitling R. The evolving art of creating genetic diversity: From directed evolution to synthetic biology. Biotechnol Adv 2021; 50:107762. [PMID: 34000294 PMCID: PMC8299547 DOI: 10.1016/j.biotechadv.2021.107762] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/21/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022]
Abstract
The ability to engineer biological systems, whether to introduce novel functionality or improved performance, is a cornerstone of biotechnology and synthetic biology. Typically, this requires the generation of genetic diversity to explore variations in phenotype, a process that can be performed at many levels, from single molecule targets (i.e., in directed evolution of enzymes) to whole organisms (e.g., in chassis engineering). Recent advances in DNA synthesis technology and automation have enhanced our ability to create variant libraries with greater control and throughput. This review highlights the latest developments in approaches to create such a hierarchy of diversity from the enzyme level to entire pathways in vitro, with a focus on the creation of combinatorial libraries that are required to navigate a target's vast design space successfully to uncover significant improvements in function.
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Affiliation(s)
- Andrew Currin
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
| | - Steven Parker
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Christopher J Robinson
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S Scrutton
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
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7
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Tizei PAG, Harris E, Withanage S, Renders M, Pinheiro VB. A novel framework for engineering protein loops exploring length and compositional variation. Sci Rep 2021; 11:9134. [PMID: 33911147 PMCID: PMC8080606 DOI: 10.1038/s41598-021-88708-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/12/2021] [Indexed: 02/02/2023] Open
Abstract
Insertions and deletions (indels) are known to affect function, biophysical properties and substrate specificity of enzymes, and they play a central role in evolution. Despite such clear significance, this class of mutation remains an underexploited tool in protein engineering with few available platforms capable of systematically generating and analysing libraries of varying sequence composition and length. We present a novel DNA assembly platform (InDel assembly), based on cycles of endonuclease restriction digestion and ligation of standardised dsDNA building blocks, that can generate libraries exploring both composition and sequence length variation. In addition, we developed a framework to analyse the output of selection from InDel-generated libraries, combining next generation sequencing and alignment-free strategies for sequence analysis. We demonstrate the approach by engineering the well-characterized TEM-1 β-lactamase Ω-loop, involved in substrate specificity, identifying multiple novel extended spectrum β-lactamases with loops of modified length and composition-areas of the sequence space not previously explored. Together, the InDel assembly and analysis platforms provide an efficient route to engineer protein loops or linkers where sequence length and composition are both essential functional parameters.
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Affiliation(s)
- Pedro A. G. Tizei
- grid.83440.3b0000000121901201Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Emma Harris
- grid.4464.20000 0001 2161 2573Department of Biological Sciences, University of London, Malet Street, Birkbeck, WC1E 7HX UK
| | - Shamal Withanage
- grid.415751.3KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Marleen Renders
- grid.415751.3KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Vitor B. Pinheiro
- grid.83440.3b0000000121901201Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK ,grid.4464.20000 0001 2161 2573Department of Biological Sciences, University of London, Malet Street, Birkbeck, WC1E 7HX UK ,grid.415751.3KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
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8
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Lindenburg L, Huovinen T, van de Wiel K, Herger M, Snaith MR, Hollfelder F. Split & mix assembly of DNA libraries for ultrahigh throughput on-bead screening of functional proteins. Nucleic Acids Res 2020; 48:e63. [PMID: 32383757 PMCID: PMC7293038 DOI: 10.1093/nar/gkaa270] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/02/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
Site-saturation libraries reduce protein screening effort in directed evolution campaigns by focusing on a limited number of rationally chosen residues. However, uneven library synthesis efficiency leads to amino acid bias, remedied at high cost by expensive custom synthesis of oligonucleotides, or through use of proprietary library synthesis platforms. To address these shortcomings, we have devised a method where DNA libraries are constructed on the surface of microbeads by ligating dsDNA fragments onto growing, surface-immobilised DNA, in iterative split-and-mix cycles. This method-termed SpliMLiB for Split-and-Mix Library on Beads-was applied towards the directed evolution of an anti-IgE Affibody (ZIgE), generating a 160,000-membered, 4-site, saturation library on the surface of 8 million monoclonal beads. Deep sequencing confirmed excellent library balance (5.1% ± 0.77 per amino acid) and coverage (99.3%). As SpliMLiB beads are monoclonal, they were amenable to direct functional screening in water-in-oil emulsion droplets with cell-free expression. A FACS-based sorting of the library beads allowed recovery of hits improved in Kd over wild-type ZIgE by up to 3.5-fold, while a consensus mutant of the best hits provided a 10-fold improvement. With SpliMLiB, directed evolution workflows are accelerated by integrating high-quality DNA library generation with an ultra-high throughput protein screening platform.
