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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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2
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Melnikov SV, Khabibullina NF, Mairhofer E, Vargas-Rodriguez O, Reynolds NM, Micura R, Söll D, Polikanov YS. Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site. Nucleic Acids Res 2019; 47:2089-2100. [PMID: 30520988 PMCID: PMC6393236 DOI: 10.1093/nar/gky1211] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/14/2018] [Accepted: 11/20/2018] [Indexed: 12/24/2022] Open
Abstract
During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, no structures have ever been reported that would explain the poor reactivity of D-amino acids. Here we report a 3.7Å-resolution crystal structure of a bacterial ribosome in complex with a D-aminoacyl-tRNA analog bound to the A site. Although at this resolution we could not observe individual chemical groups, we could unambiguously define the positions of the D-amino acid side chain and the amino group based on chemical restraints. The structure reveals that similarly to L-amino acids, the D-amino acid binds the ribosome by inserting its side chain into the ribosomal A-site cleft. This binding mode does not allow optimal nucleophilic attack of the peptidyl-tRNA by the reactive α-amino group of a D-amino acid. Also, our structure suggests that the D-amino acid cannot participate in hydrogen-bonding with the P-site tRNA that is required for the efficient proton transfer during peptide bond formation. