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Opuu V, Nigro G, Lazennec‐Schurdevin C, Mechulam Y, Schmitt E, Simonson T. Redesigning methionyl-tRNA synthetase for β-methionine activity with adaptive landscape flattening and experiments. Protein Sci 2023; 32:e4738. [PMID: 37518893 PMCID: PMC10451022 DOI: 10.1002/pro.4738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/01/2023]
Abstract
Amino acids (AAs) with a noncanonical backbone would be a valuable tool for protein engineering, enabling new structural motifs and building blocks. To incorporate them into an expanded genetic code, the first, key step is to obtain an appropriate aminoacyl-tRNA synthetase. Currently, directed evolution is not available to optimize AAs with noncanonical backbones, since an appropriate selective pressure has not been discovered. Computational protein design (CPD) is an alternative. We used a new CPD method to redesign MetRS and increase its activity towards β-Met, which has an extra backbone methylene. The new method considered a few active site positions for design and used a Monte Carlo exploration of the corresponding sequence space. During the exploration, a bias energy was adaptively learned, such that the free energy landscape of the apo enzyme was flattened. Enzyme variants could then be sampled, in the presence of the ligand and the bias energy, according to their β-Met binding affinities. Eighteen predicted variants were chosen for experimental testing; 10 exhibited detectable activity for β-Met adenylation. Top predicted hits were characterized experimentally in detail. Dissociation constants, catalytic rates, and Michaelis constants for both α-Met and β-Met were measured. The best mutant retained a preference for α-Met over β-Met; however, the preference was reduced, compared to the wildtype, by a factor of 29. For this mutant, high resolution crystal structures were obtained in complex with both α-Met and β-Met, indicating that the predicted, active conformation of β-Met in the active site was retained.
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Affiliation(s)
- Vaitea Opuu
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Giuliano Nigro
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Christine Lazennec‐Schurdevin
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
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Opuu V, Simonson T. Enzyme redesign and genetic code expansion. Protein Eng Des Sel 2023; 36:gzad017. [PMID: 37879093 DOI: 10.1093/protein/gzad017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
Enzyme design is an important application of computational protein design (CPD). It can benefit enormously from the additional chemistries provided by noncanonical amino acids (ncAAs). These can be incorporated into an 'expanded' genetic code, and introduced in vivo into target proteins. The key step for genetic code expansion is to engineer an aminoacyl-transfer RNA (tRNA) synthetase (aaRS) and an associated tRNA that handles the ncAA. Experimental directed evolution has been successfully used to engineer aaRSs and incorporate over 200 ncAAs into expanded codes. But directed evolution has severe limits, and is not yet applicable to noncanonical AA backbones. CPD can help address several of its limitations, and has begun to be applied to this problem. We review efforts to redesign aaRSs, studies that designed new proteins and functionalities with the help of ncAAs, and some of the method developments that have been used, such as adaptive landscape flattening Monte Carlo, which allows an enzyme to be redesigned with substrate or transition state binding as the design target.
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Affiliation(s)
- Vaitea Opuu
- Institut Chimie Biologie Innovation (CNRS UMR8231), Ecole Supérieure de Physique et Chimie de Paris (ESPCI), 75005 Paris, France
| | - Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
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3
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Porter JJ, Heil CS, Lueck JD. Therapeutic promise of engineered nonsense suppressor tRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1641. [PMID: 33567469 PMCID: PMC8244042 DOI: 10.1002/wrna.1641] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022]
Abstract
Nonsense mutations change an amino acid codon to a premature termination codon (PTC) generally through a single-nucleotide substitution. The generation of a PTC results in a defective truncated protein and often in severe forms of disease. Because of the exceedingly high prevalence of nonsense-associated diseases and a unifying mechanism, there has been a concerted effort to identify PTC therapeutics. Most clinical trials for PTC therapeutics have been conducted with small molecules that promote PTC read through and incorporation of a near-cognate amino acid. However, there is a need for PTC suppression agents that recode PTCs with the correct amino acid while being applicable to PTC mutations in many different genomic landscapes. With these characteristics, a single therapeutic will be able to treat several disease-causing PTCs. In this review, we will focus on the use of nonsense suppression technologies, in particular, suppressor tRNAs (sup-tRNAs), as possible therapeutics for correcting PTCs. Sup-tRNAs have many attractive qualities as possible therapeutic agents although there are knowledge gaps on their function in mammalian cells and technical hurdles that need to be overcome before their promise is realized. This article is categorized under: RNA Processing > tRNA Processing Translation > Translation Regulation.