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Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Tuomas Huovinen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Kayleigh van de Wiel
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Michael Herger
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
- AstraZeneca Medimmune Cambridge, Antibody Discovery and Protein Engineering, Cambridge, UK
| | - Michael R Snaith
- AstraZeneca Medimmune Cambridge, Antibody Discovery and Protein Engineering, Cambridge, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
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9
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Small design from big alignment: engineering proteins with multiple sequence alignment as the starting point. Biotechnol Lett 2020; 42:1305-1315. [PMID: 32430802 DOI: 10.1007/s10529-020-02914-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/14/2020] [Indexed: 02/08/2023]
Abstract
Multiple sequence alignment (MSA) is a fundamental way to gain information that cannot be obtained from the analysis of any individual sequence included in the alignment. It provides ways to investigate the relationship between sequence and function from a perspective of evolution. Thus, the MSA of proteins can be employed as a reference for protein engineering. In this paper, we reviewed the recent advances to highlight how protein engineering was benefited from the MSA of proteins. These methods include (1) engineering the thermostability or solubility of proteins by making it closer to the consensus sequence of the alignment through introducing site mutations; (2) structure-based engineering proteins with comparative modeling; (3) creating paleoenzymes featured with high thermostability and promiscuity by constructing the ancestral sequences derived from multiple sequence alignment; and (4) incorporating site-mutations targeting the evolutionarily coupled sites identified from multiple sequence alignment.
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10
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Bozovičar K, Bratkovič T. Evolving a Peptide: Library Platforms and Diversification Strategies. Int J Mol Sci 2019; 21:E215. [PMID: 31892275 PMCID: PMC6981544 DOI: 10.3390/ijms21010215] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/22/2019] [Accepted: 12/25/2019] [Indexed: 12/22/2022] Open
Abstract
Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.
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Affiliation(s)
| | - Tomaž Bratkovič
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, SI-1000 Ljubljana, Slovenia;
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11
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Lim CC, Choong YS, Lim TS. Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation. Int J Mol Sci 2019; 20:E1861. [PMID: 30991723 PMCID: PMC6515083 DOI: 10.3390/ijms20081861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Antibodies leverage on their unique architecture to bind with an array of antigens. The strength of interaction has a direct relation to the affinity of the antibodies towards the antigen. In vivo affinity maturation is performed through multiple rounds of somatic hypermutation and selection in the germinal centre. This unique process involves intricate sequence rearrangements at the gene level via molecular mechanisms. The emergence of in vitro display technologies, mainly phage display and recombinant DNA technology, has helped revolutionize the way antibody improvements are being carried out in the laboratory. The adaptation of molecular approaches in vitro to replicate the in vivo processes has allowed for improvements in the way recombinant antibodies are designed and tuned. Combinatorial libraries, consisting of a myriad of possible antibodies, are capable of replicating the diversity of the natural human antibody repertoire. The isolation of target-specific antibodies with specific affinity characteristics can also be accomplished through modification of stringent protocols. Despite the ability to screen and select for high-affinity binders, some 'fine tuning' may be required to enhance antibody binding in terms of its affinity. This review will provide a brief account of phage display technology used for antibody generation followed by a summary of different combinatorial library characteristics. The review will focus on available strategies, which include molecular approaches, next generation sequencing, and in silico approaches used for antibody affinity maturation in both therapeutic and diagnostic applications.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
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12
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A C-terminal cysteine residue is required for peptide-based inhibition of the NGF/TrkA interaction at nM concentrations: implications for peptide-based analgesics. Sci Rep 2019; 9:930. [PMID: 30700786 PMCID: PMC6353895 DOI: 10.1038/s41598-018-37585-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/07/2018] [Indexed: 11/12/2022] Open
Abstract
