1
|
Newton MS, Cabezas-Perusse Y, Tong CL, Seelig B. In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display. ACS Synth Biol 2020; 9:181-190. [PMID: 31891492 DOI: 10.1021/acssynbio.9b00419] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
mRNA display is a robust in vitro selection technique that allows the selection of peptides and proteins with desired functions from libraries of trillions of variants. mRNA display relies upon a covalent linkage between a protein and its encoding mRNA molecule; the power of the technique stems from the stability of this link, and the large degree of control over experimental conditions afforded to the researcher. This article describes the major advantages that make mRNA display the method of choice among comparable in vivo and in vitro methods, including cell-surface display, phage display, and ribosomal display. We also describe innovative techniques that harness mRNA display for directed evolution, protein engineering, and drug discovery.
Collapse
Affiliation(s)
- Matilda S. Newton
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
- Department of Molecular, Cellular, and Developmental Biology & Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yari Cabezas-Perusse
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Cher Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| |
Collapse
|
2
|
Menon BRK, Latham J, Dunstan MS, Brandenburger E, Klemstein U, Leys D, Karthikeyan C, Greaney MF, Shepherd SA, Micklefield J. Structure and biocatalytic scope of thermophilic flavin-dependent halogenase and flavin reductase enzymes. Org Biomol Chem 2018; 14:9354-9361. [PMID: 27714222 DOI: 10.1039/c6ob01861k] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Flavin-dependent halogenase (Fl-Hal) enzymes have been shown to halogenate a range of synthetic as well as natural aromatic compounds. The exquisite regioselectively of Fl-Hal enzymes can provide halogenated building blocks which are inaccessible using standard halogenation chemistries. Consequently, Fl-Hal are potentially useful biocatalysts for the chemoenzymatic synthesis of pharmaceuticals and other valuable products, which are derived from haloaromatic precursors. However, the application of Fl-Hal enzymes, in vitro, has been hampered by their poor catalytic activity and lack of stability. To overcome these issues, we identified a thermophilic tryptophan halogenase (Th-Hal), which has significantly improved catalytic activity and stability, compared with other Fl-Hal characterised to date. When used in combination with a thermostable flavin reductase, Th-Hal can efficiently halogenate a number of aromatic substrates. X-ray crystal structures of Th-Hal, and the reductase partner (Th-Fre), provide insights into the factors that contribute to enzyme stability, which could guide the discovery and engineering of more robust and productive halogenase biocatalysts.
Collapse
Affiliation(s)
- Binuraj R K Menon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Jonathan Latham
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Mark S Dunstan
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Eileen Brandenburger
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Ulrike Klemstein
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - David Leys
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Chinnan Karthikeyan
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Michael F Greaney
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Sarah A Shepherd
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| |
Collapse
|
3
|
Latham J, Brandenburger E, Shepherd SA, Menon BRK, Micklefield J. Development of Halogenase Enzymes for Use in Synthesis. Chem Rev 2017; 118:232-269. [PMID: 28466644 DOI: 10.1021/acs.chemrev.7b00032] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature has evolved halogenase enzymes to regioselectively halogenate a diverse range of biosynthetic precursors, with the halogens introduced often having a profound effect on the biological activity of the resulting natural products. Synthetic endeavors to create non-natural bioactive small molecules for pharmaceutical and agrochemical applications have also arrived at a similar conclusion: halogens can dramatically improve the properties of organic molecules for selective modulation of biological targets in vivo. Consequently, a high proportion of pharmaceuticals and agrochemicals on the market today possess halogens. Halogenated organic compounds are also common intermediates in synthesis and are particularly valuable in metal-catalyzed cross-coupling reactions. Despite the potential utility of organohalogens, traditional nonenzymatic halogenation chemistry utilizes deleterious reagents and often lacks regiocontrol. Reliable, facile, and cleaner methods for the regioselective halogenation of organic compounds are therefore essential in the development of economical and environmentally friendly industrial processes. A potential avenue toward such methods is the use of halogenase enzymes, responsible for the biosynthesis of halogenated natural products, as biocatalysts. This Review will discuss advances in developing halogenases for biocatalysis, potential untapped sources of such biocatalysts and how further optimization of these enzymes is required to achieve the goal of industrial scale biohalogenation.
Collapse
Affiliation(s)
- Jonathan Latham
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Eileen Brandenburger
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sarah A Shepherd
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Binuraj R K Menon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
4
|
Jongkees SAK, Hipolito CJ, Rogers JM, Suga H. Model foldamers: applications and structures of stable macrocyclic peptides identified using in vitro selection. NEW J CHEM 2015. [DOI: 10.1039/c4nj01633e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A survey of crystal- and solution-structure information for macrocyclic peptides, illustrating common folding patterns and target binding effects.
