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Robinson JP, Ostafe R, Iyengar SN, Rajwa B, Fischer R. Flow Cytometry: The Next Revolution. Cells 2023; 12:1875. [PMID: 37508539 PMCID: PMC10378642 DOI: 10.3390/cells12141875] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Unmasking the subtleties of the immune system requires both a comprehensive knowledge base and the ability to interrogate that system with intimate sensitivity. That task, to a considerable extent, has been handled by an iterative expansion in flow cytometry methods, both in technological capability and also in accompanying advances in informatics. As the field of fluorescence-based cytomics matured, it reached a technological barrier at around 30 parameter analyses, which stalled the field until spectral flow cytometry created a fundamental transformation that will likely lead to the potential of 100 simultaneous parameter analyses within a few years. The simultaneous advance in informatics has now become a watershed moment for the field as it competes with mature systematic approaches such as genomics and proteomics, allowing cytomics to take a seat at the multi-omics table. In addition, recent technological advances try to combine the speed of flow systems with other detection methods, in addition to fluorescence alone, which will make flow-based instruments even more indispensable in any biological laboratory. This paper outlines current approaches in cell analysis and detection methods, discusses traditional and microfluidic sorting approaches as well as next-generation instruments, and provides an early look at future opportunities that are likely to arise.
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Affiliation(s)
- J Paul Robinson
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Raluca Ostafe
- Molecular Evolution, Protein Engineering and Production Facility (PI4D), Purdue University, West Lafayette, IN 47907, USA
| | | | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Rainer Fischer
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, IN 47907, USA
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Xu G, Yang S. Diverse evolutionary origins of microbial [4 + 2]-cyclases in natural product biosynthesis. Int J Biol Macromol 2021; 182:154-161. [PMID: 33836196 DOI: 10.1016/j.ijbiomac.2021.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
Natural [4 + 2]-cyclases catalyze concerted cycloaddition during biosynthesis of over 400 natural products reported. Microbial [4 + 2]-cyclases are structurally diverse with a broad range of substrates. Thus far, about 52 putative microbial [4 + 2]-cyclases of 13 different types have been characterized, with over 20 crystal structures. However, how these cyclases have evolved during natural product biosynthesis remains elusive. Structural and phylogenetic analyses suggest that these different types of [4 + 2]-cyclases might have diverse evolutionary origins, such as reductases, dehydratases, methyltransferases, oxidases, etc. Divergent evolution of enzyme function might have occurred in these different families. Understanding the independent evolutionary history of these cyclases would provide new insights into their catalysis mechanisms and the biocatalyst design.
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Affiliation(s)
- Gangming Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Suiqun Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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3
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Hydrogen overproducing nitrogenases obtained by random mutagenesis and high-throughput screening. Sci Rep 2016; 6:38291. [PMID: 27910898 PMCID: PMC5133592 DOI: 10.1038/srep38291] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/07/2016] [Indexed: 02/05/2023] Open
Abstract
When produced biologically, especially by photosynthetic organisms, hydrogen gas (H2) is arguably the cleanest fuel available. An important limitation to the discovery or synthesis of better H2-producing enzymes is the absence of methods for the high-throughput screening of H2 production in biological systems. Here, we re-engineered the natural H2 sensing system of Rhodobacter capsulatus to direct the emission of LacZ-dependent fluorescence in response to nitrogenase-produced H2. A lacZ gene was placed under the control of the hupA H2-inducible promoter in a strain lacking the uptake hydrogenase and the nifH nitrogenase gene. This system was then used in combination with fluorescence-activated cell sorting flow cytometry to screen large libraries of nitrogenase Fe protein variants generated by random mutagenesis. Exact correlation between fluorescence emission and H2 production levels was found for all automatically selected strains. One of the selected H2-overproducing Fe protein variants lacked 40% of the wild-type amino acid sequence, a surprising finding for a protein that is highly conserved in nature. We propose that this method has great potential to improve microbial H2 production by allowing powerful approaches such as the directed evolution of nitrogenases and hydrogenases.
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Zhou X, Gao L, Yang G, Liu D, Bai A, Li B, Deng Z, Feng Y. Design of hyperthermophilic lipase chimeras by key motif-directed recombination. Chembiochem 2014; 16:455-62. [PMID: 25530200 DOI: 10.1002/cbic.201402456] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Indexed: 11/12/2022]
Abstract
Recombination of diverse natural evolved domains within a superfamily offers greater opportunity for enzyme function leaps. How to recombine protein modules from distant parents with less disruption in cross-interfaces is a challenging issue. Here, we identified the existence of a key motif, the sequence VVSVN(D)YR, within a structural motif ψ loop in the α/β-hydrolase fold superfamily, by using a MEME server and the PROMOTIF program. To obtain thermostable lipase-like enzymes, two chimeras were engineered at the key motif regions through recombination of domains from a mesophilic lipase and a hyperthermophilic esterase/peptidase with amino acid identity less than 21 %. The chimeras retained the desirable substrate preference of their mesophilic parent and exhibited more than 100-fold increased thermostability at 50 °C. Through site-directed mutation, we further improved activity of the chimera by 4.6-fold. The recombination strategy presented here enables the creation of novel catalysts.