Inhibition of the NGF/TrkA interaction presents an interesting alternative to the use of non-steroidal anti-inflammatories and/or opioids for the control of inflammatory, chronic and neuropathic pain. Most prominent of the current approaches to this therapy is the antibody Tanezumab, which is a late-stage development humanized monoclonal antibody that targets NGF. We sought to determine whether peptides might similarly inhibit the NGF/TrkA interaction and so serve as future therapeutic leads. Starting from two peptides that inhibit the NGF/TrkA interaction, we sought to eliminate a cysteine residue close to the C-terminal of both sequences, by an approach of mutagenic analysis and saturation mutagenesis of mutable residues. Elimination of cysteine from a therapeutic lead is desirable to circumvent manufacturing difficulties resulting from oxidation. Our analyses determined that the cysteine residue is not required for NGF binding, but is essential for inhibition of the NGF/TrkA interaction at pharmacologically relevant peptide concentrations. We conclude that a cysteine residue is required within potential peptide-based therapeutic leads and hypothesise that these peptides likely act as dimers, mirroring the dimeric structure of the TrkA receptor.
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13
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Mason DM, Weber CR, Parola C, Meng SM, Greiff V, Kelton WJ, Reddy ST. High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis. Nucleic Acids Res 2018; 46:7436-7449. [PMID: 29931269 PMCID: PMC6101513 DOI: 10.1093/nar/gky550] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 12/26/2022] Open
Abstract
Antibody engineering is often performed to improve therapeutic properties by directed evolution, usually by high-throughput screening of phage or yeast display libraries. Engineering antibodies in mammalian cells offer advantages associated with expression in their final therapeutic format (full-length glycosylated IgG); however, the inability to express large and diverse libraries severely limits their potential throughput. To address this limitation, we have developed homology-directed mutagenesis (HDM), a novel method which extends the concept of CRISPR/Cas9-mediated homology-directed repair (HDR). HDM leverages oligonucleotides with degenerate codons to generate site-directed mutagenesis libraries in mammalian cells. By improving HDR to a robust efficiency of 15-35% and combining mammalian display screening with next-generation sequencing, we validated this approach can be used for key applications in antibody engineering at high-throughput: rational library construction, novel variant discovery, affinity maturation and deep mutational scanning (DMS). We anticipate that HDM will be a valuable tool for engineering and optimizing antibodies in mammalian cells, and eventually enable directed evolution of other complex proteins and cellular therapeutics.
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Affiliation(s)
- Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
- Life Science Graduate School, Systems Biology, ETH Zürich, University of Zurich, Zurich 8057, Switzerland
| | - Simon M Meng
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - William J Kelton
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
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14
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Baxter D, Ullman CG, Frigotto L, Mason JM. Exploiting Overlapping Advantages of In Vitro and In Cellulo Selection Systems to Isolate a Novel High-Affinity cJun Antagonist. ACS Chem Biol 2017; 12:2579-2588. [PMID: 28880076 DOI: 10.1021/acschembio.7b00693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have combined two peptide library-screening systems, exploiting the benefits offered by both to select novel antagonistic agents of cJun. CIS display is an in vitro cell-free system that allows very large libraries (≤1014) to be interrogated. However, affinity-based screening conditions can poorly reflect those relevant to therapeutic application, particularly for difficult intracellular targets, and can lead to false positives. In contrast, an in cellulo screening system such as the Protein-fragment Complementation Assay (PCA) selects peptides with high target affinity while additionally profiling for target specificity, protease resistance, solubility, and lack of toxicity in a more relevant context. A disadvantage is the necessity to transform cells, limiting library sizes that can be screened to ≤106. However, by combining both cell-free and cell-based systems, we isolated a peptide (CPW) from a ∼1010 member library, which forms a highly stable interaction with cJun (Tm = 63 °C, Kd = 750 nM, ΔG = -8.2 kcal/mol) using the oncogenic transcriptional regulator Activator Protein-1 (AP-1) as our exemplar target. In contrast, CIS display alone selected a peptide with low affinity for cJun (Tm = 34 °C, Kd = 25 μM, ΔG = -6.2 kcal/mol), highlighting the benefit of CIS → PCA. Furthermore, increased library size with CIS → PCA vs PCA alone allows the freedom to introduce noncanonical options, such as interfacial aromatics, and solvent exposed options that may allow the molecule to explore alternative structures and interact with greater affinity and efficacy with the target. CIS → PCA therefore offers significant potential as a peptide-library screening platform by synergistically combining the relative attributes of both assays to generate therapeutically interesting compounds that may otherwise not be identified.