Collapse
Affiliation(s)
- Seino A. K. Jongkees
- Department of Chemistry
- Graduate School of Science
- University of Tokyo
- Tokyo 113-0033
- Japan
| | | | - Joseph M. Rogers
- Department of Chemistry
- Graduate School of Science
- University of Tokyo
- Tokyo 113-0033
- Japan
| | - Hiroaki Suga
- Department of Chemistry
- Graduate School of Science
- University of Tokyo
- Tokyo 113-0033
- Japan
| |
Collapse
|
5
|
Thermostable artificial enzyme isolated by in vitro selection. PLoS One 2014; 9:e112028. [PMID: 25393375 PMCID: PMC4230948 DOI: 10.1371/journal.pone.0112028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 10/11/2014] [Indexed: 12/30/2022] Open
Abstract
Artificial enzymes hold the potential to catalyze valuable reactions not observed in nature. One approach to build artificial enzymes introduces mutations into an existing protein scaffold to enable a new catalytic activity. This process commonly results in a simultaneous reduction of protein stability as an undesired side effect. While protein stability can be increased through techniques like directed evolution, care needs to be taken that added stability, conversely, does not sacrifice the desired activity of the enzyme. Ideally, enzymatic activity and protein stability are engineered simultaneously to ensure that stable enzymes with the desired catalytic properties are isolated. Here, we present the use of the in vitro selection technique mRNA display to isolate enzymes with improved stability and activity in a single step. Starting with a library of artificial RNA ligase enzymes that were previously isolated at ambient temperature and were therefore mostly mesophilic, we selected for thermostable active enzyme variants by performing the selection step at 65°C. The most efficient enzyme, ligase 10C, was not only active at 65°C, but was also an order of magnitude more active at room temperature compared to related enzymes previously isolated at ambient temperature. Concurrently, the melting temperature of ligase 10C increased by 35 degrees compared to these related enzymes. While low stability and solubility of the previously selected enzymes prevented a structural characterization, the improved properties of the heat-stable ligase 10C finally allowed us to solve the three-dimensional structure by NMR. This artificial enzyme adopted an entirely novel fold that has not been seen in nature, which was published elsewhere. These results highlight the versatility of the in vitro selection technique mRNA display as a powerful method for the isolation of thermostable novel enzymes.
Collapse
|
6
|
Korch SB, Stomel JM, León MA, Hamada MA, Stevenson CR, Simpson BW, Gujulla SK, Chaput JC. ATP sequestration by a synthetic ATP-binding protein leads to novel phenotypic changes in Escherichia coli. ACS Chem Biol 2013. [PMID: 23181457 DOI: 10.1021/cb3004786] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Artificial proteins that bind key metabolites with high affinity and specificity hold great promise as new tools in synthetic biology, but little has been done to create such molecules and examine their effects on living cells. Experiments of this kind have the potential to expand our understanding of cellular systems, as certain phenotypes may be physically realistic but not yet observed in nature. Here, we examine the physiology and morphology of a population of Escherichia coli as they respond to a genetically encoded, non-biological ATP-binding protein. Unlike natural ATP-dependent proteins, which transiently bind ATP during metabolic transformations, the synthetic protein DX depletes the concentration of intracellular ATP and ADP by a mechanism of protein-mediated ligand sequestration. The resulting ATP/ADP imbalance leads to an adaptive response in which a large population of bacilli cells transition to a filamentous state with dense lipid structures that segregate the cells into compartmentalized units. A wide range of biochemical and microscopy techniques extensively characterized these novel lipid structures, which we have termed endoliposomes. We show that endoliposomes adopt well-defined box-like structures that span the full width of the cell but exclude the synthetic protein DX. We further show that prolonged DX exposure causes a large fraction of the population to enter a viable-but-non-culturable state that is not easily reversed. Both phenotypes correlate with strong intracellular changes in ATP and ADP concentration. We suggest that artificial proteins, such as DX, could be used to control and regulate specific targets in metabolic pathways.