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Affiliation(s)
- Xiaoli Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240 (P. R. China); Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130023 (P. R. China)
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5
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Acevedo-Rocha CG, Agudo R, Reetz MT. Directed evolution of stereoselective enzymes based on genetic selection as opposed to screening systems. J Biotechnol 2014; 191:3-10. [DOI: 10.1016/j.jbiotec.2014.04.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/26/2014] [Accepted: 04/07/2014] [Indexed: 01/25/2023]
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6
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Kaltenbach M, Tokuriki N. Dynamics and constraints of enzyme evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:468-87. [DOI: 10.1002/jez.b.22562] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Miriam Kaltenbach
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
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7
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Lee YJ, Lee DH, Jeong KJ. Enhanced production of human full-length immunoglobulin G1 in the periplasm of Escherichia coli. Appl Microbiol Biotechnol 2013; 98:1237-46. [PMID: 24270917 DOI: 10.1007/s00253-013-5390-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/05/2013] [Accepted: 11/07/2013] [Indexed: 11/29/2022]
Abstract
Monoclonal antibodies are currently the most important pharmaceutical proteins, and the economic production of functional immunoglobulin G (IgG) is an important issue in biotechnology. Recent successes in the development of aglycosylated IgG variants that do not require glycosylation for effector functions have increased the use of Escherichia coli as an alternative host for economic production of IgG, instead of traditional mammalian host expression systems. Here, we have developed a new E. coli host-vector system for the high-level production of full-length IgG1 by examining (1) E. coli strains, (2) modification of 5' untranslated region sequences, and (3) co-expression of periplasmic foldase. With the engineered host-vector system, fed-batch cultivations were conducted at two different conditions, and under optimized conditions, up to 362 mg/L of full-length IgG1 could be produced in a relatively short-time (22 h) cultivation. The fully assembled IgG1 from fed-batch cultivation was purified with high purity and yield. With the purified IgG1, the specific bindings to an antigen, anthrax toxin PA, and to human neonatal Fc receptor were successfully demonstrated.
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Affiliation(s)
- Yong Jae Lee
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Republic of Korea
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8
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Bioprospecting open reading frames for peptide effectors. Methods Mol Biol 2013. [PMID: 24146398 DOI: 10.1007/978-1-62703-673-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recent successes in the development of small-molecule antagonists of protein-protein interactions designed based on co-crystal structures of peptides bound to their biological targets confirm that short peptides derived from interacting proteins can be high-value ligands for pharmacologic validation of targets and for identification of druggable sites. Evolved sequence space is likely to be enriched for interacting peptides, but identifying minimal peptide effectors within genomic sequence can be labor intensive. Here we describe the use of incremental truncation to diversify genetic material on the scale of open reading frames into comprehensive libraries of constituent peptides. The approach is capable of generating peptides derived from both continuous and discontinuous sequence elements, and is compatible with the expression of free linear or backbone cyclic peptides, with peptides tethered to amino- or carboxyl-terminal fusion partners or with the expression of peptides displayed within protein scaffolds (peptide aptamers). Incremental truncation affords a valuable source of molecular diversity to interrogate the druggable genome or evaluate the therapeutic potential of candidate genes.
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Miklos AE, Kluwe C, Der BS, Pai S, Sircar A, Hughes RA, Berrondo M, Xu J, Codrea V, Buckley PE, Calm AM, Welsh HS, Warner CR, Zacharko MA, Carney JP, Gray JJ, Georgiou G, Kuhlman B, Ellington AD. Structure-based design of supercharged, highly thermoresistant antibodies. ACTA ACUST UNITED AC 2012; 19:449-55. [PMID: 22520751 DOI: 10.1016/j.chembiol.2012.01.018] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 01/02/2012] [Accepted: 01/23/2012] [Indexed: 10/28/2022]
Abstract
Mutation of surface residues to charged amino acids increases resistance to aggregation and can enable reversible unfolding. We have developed a protocol using the Rosetta computational design package that "supercharges" proteins while considering the energetic implications of each mutation. Using a homology model, a single-chain variable fragment antibody was designed that has a markedly enhanced resistance to thermal inactivation and displays an unanticipated ≈30-fold improvement in affinity. Such supercharged antibodies should prove useful for assays in resource-limited settings and for developing reagents with improved shelf lives.
