1
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Coleman T, Shin J, Silberg JJ, Shamoo Y, Atkinson JT. The Biochemical Impact of Extracting an Embedded Adenylate Kinase Domain Using Circular Permutation. Biochemistry 2024; 63:599-609. [PMID: 38357768 DOI: 10.1021/acs.biochem.3c00605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Adenylate kinases (AKs) have evolved AMP-binding and lid domains that are encoded as continuous polypeptides embedded at different locations within the discontinuous polypeptide encoding the core domain. A prior study showed that AK homologues of different stabilities consistently retain cellular activity following circular permutation that splits a region with high energetic frustration within the AMP-binding domain into discontinuous fragments. Herein, we show that mesophilic and thermophilic AKs having this topological restructuring retain activity and substrate-binding characteristics of the parental AK. While permutation decreased the activity of both AK homologues at physiological temperatures, the catalytic activity of the thermophilic AK increased upon permutation when assayed >30 °C below the melting temperature of the native AK. The thermostabilities of the permuted AKs were uniformly lower than those of native AKs, and they exhibited multiphasic unfolding transitions, unlike the native AKs, which presented cooperative thermal unfolding. In addition, proteolytic digestion revealed that permutation destabilized each AK in differing manners, and mass spectrometry suggested that the new termini within the AMP-binding domain were responsible for the increased proteolysis sensitivity. These findings illustrate how changes in contact order can be used to tune enzyme activity and alter folding dynamics in multidomain enzymes.
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Affiliation(s)
- Tom Coleman
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - John Shin
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, MS-362, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, Texas 77005, United States
| | - Yousif Shamoo
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Joshua T Atkinson
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90007, United States
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey 08544, United States
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2
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Truong A, Myerscough D, Campbell I, Atkinson J, Silberg JJ. A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase. Protein Sci 2023; 32:e4746. [PMID: 37551563 PMCID: PMC10503412 DOI: 10.1002/pro.4746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Flavodoxins (Flds) mediate the flux of electrons between oxidoreductases in diverse metabolic pathways. To investigate whether Flds can support electron transfer to a sulfite reductase (SIR) that evolved to couple with a ferredoxin, we evaluated the ability of Flds to transfer electrons from a ferredoxin-NADP reductase (FNR) to a ferredoxin-dependent SIR using growth complementation of an Escherichia coli strain with a sulfur metabolism defect. We show that Flds from cyanobacteria complement this growth defect when coexpressed with an FNR and an SIR that evolved to couple with a plant ferredoxin. When we evaluated the effect of peptide insertion on Fld-mediated electron transfer, we observed a sensitivity to insertions within regions predicted to be proximal to the cofactor and partner binding sites, while a high insertion tolerance was detected within loops distal from the cofactor and within regions of helices and sheets that are proximal to those loops. Bioinformatic analysis showed that natural Fld sequence variability predicts a large fraction of the motifs that tolerate insertion of the octapeptide SGRPGSLS. These results represent the first evidence that Flds can support electron transfer to assimilatory SIRs, and they suggest that the pattern of insertion tolerance is influenced by interactions with oxidoreductase partners.
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Affiliation(s)
- Albert Truong
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, Texas, USA
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Dru Myerscough
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Ian Campbell
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Joshua Atkinson
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, Houston, Texas, USA
- Department of Bioengineering, Rice University, Houston, Texas, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
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3
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Atkinson JT, Jones AM, Nanda V, Silberg JJ. Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts. Protein Eng Des Sel 2019; 32:489-501. [PMID: 32626892 DOI: 10.1093/protein/gzaa012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 01/08/2023] Open
Abstract
Adenylate kinase (AK) orthologs with a range of thermostabilities were subjected to random circular permutation, and deep mutational scanning was used to evaluate where new protein termini were nondisruptive to activity. The fraction of circularly permuted variants that retained function in each library correlated with AK thermostability. In addition, analysis of the positional tolerance to new termini, which increase local conformational flexibility, showed that bonds were either functionally sensitive to cleavage across all homologs, differentially sensitive, or uniformly tolerant. The mobile AMP-binding domain, which displays the highest calculated contact energies, presented the greatest tolerance to new termini across all AKs. In contrast, retention of function in the lid and core domains was more dependent upon AK melting temperature. These results show that family permutation profiling identifies primary structure that has been selected by evolution for dynamics that are critical to activity within an enzyme family. These findings also illustrate how deep mutational scanning can be applied to protein homologs in parallel to differentiate how topology, stability, and local energetics govern mutational tolerance.