Collapse
Affiliation(s)
- Shaleen B. Korch
- Department
of Pharmacology, Midwestern University,
Glendale, Arizona 85308, United
States
| | | | | | - Matt A. Hamada
- Department
of Pharmacology, Midwestern University,
Glendale, Arizona 85308, United
States
| | | | | | | | | |
Collapse
|
7
|
Artificial proteins from combinatorial approaches. Trends Biotechnol 2012; 30:512-20. [DOI: 10.1016/j.tibtech.2012.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 06/01/2012] [Accepted: 06/06/2012] [Indexed: 11/21/2022]
|
8
|
The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis. J Mol Evol 2012; 74:1-34. [PMID: 22210458 DOI: 10.1007/s00239-011-9480-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 12/12/2011] [Indexed: 12/20/2022]
Abstract
The complexity of modern biochemistry developed gradually on early Earth as new molecules and structures populated the emerging cellular systems. Here, we generate a historical account of the gradual discovery of primordial proteins, cofactors, and molecular functions using phylogenomic information in the sequence of 420 genomes. We focus on structural and functional annotations of the 54 most ancient protein domains. We show how primordial functions are linked to folded structures and how their interaction with cofactors expanded the functional repertoire. We also reveal protocell membranes played a crucial role in early protein evolution and show translation started with RNA and thioester cofactor-mediated aminoacylation. Our findings allow elaboration of an evolutionary model of early biochemistry that is firmly grounded in phylogenomic information and biochemical, biophysical, and structural knowledge. The model describes how primordial α-helical bundles stabilized membranes, how these were decorated by layered arrangements of β-sheets and α-helices, and how these arrangements became globular. Ancient forms of aminoacyl-tRNA synthetase (aaRS) catalytic domains and ancient non-ribosomal protein synthetase (NRPS) modules gave rise to primordial protein synthesis and the ability to generate a code for specificity in their active sites. These structures diversified producing cofactor-binding molecular switches and barrel structures. Accretion of domains and molecules gave rise to modern aaRSs, NRPS, and ribosomal ensembles, first organized around novel emerging cofactors (tRNA and carrier proteins) and then more complex cofactor structures (rRNA). The model explains how the generation of protein structures acted as scaffold for nucleic acids and resulted in crystallization of modern translation.
Collapse
|
9
|
Simmons CR, Magee CL, Smith DA, Lauman L, Chaput JC, Allen JP. Three-dimensional structures reveal multiple ADP/ATP binding modes for a synthetic class of artificial proteins. Biochemistry 2010; 49:8689-99. [PMID: 20822107 DOI: 10.1021/bi100398p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The creation of synthetic enzymes with predefined functions represents a major challenge in future synthetic biology applications. Here, we describe six structures of de novo proteins that have been determined using protein crystallography to address how simple enzymes perform catalysis. Three structures are of a protein, DX, selected for its stability and ability to tightly bind ATP. Despite the addition of ATP to the crystallization conditions, the presence of a bound but distorted ATP was found only under excess ATP conditions, with ADP being present under equimolar conditions or when crystallized for a prolonged period of time. A bound ADP cofactor was evident when Asp was substituted for Val at residue 65, but ATP in a linear configuration is present when Phe was substituted for Tyr at residue 43. These new structures complement previously determined structures of DX and the protein with the Phe 43 to Tyr substitution [Simmons, C. R., et al. (2009) ACS Chem. Biol. 4, 649-658] and together demonstrate the multiple ADP/ATP binding modes from which a model emerges in which the DX protein binds ATP in a configuration that represents a transitional state for the catalysis of ATP to ADP through a slow, metal-free reaction capable of multiple turnovers. This unusual observation suggests that design-free methods can be used to generate novel protein scaffolds that are tailor-made for catalysis.
Collapse
Affiliation(s)
- C R Simmons
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | | | | | | | | | | |
Collapse
|
10
|
Zhang J, Williams BAR, Nilsson MT, Chaput JC. The evolvability of lead peptides from small library screens. Chem Commun (Camb) 2010; 46:7778-80. [PMID: 20830334 DOI: 10.1039/c0cc01475c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Very little is known about the evolvability of lead peptides that are isolated from small library screens. Here we begin to explore this question by comparing the directed evolution of two peptides previously isolated from a small library screen to new ligands generated de novo by in vitro selection.
Collapse
Affiliation(s)
- Jinglei Zhang
- Center for Evolutionary Medicine and Informatics at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA
| | | | | | | |
Collapse
|
11
|
Abstract
In vitro selection coupled with directed evolution represents a powerful method for generating nucleic acids and proteins with desired functional properties. Creating high-quality libraries of random sequences is an important step in this process as it allows variants of individual molecules to be generated from a single-parent sequence. These libraries are then screened for individual molecules with interesting, and sometimes very rare, phenotypes. Here, we describe a general method to introduce random nucleotide mutations into a parent sequence that takes advantage of the polymerase chain reaction (PCR). This protocol reduces mutational bias often associated with error-prone PCR methods and allows the experimenter to control the degree of mutagenesis by controlling the number of gene-doubling events that occur in the PCR reaction. The error-prone PCR method described here was used to optimize a de novo evolved protein for improved folding stability, solubility, and ligand-binding affinity.
Collapse
Affiliation(s)
- Elizabeth O McCullum
- The Biodesign Institute, and Department of Chemistry and Biochemistry, Center for BioOptical Nanotechnology, Arizona State University, Tempe, AZ, USA
| | | | | | | |
Collapse
|
12
|
Stomel JM, Wilson JW, León MA, Stafford P, Chaput JC. A man-made ATP-binding protein evolved independent of nature causes abnormal growth in bacterial cells. PLoS One 2009; 4:e7385. [PMID: 19812699 PMCID: PMC2754611 DOI: 10.1371/journal.pone.0007385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 09/15/2009] [Indexed: 11/18/2022] Open
Abstract
Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division. We now describe a detailed investigation into the synthetic biology of this man-made protein in a living bacterial organism, and the effect that this protein has on normal cell physiology.