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Affiliation(s)
- Aleksandr E Miklos
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
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10
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MA FQ, FENG Y, YANG GY. Ultrahigh-throughput Enzymatic Screening Method Based on Fluorescence-activated Cell Sorting and Its Applications*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Increased antibody affinity confers broad in vitro protection against escape mutants of severe acute respiratory syndrome coronavirus. J Virol 2012; 86:9113-21. [PMID: 22696652 DOI: 10.1128/jvi.00233-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Even though the effect of antibody affinity on neutralization potency is well documented, surprisingly, its impact on neutralization breadth and escape has not been systematically determined. Here, random mutagenesis and DNA shuffling of the single-chain variable fragment of the neutralizing antibody 80R followed by bacterial display screening using anchored periplasmic expression (APEx) were used to generate a number of higher-affinity variants of the severe acute respiratory syndrome coronavirus (SARS-CoV)-neutralizing antibody 80R with equilibrium dissociation constants (K(D)) as low as 37 pM, a >270-fold improvement relative to that of the parental 80R single-chain variable fragment (scFv). As expected, antigen affinity was shown to correlate directly with neutralization potency toward the icUrbani strain of SARS-CoV. Additionally, the highest-affinity antibody fragment displayed 10-fold-increased broad neutralization in vitro and completely protected against several SARS-CoV strains containing substitutions associated with antibody escape. Importantly, higher affinity also led to the suppression of viral escape mutants in vitro. Escape from the highest-affinity variant required reduced selective pressure and multiple substitutions in the binding epitope. Collectively, these results support the hypothesis that engineered antibodies with picomolar dissociation constants for a neutralizing epitope can confer escape-resistant protection.
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12
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Nishikawa T, Sunami T, Matsuura T, Ichihashi N, Yomo T. Construction of a Gene Screening System Using Giant Unilamellar Liposomes and a Fluorescence-Activated Cell Sorter. Anal Chem 2012; 84:5017-24. [DOI: 10.1021/ac300678w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis. Future Med Chem 2011; 3:809-19. [PMID: 21644826 DOI: 10.4155/fmc.11.48] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To address the synthesis of increasingly structurally diverse small-molecule drugs, methods for the generation of efficient and selective biological catalysts are becoming increasingly important. 'Directed evolution' is an umbrella term referring to a variety of methods for improving or altering the function of enzymes using a nature-inspired twofold strategy of mutagenesis followed by selection. This article provides an objective assessment of the effectiveness of directed evolution campaigns in generating enzymes with improved catalytic parameters for new substrates from the last decade, excluding studies that aimed to select for only improved physical properties and those that lack kinetic characterization. An analysis of the trends of methodologies and their success rates from 81 qualifying examples in the literature reveals the average fold improvement for k (cat) (or V (max)), K (m) and k (cat)/K (m) to be 366-, 12- and 2548-fold, respectively, whereas the median fold improvements are 5.4, 3 and 15.6. Further analysis by enzyme class, library-generation methodology and screening methodology explores relationships between successful campaigns and the methodologies employed.
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15
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Jeong KJ, Rani M. High-level production of a single chain antibody against anthrax toxin in Escherichia coli by high cell density cultivation. Bioprocess Biosyst Eng 2011; 34:811-7. [DOI: 10.1007/s00449-011-0531-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Accepted: 02/12/2011] [Indexed: 10/18/2022]
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16
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Yang G, Rich JR, Gilbert M, Wakarchuk WW, Feng Y, Withers SG. Fluorescence activated cell sorting as a general ultra-high-throughput screening method for directed evolution of glycosyltransferases. J Am Chem Soc 2010; 132:10570-7. [PMID: 20662530 DOI: 10.1021/ja104167y] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycosyltransferases (GTs) offer very attractive approaches to the synthesis of complex oligosaccharides. However, the limited number of available GTs, together with their instability and strict substrate specificity, have severely hampered the broad application of these enzymes. Previous attempts to broaden the range of substrate scope and to increase the activity of GTs via protein engineering have met with limited success, partially because of the lack of effective high-throughput screening methods. Recently, we reported an ultra-high-throughput screening method for sialyltransferases based on fluorescence-activated cell sorting (Aharoni et al. Nat. Methods 2006, 3, 609-614). Here, we considerably improve this method via the introduction of a two-color screening protocol to minimize the probability of false positive mutants and demonstrate its generality through directed evolution of a neutral sugar transferase, beta-1,3-galactosyltransferase CgtB. A variant with broader substrate tolerance than the wild-type enzyme and 300-fold higher activity was identified rapidly from a library of >10(7) CgtB mutants. Importantly, the variant effected much more efficient synthesis of G(M1a) and asialo G(M1) oligosaccharides, the building blocks of important therapeutic glycosphingolipids, than did the parent enzyme. This work not only establishes a new methodology for the directed evolution of galactosyltransferases, but also suggests a powerful strategy for the screening of almost all GT activities, thereby facilitating the engineering of glycosyltransferases.