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Affiliation(s)
- Daniel Baxter
- Dept
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Christopher G. Ullman
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Laura Frigotto
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jody M. Mason
- Dept
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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15
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Ferreira Amaral MM, Frigotto L, Hine AV. Beyond the Natural Proteome: Nondegenerate Saturation Mutagenesis-Methodologies and Advantages. Methods Enzymol 2017; 585:111-133. [PMID: 28109425 DOI: 10.1016/bs.mie.2016.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Beyond the natural proteome, high-throughput mutagenesis offers the protein engineer an opportunity to "tweak" the wild-type activity of a protein to create a recombinant protein with required attributes. Of the various approaches available, saturation mutagenesis is one of the core techniques employed by protein engineers, and in recent times, nondegenerate saturation mutagenesis is emerging as the approach of choice. This review compares the current methodologies available for conducting nondegenerate saturation mutagenesis with traditional, degenerate saturation and briefly outlines the options available for screening the resulting libraries, to discover a novel protein with the required activity and/or specificity.
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Affiliation(s)
- M M Ferreira Amaral
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom
| | - L Frigotto
- Isogenica Ltd., The Mansion, Chesterford Research Park, Essex, United Kingdom
| | - A V Hine
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom.
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16
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Mingo J, Erramuzpe A, Luna S, Aurtenetxe O, Amo L, Diez I, Schepens JTG, Hendriks WJAJ, Cortés JM, Pulido R. One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections. PLoS One 2016; 11:e0160972. [PMID: 27548698 PMCID: PMC4993582 DOI: 10.1371/journal.pone.0160972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/27/2016] [Indexed: 12/30/2022] Open
Abstract
Site-directed mutagenesis (SDM) is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis.
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Affiliation(s)
- Janire Mingo
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Asier Erramuzpe
- Quantitative Biomedicine Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Sandra Luna
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Olaia Aurtenetxe
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Laura Amo
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Ibai Diez
- Quantitative Biomedicine Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Jan T. G. Schepens
- Department of Cell Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Wiljan J. A. J. Hendriks
- Department of Cell Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Jesús M. Cortés
- Quantitative Biomedicine Unit, Biocruces Health Research Institute, Barakaldo, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- * E-mail: ;
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17
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Popova B, Schubert S, Bulla I, Buchwald D, Kramer W. A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules. PLoS One 2015; 10:e0136778. [PMID: 26355961 PMCID: PMC4565649 DOI: 10.1371/journal.pone.0136778] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/08/2015] [Indexed: 11/19/2022] Open
Abstract
A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis.