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Affiliation(s)
- Joshua T Atkinson
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, TX 77005, USA.,Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
| | - Alicia M Jones
- Biochemistry and Cell Biology Graduate Program, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA.,Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, TX 77005, USA.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, TX 77005, USA
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4
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Wu B, Atkinson JT, Kahanda D, Bennett GN, Silberg JJ. Combinatorial design of chemical‐dependent protein switches for controlling intracellular electron transfer. AIChE J 2019. [DOI: 10.1002/aic.16796] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bingyan Wu
- Biochemistry & Cell Biology Graduate Program Rice University Houston Texas
- Department of Biosciences Rice University Houston Texas
| | - Joshua T. Atkinson
- Department of Biosciences Rice University Houston Texas
- Systems, Synthetic, & Physical Biology Graduate Program Rice University Houston Texas
| | | | - George N. Bennett
- Department of Biosciences Rice University Houston Texas
- Department of Chemical & Biomolecular Engineering Rice University Houston Texas
| | - Jonathan J. Silberg
- Department of Biosciences Rice University Houston Texas
- Department of Chemical & Biomolecular Engineering Rice University Houston Texas
- Department of Bioengineering Rice University Houston Texas
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5
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Atkinson JT, Jones AM, Zhou Q, Silberg JJ. Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis. Nucleic Acids Res 2019; 46:e76. [PMID: 29912470 PMCID: PMC6061844 DOI: 10.1093/nar/gky255] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/28/2018] [Indexed: 12/17/2022] Open
Abstract
Deep mutational scanning has been used to create high-resolution DNA sequence maps that illustrate the functional consequences of large numbers of point mutations. However, this approach has not yet been applied to libraries of genes created by random circular permutation, an engineering strategy that is used to create open reading frames that express proteins with altered contact order. We describe a new method, termed circular permutation profiling with DNA sequencing (CPP-seq), which combines a one-step transposon mutagenesis protocol for creating libraries with a functional selection, deep sequencing and computational analysis to obtain unbiased insight into a protein's tolerance to circular permutation. Application of this method to an adenylate kinase revealed that CPP-seq creates two types of vectors encoding each circularly permuted gene, which differ in their ability to express proteins. Functional selection of this library revealed that >65% of the sampled vectors that express proteins are enriched relative to those that cannot translate proteins. Mapping enriched sequences onto structure revealed that the mobile AMP binding and rigid core domains display greater tolerance to backbone fragmentation than the mobile lid domain, illustrating how CPP-seq can be used to relate a protein's biophysical characteristics to the retention of activity upon permutation.
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Affiliation(s)
- Joshua T Atkinson
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main MS-180, Houston, TX 77005, USA
| | - Alicia M Jones
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, TX 77005, USA
| | - Quan Zhou
- Department of Statistics, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, TX 77005, USA.,Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX 77005, USA
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6
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Atkinson JT, Wu B, Segatori L, Silberg JJ. Overcoming component limitations in synthetic biology through transposon-mediated protein engineering. Methods Enzymol 2019; 621:191-212. [DOI: 10.1016/bs.mie.2019.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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7
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Atkinson JT, Campbell IJ, Thomas EE, Bonitatibus SC, Elliott SJ, Bennett GN, Silberg JJ. Metalloprotein switches that display chemical-dependent electron transfer in cells. Nat Chem Biol 2018; 15:189-195. [PMID: 30559426 DOI: 10.1038/s41589-018-0192-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/07/2018] [Indexed: 11/09/2022]
Abstract
Biological electron transfer is challenging to directly regulate using environmental conditions. To enable dynamic, protein-level control over energy flow in metabolic systems for synthetic biology and bioelectronics, we created ferredoxin logic gates that utilize transcriptional and post-translational inputs to control energy flow through a synthetic electron transfer pathway that is required for bacterial growth. These logic gates were created by subjecting a thermostable, plant-type ferredoxin to backbone fission and fusing the resulting fragments to a pair of proteins that self-associate, a pair of proteins whose association is stabilized by a small molecule, and to the termini of a ligand-binding domain. We show that the latter domain insertion design strategy yields an allosteric ferredoxin switch that acquires an oxygen-tolerant [2Fe-2S] cluster and can use different chemicals, including a therapeutic drug and an environmental pollutant, to control the production of a reduced metabolite in Escherichia coli and cell lysates.
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Affiliation(s)
- Joshua T Atkinson
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Ian J Campbell
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, TX, USA
| | - Emily E Thomas
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, TX, USA
| | | | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, MA, USA
| | - George N Bennett
- Department of BioSciences, Rice University, Houston, TX, USA.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, Houston, TX, USA. .,Department of Bioengineering, Rice University, Houston, TX, USA.
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8
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Younger AKD, Su PY, Shepard AJ, Udani SV, Cybulski TR, Tyo KEJ, Leonard JN. Development of novel metabolite-responsive transcription factors via transposon-mediated protein fusion. Protein Eng Des Sel 2018; 31:55-63. [PMID: 29385546 DOI: 10.1093/protein/gzy001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/07/2018] [Indexed: 12/22/2022] Open
Abstract
Naturally evolved metabolite-responsive biosensors enable applications in metabolic engineering, ranging from screening large genetic libraries to dynamically regulating biosynthetic pathways. However, there are many metabolites for which a natural biosensor does not exist. To address this need, we developed a general method for converting metabolite-binding proteins into metabolite-responsive transcription factors-Biosensor Engineering by Random Domain Insertion (BERDI). This approach takes advantage of an in vitro transposon insertion reaction to generate all possible insertions of a DNA-binding domain into a metabolite-binding protein, followed by fluorescence activated cell sorting to isolate functional biosensors. To develop and evaluate the BERDI method, we generated a library of candidate biosensors in which a zinc finger DNA-binding domain was inserted into maltose binding protein, which served as a model well-studied metabolite-binding protein. Library diversity was characterized by several methods, a selection scheme was deployed, and ultimately several distinct and functional maltose-responsive transcriptional biosensors were identified. We hypothesize that the BERDI method comprises a generalizable strategy that may ultimately be applied to convert a wide range of metabolite-binding proteins into novel biosensors for applications in metabolic engineering and synthetic biology.
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Affiliation(s)
- Andrew K D Younger
- Interdisciplinary Biological Sciences (IBiS) Graduate Program, Northwestern University, 2-100 Hogan Hall, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Peter Y Su
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, 2145 Sheridan Road, Room E-136, Evanston, IL 60208, USA
| | - Andrea J Shepard
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, 2145 Sheridan Road, Room E-136, Evanston, IL 60208, USA
| | - Shreya V Udani
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Science, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Thaddeus R Cybulski
- Department of Physical Medicine and Rehabilitation, Northwestern University and Rehabilitation Institute of Chicago, 710 North Lake Shore Drive, #1022, Chicago, IL 60611, USA
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, 2145 Sheridan Road, Room E-136, Evanston, IL 60208, USA.,Chemistry of Life Processes Institute, 2170 Campus Dr, Evanston, IL 60208, USA.,Center for Synthetic Biology, Technological Institute, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, 2145 Sheridan Road, Room E-136, Evanston, IL 60208, USA.,Chemistry of Life Processes Institute, 2170 Campus Dr, Evanston, IL 60208, USA.,Center for Synthetic Biology, Technological Institute, 2145 Sheridan Road, Evanston, IL 60208, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 303 E. Superior L3-125, Chicago, IL 60611, USA
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9
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Finch AJ, Kim JR. Thermophilic Proteins as Versatile Scaffolds for Protein Engineering. Microorganisms 2018; 6:microorganisms6040097. [PMID: 30257429 PMCID: PMC6313779 DOI: 10.3390/microorganisms6040097] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 09/23/2018] [Accepted: 09/23/2018] [Indexed: 01/18/2023] Open
Abstract
Literature from the past two decades has outlined the existence of a trade-off between protein stability and function. This trade-off creates a unique challenge for protein engineers who seek to introduce new functionality to proteins. These engineers must carefully balance the mutation-mediated creation and/or optimization of function with the destabilizing effect of those mutations. Subsequent research has shown that protein stability is positively correlated with "evolvability" or the ability to support mutations which bestow new functionality on the protein. Since the ultimate goal of protein engineering is to create and/or optimize a protein's function, highly stable proteins are preferred as potential scaffolds for protein engineering. This review focuses on the application potential for thermophilic proteins as scaffolds for protein engineering. The relatively high inherent thermostability of these proteins grants them a great deal of mutational robustness, making them promising scaffolds for various protein engineering applications. Comparative studies on the evolvability of thermophilic and mesophilic proteins have strongly supported the argument that thermophilic proteins are more evolvable than mesophilic proteins. These findings indicate that thermophilic proteins may represent the scaffold of choice for protein engineering in the future.
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Affiliation(s)
- Anthony J Finch
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Jin Ryoun Kim
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA.
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10
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Zeng Y, Jones AM, Thomas EE, Nassif B, Silberg JJ, Segatori L. A Split Transcriptional Repressor That Links Protein Solubility to an Orthogonal Genetic Circuit. ACS Synth Biol 2018; 7:2126-2138. [PMID: 30089365 PMCID: PMC6858789 DOI: 10.1021/acssynbio.8b00129] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Monitoring the aggregation of proteins within the cellular environment is key to investigating the molecular mechanisms underlying the formation of off-pathway protein assemblies associated with the development of disease and testing therapeutic strategies to prevent the accumulation of non-native conformations. It remains challenging, however, to couple protein aggregation events underlying the cellular pathogenesis of a disease to genetic circuits and monitor their progression in a quantitative fashion using synthetic biology tools. To link the aggregation propensity of a target protein to the expression of an easily detectable reporter, we investigated the use of a transcriptional AND gate system based on complementation of a split transcription factor. We first identified two-fragment tetracycline repressor (TetR) variants that can be regulated via ligand-dependent induction and demonstrated that split TetR variants can function as transcriptional AND gates in both bacteria and mammalian cells. We then adapted split TetR for use as an aggregation sensor. Protein aggregation was detected by monitoring complementation between a larger TetR fragment that serves as a "detector" and a smaller TetR fragment expressed as a fusion to an aggregation-prone protein that serves as a "sensor" of the target protein aggregation status. This split TetR represents a novel genetic component that can be used for a wide range of applications in bacterial as well as mammalian synthetic biology and a much needed cell-based sensor for monitoring a protein's conformational status in complex cellular environments.
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Affiliation(s)
- Yimeng Zeng
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Alicia M. Jones
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Emily E. Thomas
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Barbara Nassif
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Jonathan J. Silberg
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
| | - Laura Segatori
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
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11
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Tyurin AA, Kabardaeva KV, Mustafaev ON, Pavlenko OS, Sadovskaya NS, Fadeev VS, Zvonova EA, Goldenkova-Pavlova IV. Expression of Soluble Active Interferon αA in Escherichia coli Periplasm by Fusion with Thermostable Lichenase Using the Domain Insertion Approach. BIOCHEMISTRY (MOSCOW) 2018; 83:259-269. [DOI: 10.1134/s0006297918030069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Thomas EE, Pandey N, Knudsen S, Ball ZT, Silberg JJ. Programming Post-Translational Control over the Metabolic Labeling of Cellular Proteins with a Noncanonical Amino Acid. ACS Synth Biol 2017; 6:1572-1583. [PMID: 28419802 PMCID: PMC6858787 DOI: 10.1021/acssynbio.7b00100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transcriptional control can be used to program cells to label proteins with noncanonical amino acids by regulating the expression of orthogonal aminoacyl tRNA synthetases (aaRSs). However, we cannot yet program cells to control labeling in response to aaRS and ligand binding. To identify aaRSs whose activities can be regulated by interactions with ligands, we used a combinatorial approach to discover fragmented variants of Escherichia coli methionyl tRNA synthetase (MetRS) that require fusion to associating proteins for maximal activity. We found that these split proteins could be leveraged to create ligand-dependent MetRS using two approaches. When a pair of MetRS fragments was fused to FKBP12 and the FKBP-rapamycin binding domain (FRB) of mTOR and mutations were introduced that direct substrate specificity toward azidonorleucine (Anl), Anl metabolic labeling was significantly enhanced in growth medium containing rapamycin, which stabilizes the FKBP12-FRB complex. In addition, fusion of MetRS fragments to the termini of the ligand-binding domain of the estrogen receptor yielded proteins whose Anl metabolic labeling was significantly enhanced when 4-hydroxytamoxifen (4-HT) was added to the growth medium. These findings suggest that split MetRS can be fused to a range of ligand-binding proteins to create aaRSs whose metabolic labeling activities depend upon post-translational interactions with ligands.
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Affiliation(s)
- Emily E. Thomas
- Department of Biosciences, Rice University, Houston, TX 77005, USA
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, TX 77005, USA
| | - Naresh Pandey
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Sarah Knudsen
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Zachary T. Ball
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Jonathan J. Silberg
- Department of Biosciences, Rice University, Houston, TX 77005, USA
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
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13
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Jones AM, Atkinson JT, Silberg JJ. PERMutation Using Transposase Engineering (PERMUTE): A Simple Approach for Constructing Circularly Permuted Protein Libraries. Methods Mol Biol 2017; 1498:295-308. [PMID: 27709583 DOI: 10.1007/978-1-4939-6472-7_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Rearrangements that alter the order of a protein's sequence are used in the lab to study protein folding, improve activity, and build molecular switches. One of the simplest ways to rearrange a protein sequence is through random circular permutation, where native protein termini are linked together and new termini are created elsewhere through random backbone fission. Transposase mutagenesis has emerged as a simple way to generate libraries encoding different circularly permuted variants of proteins. With this approach, a synthetic transposon (called a permuteposon) is randomly inserted throughout a circularized gene to generate vectors that express different permuted variants of a protein. In this chapter, we outline the protocol for constructing combinatorial libraries of circularly permuted proteins using transposase mutagenesis, and we describe the different permuteposons that have been developed to facilitate library construction.
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Affiliation(s)
- Alicia M Jones
- Biosciences Department, Rice University, MS-140, 6100 Main Street, Houston, TX, 77005, USA
| | - Joshua T Atkinson
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main MS-180, Houston, TX, 77005, USA
| | - Jonathan J Silberg
- Biosciences Department, Rice University, MS-140, 6100 Main Street, Houston, TX, 77005, USA.
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14
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Pandey N, Kuypers BE, Nassif B, Thomas EE, Alnahhas RN, Segatori L, Silberg JJ. Tolerance of a Knotted Near-Infrared Fluorescent Protein to Random Circular Permutation. Biochemistry 2016; 55:3763-73. [PMID: 27304983 DOI: 10.1021/acs.biochem.6b00258] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteriophytochrome photoreceptors (BphP) are knotted proteins that have been developed as near-infrared fluorescent protein (iRFP) reporters of gene expression. To explore how rearrangements in the peptides that interlace into the knot within the BphP photosensory core affect folding, we subjected iRFPs to random circular permutation using an improved transposase mutagenesis strategy and screened for variants that fluoresce. We identified 27 circularly permuted iRFPs that display biliverdin-dependent fluorescence in Escherichia coli. The variants with the brightest whole cell fluorescence initiated translation at residues near the domain linker and knot tails, although fluorescent variants that initiated translation within the PAS and GAF domains were discovered. Circularly permuted iRFPs retained sufficient cofactor affinity to fluoresce in tissue culture without the addition of biliverdin, and one variant displayed enhanced fluorescence when expressed in bacteria and tissue culture. This variant displayed a quantum yield similar to that of iRFPs but exhibited increased resistance to chemical denaturation, suggesting that the observed increase in the magnitude of the signal arose from more efficient protein maturation. These results show how the contact order of a knotted BphP can be altered without disrupting chromophore binding and fluorescence, an important step toward the creation of near-infrared biosensors with expanded chemical sensing functions for in vivo imaging.
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Affiliation(s)
- Naresh Pandey
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Biochemistry and Cell Biology Graduate Program, Rice University , Houston, Texas 77005, United States
| | - Brianna E Kuypers
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University , Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University , Houston, Texas 77005, United States
| | - Barbara Nassif
- Department of Biosciences, Rice University , Houston, Texas 77005, United States
| | - Emily E Thomas
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Biochemistry and Cell Biology Graduate Program, Rice University , Houston, Texas 77005, United States
| | - Razan N Alnahhas
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Biochemistry and Cell Biology Graduate Program, Rice University , Houston, Texas 77005, United States
| | - Laura Segatori
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University , Houston, Texas 77005, United States.,Department of Bioengineering, Rice University , Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Department of Bioengineering, Rice University , Houston, Texas 77005, United States
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15
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Jones AM, Mehta MM, Thomas EE, Atkinson JT, Segall-Shapiro TH, Liu S, Silberg JJ. The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation. ACS Synth Biol 2016; 5:415-25. [PMID: 26976658 DOI: 10.1021/acssynbio.5b00305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins can be engineered for synthetic biology through circular permutation, a sequence rearrangement in which native protein termini become linked and new termini are created elsewhere through backbone fission. However, it remains challenging to anticipate a protein's functional tolerance to circular permutation. Here, we describe new transposons for creating libraries of randomly circularly permuted proteins that minimize peptide additions at their termini, and we use transposase mutagenesis to study the tolerance of a thermophilic adenylate kinase (AK) to circular permutation. We find that libraries expressing permuted AKs with either short or long peptides amended to their N-terminus yield distinct sets of active variants and present evidence that this trend arises because permuted protein expression varies across libraries. Mapping all sites that tolerate backbone cleavage onto AK structure reveals that the largest contiguous regions of sequence that lack cleavage sites are proximal to the phosphotransfer site. A comparison of our results with a range of structure-derived parameters further showed that retention of function correlates to the strongest extent with the distance to the phosphotransfer site, amino acid variability in an AK family sequence alignment, and residue-level deviations in superimposed AK structures. Our work illustrates how permuted protein libraries can be created with minimal peptide additions using transposase mutagenesis, and it reveals a challenge of maintaining consistent expression across permuted variants in a library that minimizes peptide additions. Furthermore, these findings provide a basis for interpreting responses of thermophilic phosphotransferases to circular permutation by calibrating how different structure-derived parameters relate to retention of function in a cellular selection.
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Affiliation(s)
- Alicia M. Jones
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Manan M. Mehta
- Medical
Scientist Training Program, Northwestern University, 303 East
Chicago Avenue, Morton 1-670, Chicago, Illinois 60611, United States
| | - Emily E. Thomas
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Joshua T. Atkinson
- Systems,
Synthetic, and Physical Biology Graduate Program, Rice University, 6100
Main MS-180, Houston, Texas 77005, United States
| | - Thomas H. Segall-Shapiro
- Department
of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 500 Technology Square, NE47-257, Cambridge, Massachusetts 02139, United States
| | - Shirley Liu
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J. Silberg
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
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16
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Pandey N, Nobles CL, Zechiedrich L, Maresso AW, Silberg JJ. Combining random gene fission and rational gene fusion to discover near-infrared fluorescent protein fragments that report on protein-protein interactions. ACS Synth Biol 2015; 4:615-24. [PMID: 25265085 PMCID: PMC4487222 DOI: 10.1021/sb5002938] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Gene fission can convert monomeric proteins into two-piece catalysts, reporters, and transcription factors for systems and synthetic biology. However, some proteins can be challenging to fragment without disrupting function, such as near-infrared fluorescent protein (IFP). We describe a directed evolution strategy that can overcome this challenge by randomly fragmenting proteins and concomitantly fusing the protein fragments to pairs of proteins or peptides that associate. We used this method to create libraries that express fragmented IFP as fusions to a pair of associating peptides (IAAL-E3 and IAAL-K3) and proteins (CheA and CheY) and screened for fragmented IFP with detectable near-infrared fluorescence. Thirteen novel fragmented IFPs were identified, all of which arose from backbone fission proximal to the interdomain linker. Either the IAAL-E3 and IAAL-K3 peptides or CheA and CheY proteins could assist with IFP fragment complementation, although the IAAL-E3 and IAAL-K3 peptides consistently yielded higher fluorescence. These results demonstrate how random gene fission can be coupled to rational gene fusion to create libraries enriched in fragmented proteins with AND gate logic that is dependent upon a protein-protein interaction, and they suggest that these near-infrared fluorescent protein fragments will be suitable as reporters for pairs of promoters and protein-protein interactions within whole animals.
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Affiliation(s)
- Naresh Pandey
- Department
of Biosciences, Rice University, Houston, Texas 77005, United States
| | | | | | | | - Jonathan J. Silberg
- Department
of Biosciences, Rice University, Houston, Texas 77005, United States
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17
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Abstract
Split T7 RNA polymerase provides new avenues for creating synthetic gene circuits that are
decoupled from host regulatory processes—but how many times can this enzyme be split, yet
retain function? New research by Voigt and colleagues (Segall-Shapiro et al, 2014)
indicates that it may be more than you think.
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Affiliation(s)
- David L Shis
- Department of Biochemistry & Cell Biology, Rice University, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biochemistry & Cell Biology, Rice University, Houston, TX, USA
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18
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Segall-Shapiro TH, Meyer AJ, Ellington AD, Sontag ED, Voigt CA. A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase. Mol Syst Biol 2014; 10:742. [PMID: 25080493 PMCID: PMC4299498 DOI: 10.15252/msb.20145299] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Synthetic genetic systems share resources with the host, including machinery for transcription
and translation. Phage RNA polymerases (RNAPs) decouple transcription from the host and generate
high expression. However, they can exhibit toxicity and lack accessory proteins (σ factors
and activators) that enable switching between different promoters and modulation of activity. Here,
we show that T7 RNAP (883 amino acids) can be divided into four fragments that have to be
co-expressed to function. The DNA-binding loop is encoded in a C-terminal 285-aa ‘σ
fragment’, and fragments with different specificity can direct the remaining 601-aa
‘core fragment’ to different promoters. Using these parts, we have built a resource
allocator that sets the core fragment concentration, which is then shared by multiple σ
fragments. Adjusting the concentration of the core fragment sets the maximum transcriptional
capacity available to a synthetic system. Further, positive and negative regulation is implemented
using a 67-aa N-terminal ‘α fragment’ and a null (inactivated) σ
fragment, respectively. The α fragment can be fused to recombinant proteins to make promoters
responsive to their levels. These parts provide a toolbox to allocate transcriptional resources via
different schemes, which we demonstrate by building a system which adjusts promoter activity to
compensate for the difference in copy number of two plasmids.
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Affiliation(s)
- Thomas H Segall-Shapiro
- Department of Biological Engineering, Synthetic Biology Center Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam J Meyer
- Institute for Cellular and Molecular Biology University of Texas at Austin, Austin, TX, USA
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology University of Texas at Austin, Austin, TX, USA
| | - Eduardo D Sontag
- Department of Mathematics, Rutgers University, Piscataway, NJ, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center Massachusetts Institute of Technology, Cambridge, MA, USA
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19
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Mahdavi A, Segall-Shapiro TH, Kou S, Jindal GA, Hoff KG, Liu S, Chitsaz M, Ismagilov RF, Silberg JJ, Tirrell DA. A genetically encoded and gate for cell-targeted metabolic labeling of proteins. J Am Chem Soc 2013; 135:2979-82. [PMID: 23406315 DOI: 10.1021/ja400448f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We describe a genetic AND gate for cell-targeted metabolic labeling and proteomic analysis in complex cellular systems. The centerpiece of the AND gate is a bisected methionyl-tRNA synthetase (MetRS) that charges the Met surrogate azidonorleucine (Anl) to tRNA(Met). Cellular protein labeling occurs only upon activation of two different promoters that drive expression of the N- and C-terminal fragments of the bisected MetRS. Anl-labeled proteins can be tagged with fluorescent dyes or affinity reagents via either copper-catalyzed or strain-promoted azide-alkyne cycloaddition. Protein labeling is apparent within 5 min after addition of Anl to bacterial cells in which the AND gate has been activated. This method allows spatial and temporal control of proteomic labeling and identification of proteins made in specific cellular subpopulations. The approach is demonstrated by selective labeling of proteins in bacterial cells immobilized in the center of a laminar-flow microfluidic channel, where they are exposed to overlapping, opposed gradients of inducers of the N- and C-terminal MetRS fragments. The observed labeling profile is predicted accurately from the strengths of the individual input signals.