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Affiliation(s)
- Guangyu Yang
- Centre for High-throughput Biology (CHiBi) and Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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17
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Wang Q, Wu H, Wang A, Du P, Pei X, Li H, Yin X, Huang L, Xiong X. Prospecting metagenomic enzyme subfamily genes for DNA family shuffling by a novel PCR-based approach. J Biol Chem 2010; 285:41509-16. [PMID: 20962349 DOI: 10.1074/jbc.m110.139659] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA family shuffling is a powerful method for enzyme engineering, which utilizes recombination of naturally occurring functional diversity to accelerate laboratory-directed evolution. However, the use of this technique has been hindered by the scarcity of family genes with the required level of sequence identity in the genome database. We describe here a strategy for collecting metagenomic homologous genes for DNA shuffling from environmental samples by truncated metagenomic gene-specific PCR (TMGS-PCR). Using identified metagenomic gene-specific primers, twenty-three 921-bp truncated lipase gene fragments, which shared 64-99% identity with each other and formed a distinct subfamily of lipases, were retrieved from 60 metagenomic samples. These lipase genes were shuffled, and selected active clones were characterized. The chimeric clones show extensive functional and genetic diversity, as demonstrated by functional characterization and sequence analysis. Our results indicate that homologous sequences of genes captured by TMGS-PCR can be used as suitable genetic material for DNA family shuffling with broad applications in enzyme engineering.
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Affiliation(s)
- Qiuyan Wang
- Center for Biomedicine and Health, Hangzhou Normal University, Hangzhou 310012, China
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18
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Kockar F, Maresca A, Aydın M, Işık S, Turkoglu S, Sinan S, Arslan O, Güler ÖÖ, Turan Y, Supuran CT. Mutation of Phe91 to Asn in human carbonic anhydrase I unexpectedly enhanced both catalytic activity and affinity for sulfonamide inhibitors. Bioorg Med Chem 2010; 18:5498-503. [DOI: 10.1016/j.bmc.2010.06.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 06/13/2010] [Accepted: 06/16/2010] [Indexed: 10/19/2022]
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19
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Zheng W, Griswold KE, Bailey-Kellogg C. Protein fragment swapping: a method for asymmetric, selective site-directed recombination. J Comput Biol 2010; 17:459-75. [PMID: 20377457 DOI: 10.1089/cmb.2009.0189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This article presents a new approach to site-directed recombination, swapping combinations of selected discontiguous fragments from a source protein in place of corresponding fragments of a target protein. By being both asymmetric (differentiating source and target) and selective (swapping discontiguous fragments), our method focuses experimental effort on a more restricted portion of sequence space, constructing hybrids that are more likely to have the properties that are the objective of the experiment. Furthermore, since the source and target need to be structurally homologous only locally (rather than overall), our method supports swapping fragments from functionally important regions of a source into a target "scaffold" (for example, to humanize an exogenous therapeutic protein). A protein fragment swapping plan is defined by the residue position boundaries of the fragments to be swapped; it is assessed by an average potential score over the resulting hybrid library, with singleton and pairwise terms evaluating the importance and fit of the swapped residues. While we prove that it is NP-hard to choose an optimal set of fragments under such a potential score, we develop an integer programming approach, which we call Swagmer, that works very well in practice. We demonstrate the effectiveness of our method in three swapping problems: selective recombination between beta-lactamases, activity swapping between glutathione transferases, and activity swapping between carboxylases and mutases in the purE family. We show that the selective recombination approach generates better plan (in terms of resulting potential score) than traditional site-directed recombination approaches. We also show that in all cases the optimized experiments are significantly better than ones that would result from stochastic methods.
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Affiliation(s)
- Wei Zheng
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire 03755, USA
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20
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Yang G, Withers SG. Ultrahigh-throughput FACS-based screening for directed enzyme evolution. Chembiochem 2010; 10:2704-15. [PMID: 19780076 DOI: 10.1002/cbic.200900384] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Directed enzyme evolution has proven to be a powerful tool for improving a range of properties of enzymes through consecutive rounds of diversification and selection. However, its success depends heavily on the efficiency of the screening strategy employed. Fluorescence-activated cell sorting (FACS) has recently emerged as a powerful tool for screening enzyme libraries due to its high sensitivity and its ability to analyze as many as 10(8) mutants per day. Applications of FACS screening have allowed the isolation of enzyme variants with significantly improved activities, altered substrate specificities, or even novel functions. This review discusses FACS-based screening for enzymatic activity and its potential application for the directed evolution of enzymes, ribozymes, and catalytic antibodies.
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Affiliation(s)
- Guangyu Yang
- Centre for High-Throughput Biology (CHiBi) and Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C. V6T 1Z1, Canada
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21
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Seo MJ, Jeong KJ, Leysath CE, Ellington AD, Iverson BL, Georgiou G. Engineering antibody fragments to fold in the absence of disulfide bonds. Protein Sci 2009; 18:259-67. [PMID: 19177559 DOI: 10.1002/pro.31] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Disulfide bonds play a critical role in the stabilization of the immunoglobulin beta-sandwich sandwich. Under reducing conditions, such as those that prevail in the cytoplasm, disulfide bonds do not normally form and as a result most antibodies expressed in that compartment (intrabodies) accumulate in a misfolded and inactive state. We have developed a simple method for the quantitative isolation of antibody fragments that retain full activity under reducing conditions from large mutant libraries. In E. coli, inactivation of the cysteine oxidoreductase DsbA abolishes protein oxidation in the periplasm, which leads to the accumulation of scFvs and other disulfide-containing proteins in a reduced form. Libraries of mutant scFvs were tethered onto the inner membrane of dsbA cells and mutants that could bind fluorescently labeled antigen in the reducing periplasm were screened by Anchored Periplasmic Expression (APEx; Harvey et al., Proc Natl Acad Sci USA 2004;101:9193-9198.). Using this approach, we isolated scFv antibody variants that are fully active when expressed in the cytoplasm or when the four Cys residues that normally form disulfides are substituted by Ser residues.
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Affiliation(s)
- Min Jeong Seo
- Department of Chemical Engineering, University of Texas, Austin, 78712, USA
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23
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Dalton DA, Boniface C, Turner Z, Lindahl A, Kim HJ, Jelinek L, Govindarajulu M, Finger RE, Taylor CG. Physiological roles of glutathione s-transferases in soybean root nodules. PLANT PHYSIOLOGY 2009; 150:521-30. [PMID: 19279195 PMCID: PMC2675717 DOI: 10.1104/pp.109.136630] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Accepted: 03/08/2009] [Indexed: 05/17/2023]
Abstract
Glutathione S-transferases (GSTs) are ubiquitous enzymes that catalyze the conjugation of toxic xenobiotics and oxidatively produced compounds to reduced glutathione, which facilitates their metabolism, sequestration, or removal. We report here that soybean (Glycine max) root nodules contain at least 14 forms of GST, with GST9 being most prevalent, as measured by both real-time reverse transcription-polymerase chain reaction and identification of peptides in glutathione-affinity purified extracts. GST8 was prevalent in stems and uninfected roots, whereas GST2/10 prevailed in leaves. Purified, recombinant GSTs were shown to have wide-ranging kinetic properties, suggesting that the suite of GSTs could provide physiological flexibility to deal with numerous stresses. Levels of GST9 increased with aging, suggesting a role related to senescence. RNA interference studies of nodules on composite plants showed that a down-regulation of GST9 led to a decrease in nitrogenase (acetylene reduction) activity and an increase in oxidatively damaged proteins. These findings indicate that GSTs are abundant in nodules and likely function to provide antioxidant defenses that are critical to support nitrogen fixation.
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Affiliation(s)
- David A Dalton
- Biology Department, Reed College, Portland, Oregon 97202, USA.
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24
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Balamurali MM, Sharma D, Chang A, Khor D, Chu R, Li H. Recombination of protein fragments: a promising approach toward engineering proteins with novel nanomechanical properties. Protein Sci 2008; 17:1815-26. [PMID: 18628239 DOI: 10.1110/ps.036376.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Combining single molecule atomic force microscopy (AFM) and protein engineering techniques, here we demonstrate that we can use recombination-based techniques to engineer novel elastomeric proteins by recombining protein fragments from structurally homologous parent proteins. Using I27 and I32 domains from the muscle protein titin as parent template proteins, we systematically shuffled the secondary structural elements of the two parent proteins and engineered 13 hybrid daughter proteins. Although I27 and I32 are highly homologous, and homology modeling predicted that the hybrid daughter proteins fold into structures that are similar to that of parent protein, we found that only eight of the 13 daughter proteins showed beta-sheet dominated structures that are similar to parent proteins, and the other five recombined proteins showed signatures of the formation of significant alpha-helical or random coil-like structure. Single molecule AFM revealed that six recombined daughter proteins are mechanically stable and exhibit mechanical properties that are different from the parent proteins. In contrast, another four of the hybrid proteins were found to be mechanically labile and unfold at forces that are lower than the approximately 20 pN, as we could not detect any unfolding force peaks. The last three hybrid proteins showed interesting duality in their mechanical unfolding behaviors. These results demonstrate the great potential of using recombination-based approaches to engineer novel elastomeric protein domains of diverse mechanical properties. Moreover, our results also revealed the challenges and complexity of developing a recombination-based approach into a laboratory-based directed evolution approach to engineer novel elastomeric proteins.
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Affiliation(s)
- M M Balamurali
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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Bershtein S, Tawfik DS. Advances in laboratory evolution of enzymes. Curr Opin Chem Biol 2008; 12:151-8. [PMID: 18284924 DOI: 10.1016/j.cbpa.2008.01.027] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/17/2008] [Accepted: 01/24/2008] [Indexed: 11/19/2022]
Abstract
We address recent developments in the area of laboratory, or directed evolution, with a focus on enzymes and on new methodologies of generic potential. We survey three main areas: (i) library making techniques, including the application of computational and rational methods for library design; (ii) screening and selection techniques, including recent applications of enzyme screening by FACS (fluorescence activated cell sorter); (iii) new approaches for performing directed evolution, and in particular, the application of 'neutral drifts' (libraries generated by rounds of mutation and selection for the enzyme's original function) and of consensus mutations to generate highly evolvable starting points for directed evolution.