Collapse
Affiliation(s)
- Joshua M. Stomel
- Center for BioOptical Nanotechnology, Arizona State University, Tempe, Arizona, United States of America
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - James W. Wilson
- Center for Infectious Disease and Vaccinology, Arizona State University, Tempe, Arizona, United States of America
| | - Megan A. León
- Center for BioOptical Nanotechnology, Arizona State University, Tempe, Arizona, United States of America
| | - Phillip Stafford
- Center for Innovations in Medicine, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - John C. Chaput
- Center for BioOptical Nanotechnology, Arizona State University, Tempe, Arizona, United States of America
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
| |
Collapse
|
13
|
Simmons CR, Stomel JM, McConnell MD, Smith DA, Watkins JL, Allen JP, Chaput JC. A synthetic protein selected for ligand binding affinity mediates ATP hydrolysis. ACS Chem Biol 2009; 4:649-58. [PMID: 19522480 DOI: 10.1021/cb900109w] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
How primitive enzymes emerged from a primordial pool remains a fundamental unanswered question with important practical implications in synthetic biology. Here we show that a de novo evolved ATP binding protein, selected solely on the basis of its ability to bind ATP, mediates the regiospecific hydrolysis of ATP to ADP when crystallized with 1 equiv of ATP. Structural insights into this reaction were obtained by growing protein crystals under saturating ATP conditions. The resulting crystal structure refined to 1.8 A resolution reveals that this man-made protein binds ATP in an unusual bent conformation that is metal-independent and held in place by a key bridging water molecule. Removal of this interaction using a null mutant results in a variant that binds ATP in a normal linear geometry and is incapable of ATP hydrolysis. Biochemical analysis, including high-resolution mass spectrometry performed on dissolved protein crystals, confirms that the reaction is accelerated in the crystalline environment. This observation suggests that proteins with weak chemical reactivity can emerge from high affinity ligand binding sites and that constrained ligand-binding geometries could have helped to facilitate the emergence of early protein enzymes.
Collapse
Affiliation(s)
- Chad R. Simmons
- Center for BioOptical Nanotechnology, The Biodesign Institute
- Department of Chemistry and Biochemistry
| | - Joshua M. Stomel
- Center for BioOptical Nanotechnology, The Biodesign Institute
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-5201
| | - Michael D. McConnell
- Center for BioOptical Nanotechnology, The Biodesign Institute
- Department of Chemistry and Biochemistry
| | - Daniel A. Smith
- Center for BioOptical Nanotechnology, The Biodesign Institute
- Department of Chemistry and Biochemistry
| | - Jennifer L. Watkins
- Center for BioOptical Nanotechnology, The Biodesign Institute
- Department of Chemistry and Biochemistry
| | | | - John C. Chaput
- Center for BioOptical Nanotechnology, The Biodesign Institute
- Department of Chemistry and Biochemistry
| |
Collapse
|
14
|
Chaput JC, Woodbury NW, Stearns LA, Williams BAR. Creating protein biocatalysts as tools for future industrial applications. Expert Opin Biol Ther 2008; 8:1087-98. [PMID: 18613761 DOI: 10.1517/14712598.8.8.1087] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Biocatalysts provide an economical and energy-efficient alternative to traditional chemical manufacturing processes. For processes where biocatalysts currently do not exist or existing protein catalysts function poorly, there is a tremendous need to discover new protein catalysts that function in industrial settings. The protein engineering community has traditionally relied on cell-based techniques in 96-well format to evolve new catalysts or improve existing enzymes. OBJECTIVE This review examines recent progress made in many display technologies, providing powerful alternatives for generating novel enzymes with altered specificity or altogether new types of function. METHODS Library creation methods and display technologies that are commonly used in conjunction with enzyme evolution are discussed. CONCLUSION We conclude with an expert opinion on future trans-disciplinary approaches that combine directed evolution with computational design as novel platforms for rapidly discovering new types of catalytic function.
Collapse
Affiliation(s)
- John C Chaput
- Center for BioOptical Nanotechnology, The Biodesign Institute, Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5201, USA.
| | | | | | | |
Collapse
|
15
|
Watkins JL, Chaput JC. Searching combinatorial libraries for native proteins with novel folds. Chembiochem 2008; 9:1361-3. [PMID: 18464233 DOI: 10.1002/cbic.200800147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jennifer L Watkins
- Center for BioOptical Nanotechnology, The Biodesign Institute, Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5201, USA
| | | |
Collapse
|