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Affiliation(s)
- Joseph J. Porter
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Christina S. Heil
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - John D. Lueck
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Department of NeurologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
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Tawfik DS, Gruic-Sovulj I. How evolution shapes enzyme selectivity - lessons from aminoacyl-tRNA synthetases and other amino acid utilizing enzymes. FEBS J 2020; 287:1284-1305. [PMID: 31891445 DOI: 10.1111/febs.15199] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/08/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022]
Abstract
Aminoacyl-tRNA synthetases (AARSs) charge tRNA with their cognate amino acids. Many other enzymes use amino acids as substrates, yet discrimination against noncognate amino acids that threaten the accuracy of protein translation is a hallmark of AARSs. Comparing AARSs to these other enzymes allowed us to recognize patterns in molecular recognition and strategies used by evolution for exercising selectivity. Overall, AARSs are 2-3 orders of magnitude more selective than most other amino acid utilizing enzymes. AARSs also reveal the physicochemical limits of molecular discrimination. For example, amino acids smaller by a single methyl moiety present a discrimination ceiling of ~200, while larger ones can be discriminated by up to 105 -fold. In contrast, substrates larger by a hydroxyl group challenge AARS selectivity, due to promiscuous H-bonding with polar active site groups. This 'hydroxyl paradox' is resolved by editing. Indeed, when the physicochemical discrimination limits are reached, post-transfer editing - hydrolysis of tRNAs charged with noncognate amino acids, evolved. The editing site often selectively recognizes the edited noncognate substrate using the very same feature that the synthetic site could not efficiently discriminate against. Finally, the comparison to other enzymes also reveals that the selectivity of AARSs is an explicitly evolved trait, showing some clear examples of how selection acted not only to optimize catalytic efficiency with the target substrate, but also to abolish activity with noncognate threat substrates ('negative selection').
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Affiliation(s)
- Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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Canu N, Belin P, Thai R, Correia I, Lequin O, Seguin J, Moutiez M, Gondry M. Incorporation of Non-canonical Amino Acids into 2,5-Diketopiperazines by Cyclodipeptide Synthases. Angew Chem Int Ed Engl 2018; 57:3118-3122. [DOI: 10.1002/anie.201712536] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Nicolas Canu
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Pascal Belin
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Robert Thai
- SIMOPRO; CEA-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Isabelle Correia
- Sorbonne Université; Ecole Normale Supérieure; PSL University; CNRS; Laboratoire des Biomolécules (LBM); 75005 Paris France
| | - Olivier Lequin
- Sorbonne Université; Ecole Normale Supérieure; PSL University; CNRS; Laboratoire des Biomolécules (LBM); 75005 Paris France
| | - Jérôme Seguin
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Mireille Moutiez
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Muriel Gondry
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
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6
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Canu N, Belin P, Thai R, Correia I, Lequin O, Seguin J, Moutiez M, Gondry M. Incorporation of Non-canonical Amino Acids into 2,5-Diketopiperazines by Cyclodipeptide Synthases. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Nicolas Canu
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Pascal Belin
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Robert Thai
- SIMOPRO; CEA-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Isabelle Correia
- Sorbonne Université; Ecole Normale Supérieure; PSL University; CNRS; Laboratoire des Biomolécules (LBM); 75005 Paris France
| | - Olivier Lequin
- Sorbonne Université; Ecole Normale Supérieure; PSL University; CNRS; Laboratoire des Biomolécules (LBM); 75005 Paris France
| | - Jérôme Seguin
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Mireille Moutiez
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Muriel Gondry
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
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Chaliotis A, Vlastaridis P, Mossialos D, Ibba M, Becker HD, Stathopoulos C, Amoutzias GD. The complex evolutionary history of aminoacyl-tRNA synthetases. Nucleic Acids Res 2017; 45:1059-1068. [PMID: 28180287 PMCID: PMC5388404 DOI: 10.1093/nar/gkw1182] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/20/2016] [Accepted: 11/16/2016] [Indexed: 12/15/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) are a superfamily of enzymes responsible for the faithful translation of the genetic code and have lately become a prominent target for synthetic biologists. Our large-scale analysis of >2500 prokaryotic genomes reveals the complex evolutionary history of these enzymes and their paralogs, in which horizontal gene transfer played an important role. These results show that a widespread belief in the evolutionary stability of this superfamily is misconceived. Although AlaRS, GlyRS, LeuRS, IleRS, ValRS are the most stable members of the family, GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes. In the course of this analysis, highly conserved protein motifs and domains within each of the AARS loci were identified and used to build a web-based computational tool for the genome-wide detection of AARS coding sequences. This is based on hidden Markov models (HMMs) and is available together with a cognate database that may be used for specific analyses. The bioinformatics tools that we have developed may also help to identify new antibiotic agents and targets using these essential enzymes. These tools also may help to identify organisms with alternative pathways that are involved in maintaining the fidelity of the genetic code.