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Affiliation(s)
- Shimon Bershtein
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Cobaugh CW, Almagro JC, Pogson M, Iverson B, Georgiou G. Synthetic antibody libraries focused towards peptide ligands. J Mol Biol 2008; 378:622-33. [PMID: 18384812 DOI: 10.1016/j.jmb.2008.02.037] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 02/14/2008] [Accepted: 02/16/2008] [Indexed: 11/27/2022]
Abstract
Synthetic antibody libraries have proven immensely useful for the de novo isolation of antibodies without the need for animal immunization. Recently, focused libraries designed to recognize particular classes of ligands, such as haptens or proteins, have been employed to facilitate the selection of high-affinity antibodies. Focused libraries are built using V regions encoding combinations of canonical structures that resemble the structural features of antibodies that bind the desired class of ligands and sequence diversity is introduced at residues typically involved in recognition. Here we describe the generation and experimental validation of two different single-chain antibody variable fragment libraries that efficiently generate binders to peptides, a class of molecules that has proven to be a difficult target for antibody generation. First, a human anti-peptide library was constructed by diversifying a scaffold: the human variable heavy chain (V(H)) germ line gene 3-23, which was fused to a variant of the human variable light chain (V(L)) germ line gene A27, in which L1 was modified to encode the canonical structure found in anti-peptide antibodies. The sequence diversity was introduced into 3-23 (V(H)) only, targeting for diversification residues commonly found in contact with protein and peptide antigens. Second, a murine library was generated using the antibody 26-10, which was initially isolated based on its affinity to the hapten digoxin, but also binds peptides and exhibits a canonical structure pattern typical of anti-peptide antibodies. Diversity was introduced in the V(H) only using the profile of amino acids found at positions that frequently contact peptide antigens. Both libraries yielded binders to two model peptides, angiotensin and neuropeptide Y, following screening by solution phage panning. The mouse library yielded antibodies with affinities below 20 nM to both targets, although only the V(H) had been subjected to diversification.
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Affiliation(s)
- Christian W Cobaugh
- Institute for Cell and Molecular Biology, University of Texas at Austin, 2500 Speedway MBB 3.312, Austin, TX 78712, USA
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27
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Chaparro-Riggers JF, Loo BL, Polizzi KM, Gibbs PR, Tang XS, Nelson MJ, Bommarius AS. Revealing biases inherent in recombination protocols. BMC Biotechnol 2007; 7:77. [PMID: 18001472 PMCID: PMC2203992 DOI: 10.1186/1472-6750-7-77] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 11/14/2007] [Indexed: 11/23/2022] Open
Abstract
Background The recombination of homologous genes is an effective protein engineering tool to evolve proteins. DNA shuffling by gene fragmentation and reassembly has dominated the literature since its first publication, but this fragmentation-based method is labor intensive. Recently, a fragmentation-free PCR based protocol has been published, termed recombination-dependent PCR, which is easy to perform. However, a detailed comparison of both methods is still missing. Results We developed different test systems to compare and reveal biases from DNA shuffling and recombination-dependent PCR (RD-PCR), a StEP-like recombination protocol. An assay based on the reactivation of β-lactamase was developed to simulate the recombination of point mutations. Both protocols performed similarly here, with slight advantages for RD-PCR. However, clear differences in the performance of the recombination protocols were observed when applied to homologous genes of varying DNA identities. Most importantly, the recombination-dependent PCR showed a less pronounced bias of the crossovers in regions with high sequence identity. We discovered that template variations, including engineered terminal truncations, have significant influence on the position of the crossovers in the recombination-dependent PCR. In comparison, DNA shuffling can produce higher crossover numbers, while the recombination-dependent PCR frequently results in one crossover. Lastly, DNA shuffling and recombination-dependent PCR both produce counter-productive variants such as parental sequences and have chimeras that are over-represented in a library, respectively. Lastly, only RD-PCR yielded chimeras in the low homology situation of GFP/mRFP (45% DNA identity level). Conclusion By comparing different recombination scenarios, this study expands on existing recombination knowledge and sheds new light on known biases, which should improve library-creation efforts. It could be shown that the recombination-dependent PCR is an easy to perform alternative to DNA shuffling.
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Affiliation(s)
- Javier F Chaparro-Riggers
- School of Chemical and Biomolecular Engineering, Parker H. Petit Institute of Bioengineering and Bioscience, 315 Ferst Drive, Atlanta, GA 30332-0363, USA.
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Link AJ, Jeong KJ, Georgiou G. Beyond toothpicks: new methods for isolating mutant bacteria. Nat Rev Microbiol 2007; 5:680-8. [PMID: 17676054 DOI: 10.1038/nrmicro1715] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Over the past 50 years genetic analysis in microbiology has relied predominantly on selections and plate assays using chromogenic enzyme substrates - for example, X-gal assays for the detection of beta-galactosidase activity. Recent advances in fluorescent assays and high throughput screening technologies have paved the way for the rapid isolation of mutants that confer complex phenotypes and for the quantitative analysis of the evolution of new traits in bacterial populations. This Review highlights the power of novel single-cell screening technologies and their applications to genetics, evolution and the biotechnological uses of bacteria.