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Affiliation(s)
- Alborz Mahdavi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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20
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Mehta MM, Liu S, Silberg JJ. A transposase strategy for creating libraries of circularly permuted proteins. Nucleic Acids Res 2012; 40:e71. [PMID: 22319214 PMCID: PMC3351165 DOI: 10.1093/nar/gks060] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A simple approach for creating libraries of circularly permuted proteins is described that is called PERMutation Using Transposase Engineering (PERMUTE). In PERMUTE, the transposase MuA is used to randomly insert a minitransposon that can function as a protein expression vector into a plasmid that contains the open reading frame (ORF) being permuted. A library of vectors that express different permuted variants of the ORF-encoded protein is created by: (i) using bacteria to select for target vectors that acquire an integrated minitransposon; (ii) excising the ensemble of ORFs that contain an integrated minitransposon from the selected vectors; and (iii) circularizing the ensemble of ORFs containing integrated minitransposons using intramolecular ligation. Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods. In addition, selection of this library for variants that complement the growth of Escherichia coli with a temperature-sensitive AK identified functional proteins with novel architectures, suggesting that PERMUTE will be useful for the directed evolution of proteins with new functions.
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Affiliation(s)
- Manan M Mehta
- Department of Biochemistry and Cell Biology Rice University, Houston, TX 77251, USA
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21
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Daily MD, Phillips GN, Cui Q. Interconversion of functional motions between mesophilic and thermophilic adenylate kinases. PLoS Comput Biol 2011; 7:e1002103. [PMID: 21779157 PMCID: PMC3136430 DOI: 10.1371/journal.pcbi.1002103] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 05/12/2011] [Indexed: 11/21/2022] Open
Abstract
Dynamic properties are functionally important in many proteins, including the enzyme adenylate kinase (AK), for which the open/closed transition limits the rate of catalytic turnover. Here, we compare our previously published coarse-grained (double-well Gō) simulation of mesophilic AK from E. coli (AKmeso) to simulations of thermophilic AK from Aquifex aeolicus (AKthermo). In AKthermo, as with AKmeso, the LID domain prefers to close before the NMP domain in the presence of ligand, but LID rigid-body flexibility in the open (O) ensemble decreases significantly. Backbone foldedness in O and/or transition state (TS) ensembles increases significantly relative to AKmeso in some interdomain backbone hinges and within LID. In contact space, the TS of AKthermo has fewer contacts at the CORE-LID interface but a stronger contact network surrounding the CORE-NMP interface than the TS of AKmeso. A “heated” simulation of AKthermo at 375K slightly increases LID rigid-body flexibility in accordance with the “corresponding states” hypothesis. Furthermore, while computational mutation of 7 prolines in AKthermo to their AKmeso counterparts produces similar small perturbations, mutation of these sites, especially positions 8 and 155, to glycine is required to achieve LID rigid-body flexibility and hinge flexibilities comparable to AKmeso. Mutating the 7 sites to proline in AKmeso reduces some hinges' flexibilities, especially hinge 2, but does not reduce LID rigid-body flexibility, suggesting that these two types of motion are decoupled in AKmeso. In conclusion, our results suggest that hinge flexibility and global functional motions alike are correlated with but not exclusively determined by the hinge residues. This mutational framework can inform the rational design of functionally important flexibility and allostery in other proteins toward engineering novel biochemical pathways. Dynamic properties are functionally important in many proteins, including the enzyme adenylate kinase (AK), which undergoes chemically rate-limiting domain motions coupled to substrate binding. Since mesophiles and thermophiles often differ in functionally important motions, we compare coarse-grained simulations of AKmeso and AKthermo as well as several proline and glycine mutational variants designed to interconvert the dynamics. As might be expected, both domain motions and local unfolding motions are reduced in AKthermo relative to AKmeso. In AKthermo, both of these types of motions can be partially shifted toward more flexible AKmeso by heating or by mutating hinge prolines. However, only mutation to highly flexible glycine produces motions like those of AKmeso. Thus, the rate-limiting global transition likely depends on a combination of hinge flexibility and stability within the LID and NMP domains. Finally, this mutagenic framework can inform the rational design of flexibility and allostery in other proteins toward engineering novel biological control systems.
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Affiliation(s)
- Michael D. Daily
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Computation and Informatics in Biology and Medicine Training Program, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - George N. Phillips
- Departments of Biochemistry and Computer Sciences, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Theoretical Chemical Institute, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- * E-mail:
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