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Affiliation(s)
- Blagovesta Popova
- Department Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Department Molecular Genetics and Preparative Molecular Biology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- * E-mail:
| | - Steffen Schubert
- Department Molecular Genetics and Preparative Molecular Biology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Department Dermatology, Venereology and Allergology, University Medical Center, Göttingen, Germany
- Information Network of Departments of Dermatology (IVDK), Göttingen, Germany
| | - Ingo Bulla
- Theoretical Biology and Biophysics, Group T-6, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Institute for Mathematics and Informatics, Universität Greifswald, Greifswald, Germany
- Department Bioinformatics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Daniela Buchwald
- Department Bioinformatics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Neurobiology Laboratory, German Primate Center GmbH, Göttingen, Germany
| | - Wilfried Kramer
- Department Molecular Genetics and Preparative Molecular Biology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Department Molecular Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
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18
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Library construction, selection and modification strategies to generate therapeutic peptide-based modulators of protein-protein interactions. Future Med Chem 2015; 6:2073-92. [PMID: 25531969 DOI: 10.4155/fmc.14.134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In the modern age of proteomics, vast numbers of protein-protein interactions (PPIs) are being identified as causative agents in pathogenesis, and are thus attractive therapeutic targets for intervention. Although traditionally regarded unfavorably as druggable agents relative to small molecules, peptides in recent years have gained considerable attention. Their previous dismissal had been largely due to the susceptibility of unmodified peptides to the barriers and pressures exerted by the circulation, immune system, proteases, membranes and other stresses. However, recent advances in high-throughput peptide isolation techniques, as well as a huge variety of direct modification options and approaches to allow targeted delivery, mean that peptides and their mimetics can now be designed to circumvent many of these traditional barriers. As a result, an increasing number of peptide-based drugs are reaching clinical trials and patients beyond.
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19
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Acevedo-Rocha CG, Reetz MT, Nov Y. Economical analysis of saturation mutagenesis experiments. Sci Rep 2015; 5:10654. [PMID: 26190439 PMCID: PMC4507136 DOI: 10.1038/srep10654] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/20/2015] [Indexed: 11/15/2022] Open
Abstract
Saturation mutagenesis is a powerful technique for engineering proteins, metabolic pathways and genomes. In spite of its numerous applications, creating high-quality saturation mutagenesis libraries remains a challenge, as various experimental parameters influence in a complex manner the resulting diversity. We explore from the economical perspective various aspects of saturation mutagenesis library preparation: We introduce a cheaper and faster control for assessing library quality based on liquid media; analyze the role of primer purity and supplier in libraries with and without redundancy; compare library quality, yield, randomization efficiency, and annealing bias using traditional and emergent randomization schemes based on mixtures of mutagenic primers; and establish a methodology for choosing the most cost-effective randomization scheme given the screening costs and other experimental parameters. We show that by carefully considering these parameters, laboratory expenses can be significantly reduced.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- 1] Department of Organic Synthesis, Max-Planck-Institut für Kohlenforschung, Mulheim, 45470, Germany [2] Department of Chemistry, Philipps-Universität Marburg, 35032, Germany [3] Prokaryotic Small RNA Biology Group, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, 35043, Germany [4] Landes-Offensive zur Entwicklung Wissenschafltich-ökonomischer Exzellenz (LOEWE) Centre for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032, Germany
| | - Manfred T Reetz
- 1] Department of Organic Synthesis, Max-Planck-Institut für Kohlenforschung, Mulheim, 45470, Germany [2] Department of Chemistry, Philipps-Universität Marburg, 35032, Germany
| | - Yuval Nov
- Department of Statistics, University of Haifa, Haifa, 31905, Israel
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20
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Sieber T, Hare E, Hofmann H, Trepel M. Biomathematical description of synthetic peptide libraries. PLoS One 2015; 10:e0129200. [PMID: 26042419 PMCID: PMC4456392 DOI: 10.1371/journal.pone.0129200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 05/07/2015] [Indexed: 12/28/2022] Open
Abstract
Libraries of randomised peptides displayed on phages or viral particles are essential tools in a wide spectrum of applications. However, there is only limited understanding of a library's fundamental dynamics and the influences of encoding schemes and sizes on their quality. Numeric properties of libraries, such as the expected number of different peptides and the library's coverage, have long been in use as measures of a library's quality. Here, we present a graphical framework of these measures together with a library's relative efficiency to help to describe libraries in enough detail for researchers to plan new experiments in a more informed manner. In particular, these values allow us to answer-in a probabilistic fashion-the question of whether a specific library does indeed contain one of the "best" possible peptides. The framework is implemented in a web-interface based on two packages, discreteRV and peptider, to the statistical software environment R. We further provide a user-friendly web-interface called PeLiCa (Peptide Library Calculator, http://www.pelica.org), allowing scientists to plan and analyse their peptide libraries.
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Affiliation(s)
- Timo Sieber
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eric Hare
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Heike Hofmann
- Department of Statistics, Iowa State University, Ames, IA, USA
- * E-mail:
| | - Martin Trepel
- Department of Hematology and Oncology, Augsburg Medical Center, Interdisciplinary Cancer Center, Augsburg, Germany
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21
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Codon-Precise, Synthetic, Antibody Fragment Libraries Built Using Automated Hexamer Codon Additions and Validated through Next Generation Sequencing. Antibodies (Basel) 2015. [DOI: 10.3390/antib4020088] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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22
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Hoebenreich S, Zilly FE, Acevedo-Rocha CG, Zilly M, Reetz MT. Speeding up directed evolution: Combining the advantages of solid-phase combinatorial gene synthesis with statistically guided reduction of screening effort. ACS Synth Biol 2015; 4:317-31. [PMID: 24921161 DOI: 10.1021/sb5002399] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Efficient and economic methods in directed evolution at the protein, metabolic, and genome level are needed for biocatalyst development and the success of synthetic biology. In contrast to random strategies, semirational approaches such as saturation mutagenesis explore the sequence space in a focused manner. Although several combinatorial libraries based on saturation mutagenesis have been reported using solid-phase gene synthesis, direct comparison with traditional PCR-based methods is currently lacking. In this work, we compare combinatorial protein libraries created in-house via PCR versus those generated by commercial solid-phase gene synthesis. Using descriptive statistics and probabilistic distributions on amino acid occurrence frequencies, the quality of the libraries was assessed and compared, revealing that the outsourced libraries are characterized by less bias and outliers than the PCR-based ones. Afterward, we screened all libraries following a traditional algorithm for almost complete library coverage and compared this approach with an emergent statistical concept suggesting screening a lower portion of the protein sequence space. Upon analyzing the biocatalytic landscapes and best hits of all combinatorial libraries, we show that the screening effort could have been reduced in all cases by more than 50%, while still finding at least one of the best mutants.
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Affiliation(s)
- Sabrina Hoebenreich
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Felipe E. Zilly
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Matías Zilly
- Fakultät
für Physik, Universität Duisburg-Essen, Lotharstraße 1, 47048 Duisburg, Germany
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
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23
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MDC-Analyzer: a novel degenerate primer design tool for the construction of intelligent mutagenesis libraries with contiguous sites. Biotechniques 2014; 56:301-2, 304, 306-8, passim. [PMID: 24924390 DOI: 10.2144/000114177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 04/03/2014] [Indexed: 11/23/2022] Open
Abstract
Recent computational and bioinformatics advances have enabled the efficient creation of novel biocatalysts by reducing amino acid variability at hot spot regions. To further expand the utility of this strategy, we present here a tool called Multi-site Degenerate Codon Analyzer (MDC-Analyzer) for the automated design of intelligent mutagenesis libraries that can completely cover user-defined randomized sequences, especially when multiple contiguous and/or adjacent sites are targeted. By initially defining an objective function, the possible optimal degenerate PCR primer profiles could be automatically explored using the heuristic approach of Greedy Best-First-Search. Compared to the previously developed DC-Analyzer, MDC-Analyzer allows for the existence of a small amount of undesired sequences as a tradeoff between the number of degenerate primers and the encoded library size while still providing all the benefits of DC-Analyzer with the ability to randomize multiple contiguous sites. MDC-Analyzer was validated using a series of randomly generated mutation schemes and experimental case studies on the evolution of halohydrin dehalogenase, which proved that the MDC methodology is more efficient than other methods and is particularly well-suited to exploring the sequence space of proteins using data-driven protein engineering strategies.
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