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Affiliation(s)
- A James Link
- Department of Chemical Engineering, University of Texas, 1 University Station, Austin, Texas 78712, USA
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Landwehr M, Carbone M, Otey CR, Li Y, Arnold FH. Diversification of catalytic function in a synthetic family of chimeric cytochrome p450s. ACTA ACUST UNITED AC 2007; 14:269-78. [PMID: 17379142 PMCID: PMC1991292 DOI: 10.1016/j.chembiol.2007.01.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 01/22/2007] [Indexed: 10/23/2022]
Abstract
We report initial characterization of a synthetic family of more than 3000 cytochrome P450s made by SCHEMA recombination of 3 bacterial CYP102s. A total of 16 heme domains and their holoenzyme fusions with each of the 3 parental reductase domains were tested for activity on 11 different substrates. The results show that the chimeric enzymes have acquired significant functional diversity, including the ability to accept substrates not accepted by the parent enzymes. K-means clustering analysis of the activity data allowed the enzymes to be classified into five distinct groups based on substrate specificity. The substrates can also be grouped such that one can be a "surrogate" for others in the group. Fusion of a functional chimeric heme domain with a parental reductase domain always reconstituted a functional holoenzyme, indicating that key interdomain interactions are conserved upon reductase swapping.
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Affiliation(s)
- Marco Landwehr
- Division of Chemistry and Chemical Engineering, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
| | - Martina Carbone
- Division of Chemistry and Chemical Engineering, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
| | - Christopher R. Otey
- Biochemistry and Molecular Biophysics, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
| | - Yougen Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
- Biochemistry and Molecular Biophysics, California Institute of Technology, mail code 210-41, Pasadena, California 91125, USA
- ¶ Correspondence should be addressed to: Prof. Frances H. Arnold, Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, Tel: (626) 395-4162, Fax: (626) 568-8743, E-mail:
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Gerth ML, Lutz S. Non-homologous recombination of deoxyribonucleoside kinases from human and Drosophila melanogaster yields human-like enzymes with novel activities. J Mol Biol 2007; 370:742-51. [PMID: 17543337 PMCID: PMC1986717 DOI: 10.1016/j.jmb.2007.05.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2007] [Revised: 04/29/2007] [Accepted: 05/02/2007] [Indexed: 11/26/2022]
Abstract
In antiviral and cancer therapy, deoxyribonucleoside kinases (dNKs) are often the rate-limiting step in activating nucleoside analog (NA) prodrugs into their cytotoxic, phosphorylated forms. We have constructed libraries of hybrid enzymes by non-homologous recombination of the pyrimidine-specific human thymidine kinase 2 and the broad-specificity dNK from Drosophila melanogaster; their low sequence identity has precluded engineering by conventional, homology-dependent shuffling techniques. From these libraries, we identified chimeras that phosphorylate nucleoside analogs with higher activity than either parental enzyme, and that possess new activity towards the anti-HIV prodrug 2',3'-didehydro-3'-deoxythymidine (d4T). These results demonstrate the potential of non-homologous recombination within the dNK family for creating enzymes with new and improved activities towards nucleoside analogs. In addition, our results exposed a previously unknown role for the C-terminal regions of these dNKs in determining substrate selectivity.
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Jeong KJ, Seo MJ, Iverson BL, Georgiou G. APEx 2-hybrid, a quantitative protein-protein interaction assay for antibody discovery and engineering. Proc Natl Acad Sci U S A 2007; 104:8247-52. [PMID: 17494738 PMCID: PMC1895937 DOI: 10.1073/pnas.0702650104] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have developed a bacterial system for the discovery of interacting proteins that, unlike other two-hybrid technologies, allows for the selection of protein pairs on the basis of affinity or expression. This technology relies on the anchored periplasmic expression (APEx) of one protein (bait) on the periplasmic side of the inner membrane of Escherichia coli and its interacting partner (prey) as a soluble, epitope-tagged, periplasmic protein. Upon removal of the outer membrane by spheroplasting, periplasmic proteins, including any unbound epitope-tagged prey, are released into the extracellular fluid. However, if the epitope-tagged prey can bind to the membrane-anchored bait, it remains associated with the cell and can be detected quantitatively by using fluorescent anti-epitope tag antibodies. Cells expressing prey:bait pairs exhibiting different affinities can be readily distinguished by flow cytometry. The utility of this technology, called APEx two-hybrid, was demonstrated in two demanding antibody engineering applications: First, single-chain variable fragment (scFvs) with increased affinity to the protective antigen of Bacillus anthracis were isolated from cells coexpressing libraries of scFv random mutants, together with endogenously expressed antigen. Second, APEx two-hybrid coupled with multicolor FACS analysis to account for protein expression was used for the selection of mutant Fab antibody fragments exhibiting improved expression in the bacterial periplasm.