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Affiliation(s)
- Anargyros Chaliotis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Panayotis Vlastaridis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Dimitris Mossialos
- Molecular Microbiology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Hubert D Becker
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, 4 allée Konrad Röntgen, Strasbourg Cedex, France
| | | | - Grigorios D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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8
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Cvetesic N, Gruic-Sovulj I. Synthetic and editing reactions of aminoacyl-tRNA synthetases using cognate and non-cognate amino acid substrates. Methods 2016; 113:13-26. [PMID: 27713080 DOI: 10.1016/j.ymeth.2016.09.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/29/2016] [Accepted: 09/29/2016] [Indexed: 11/19/2022] Open
Abstract
The covalent coupling of cognate amino acid-tRNA pairs by corresponding aminoacyl-tRNA synthetases (aaRS) defines the genetic code and provides aminoacylated tRNAs for ribosomal protein synthesis. Besides the cognate substrate, some non-cognate amino acids may also compete for tRNA aminoacylation. However, their participation in protein synthesis is generally prevented by an aaRS proofreading activity located in the synthetic site and in a separate editing domain. These mechanisms, coupled with the ability of certain aaRSs to discriminate well against non-cognate amino acids in the synthetic reaction alone, define the accuracy of the aminoacylation reaction. aaRS quality control may also act as a gatekeeper for the standard genetic code and prevents infiltration by natural amino acids that are not normally coded for protein biosynthesis. This latter finding has reinforced interest in understanding the principles that govern discrimination against a range of potential non-cognate amino acids. This paper presents an overview of the kinetic assays that have been established for monitoring synthetic and editing reactions with cognate and non-cognate amino acid substrates. Taking into account the peculiarities of non-cognate reactions, the specific controls needed and the dedicated experimental designs are discussed in detail. Kinetic partitioning within the synthetic and editing sites controls the balance between editing and aminoacylation. We describe in detail steady-state and single-turnover approaches for the analysis of synthetic and editing reactions, which ultimately enable mechanisms of amino acid discrimination to be determined.
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Affiliation(s)
- Nevena Cvetesic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
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9
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Lajoie MJ, Söll D, Church GM. Overcoming Challenges in Engineering the Genetic Code. J Mol Biol 2016; 428:1004-21. [PMID: 26348789 PMCID: PMC4779434 DOI: 10.1016/j.jmb.2015.09.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/19/2015] [Accepted: 09/01/2015] [Indexed: 11/24/2022]
Abstract
Withstanding 3.5 billion years of genetic drift, the canonical genetic code remains such a fundamental foundation for the complexity of life that it is highly conserved across all three phylogenetic domains. Genome engineering technologies are now making it possible to rationally change the genetic code, offering resistance to viruses, genetic isolation from horizontal gene transfer, and prevention of environmental escape by genetically modified organisms. We discuss the biochemical, genetic, and technological challenges that must be overcome in order to engineer the genetic code.
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Affiliation(s)
- M J Lajoie
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - D Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - G M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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Rauch BJ, Porter JJ, Mehl RA, Perona JJ. Improved Incorporation of Noncanonical Amino Acids by an Engineered tRNA(Tyr) Suppressor. Biochemistry 2016; 55:618-28. [PMID: 26694948 DOI: 10.1021/acs.biochem.5b01185] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Methanocaldcoccus jannaschii tyrosyl-tRNA synthetase (TyrRS):tRNA(Tyr) cognate pair has been used to incorporate a large number of noncanonical amino acids (ncAAs) into recombinant proteins in Escherichia coli. However, the structural elements of the suppressor tRNA(Tyr) used in these experiments have not been examined for optimal performance. Here, we evaluate the steady-state kinetic parameters of wild-type M. jannaschii TyrRS and an evolved 3-nitrotyrosyl-tRNA synthetase (nitroTyrRS) toward several engineered tRNA(Tyr) suppressors, and we correlate aminoacylation properties with the efficiency and fidelity of superfolder green fluorescent protein (sfGFP) synthesis in vivo. Optimal ncAA-sfGFP synthesis correlates with improved aminoacylation kinetics for a tRNA(Tyr) amber suppressor with two substitutions in the anticodon loop (G34C/G37A), while four additional mutations in the D and variable loops, present in the tRNA(Tyr) used in all directed evolution experiments to date, are deleterious to function both in vivo and in vitro. These findings extend to three of four other evolved TyrRS enzymes that incorporate distinct ncAAs. Suppressor tRNAs elicit decreases in amino acid Km values for both TyrRS and nitroTyrRS, suggesting that direct anticodon recognition by TyrRS need not be an impediment to superior performance of this orthogonal system and offering insight into novel approaches for directed evolution. The G34C/G37A tRNA(Tyr) may enhance future incorporation of many ncAAs by engineered TyrRS enzymes.
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Affiliation(s)
- Benjamin J Rauch
- Department of Chemistry, Portland State University , P.O. Box 751, Portland, Oregon 97207, United States.,Department of Biochemistry & Molecular Biology, Oregon Health & Sciences University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Joseph J Porter
- Department of Biochemistry and Biophysics, Oregon State University , 2011 Agriculture and Life Sciences Building, Corvallis, Oregon 97331, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University , 2011 Agriculture and Life Sciences Building, Corvallis, Oregon 97331, United States
| | - John J Perona
- Department of Chemistry, Portland State University , P.O. Box 751, Portland, Oregon 97207, United States.,Department of Biochemistry & Molecular Biology, Oregon Health & Sciences University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
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