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Affiliation(s)
- Ki Jun Jeong
- Departments of *Chemical Engineering
- Institute for Cellular and Molecular Biology, and
| | - Min Jeong Seo
- Departments of *Chemical Engineering
- Institute for Cellular and Molecular Biology, and
| | | | - George Georgiou
- Departments of *Chemical Engineering
- Biomedical Engineering
- Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712
- To whom correspondence should be addressed. E-mail:
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Griswold KE, Aiyappan NS, Iverson BL, Georgiou G. The Evolution of Catalytic Efficiency and Substrate Promiscuity in Human Theta Class 1-1 Glutathione Transferase. J Mol Biol 2006; 364:400-10. [PMID: 17011574 PMCID: PMC1995603 DOI: 10.1016/j.jmb.2006.09.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Revised: 08/31/2006] [Accepted: 09/01/2006] [Indexed: 11/29/2022]
Abstract
Theta class glutathione transferases (GST) from various species exhibit markedly different catalytic activities in conjugating the tripeptide glutathione (GSH) to a variety of electrophilic substrates. For example, the human theta 1-1 enzyme (hGSTT1-1) is 440-fold less efficient than the rat theta 2-2 enzyme (rGSTT2-2) with the fluorogenic substrate 7-amino-4-chloromethyl coumarin (CMAC). Large libraries of hGSTT1-1 constructed by error-prone PCR, DNA shuffling, or saturation mutagenesis were screened for improved catalytic activity towards CMAC in a quantitative fashion using flow cytometry. An iterative directed evolution approach employing random mutagenesis in conjunction with homologous recombination gave rise to enzymes exhibiting up to a 20,000-fold increase in k(cat)/K(M) compared to hGSTT1-1. All highly active clones encoded one or more mutations at residues 32, 176, or 234. Combinatorial saturation mutagenesis was used to evaluate the full complement of natural amino acids at these positions, and resulted in the isolation of enzymes with catalytic rates comparable to those exhibited by the fastest mutants obtained via directed evolution. The substrate selectivities of enzymes resulting from random mutagenesis, DNA shuffling, and combinatorial saturation mutagenesis were evaluated using a series of distinct electrophiles. The results revealed that promiscuous substrate activities arose in a stochastic manner, as they did not correlate with catalytic efficiency towards the CMAC selection substrate. In contrast, chimeric enzymes previously constructed by homology-independent recombination of hGSTT-1 and rGSTT2-2 exhibited very different substrate promiscuity profiles, and showed a more defined relationship between evolved and promiscuous activities.
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Affiliation(s)
- Karl E. Griswold
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Nandini S. Aiyappan
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
| | - Brent L. Iverson
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
- ‡ To whom correspondence should be addressed: , Department of Chemistry and Biochemistry, WEL 5.320, University of Texas at Austin, Austin, TX 78712, Phone 512-471-5053, Fax 512-471-8615, , Department of Chemical Engineering, CPE 4.410, University of Texas at Austin, Austin, TX 78712, Phone 512-471-6975, Fax 512-471-7963
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
- ‡ To whom correspondence should be addressed: , Department of Chemistry and Biochemistry, WEL 5.320, University of Texas at Austin, Austin, TX 78712, Phone 512-471-5053, Fax 512-471-8615, , Department of Chemical Engineering, CPE 4.410, University of Texas at Austin, Austin, TX 78712, Phone 512-471-6975, Fax 512-471-7963
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Sharma D, Cao Y, Li H. Engineering Proteins with Novel Mechanical Properties by Recombination of Protein Fragments. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sharma D, Cao Y, Li H. Engineering Proteins with Novel Mechanical Properties by Recombination of Protein Fragments. Angew Chem Int Ed Engl 2006; 45:5633-8. [PMID: 16856192 DOI: 10.1002/anie.200600382] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Deepak Sharma
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver BC, V6T 1Z1, Canada
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Saraf MC, Moore GL, Goodey NM, Cao VY, Benkovic SJ, Maranas CD. IPRO: an iterative computational protein library redesign and optimization procedure. Biophys J 2006; 90:4167-80. [PMID: 16513775 PMCID: PMC1459523 DOI: 10.1529/biophysj.105.079277] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A number of computational approaches have been developed to reengineer promising chimeric proteins one at a time through targeted point mutations. In this article, we introduce the computational procedure IPRO (iterative protein redesign and optimization procedure) for the redesign of an entire combinatorial protein library in one step using energy-based scoring functions. IPRO relies on identifying mutations in the parental sequences, which when propagated downstream in the combinatorial library, improve the average quality of the library (e.g., stability, binding affinity, specific activity, etc.). Residue and rotamer design choices are driven by a globally convergent mixed-integer linear programming formulation. Unlike many of the available computational approaches, the procedure allows for backbone movement as well as redocking of the associated ligands after a prespecified number of design iterations. IPRO can also be used, as a limiting case, for the redesign of a single or handful of individual sequences. The application of IPRO is highlighted through the redesign of a 16-member library of Escherichia coli/Bacillus subtilis dihydrofolate reductase hybrids, both individually and through upstream parental sequence redesign, for improving the average binding energy. Computational results demonstrate that it is indeed feasible to improve the overall library quality as exemplified by binding energy scores through targeted mutations in the parental sequences.
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Affiliation(s)
- Manish C Saraf
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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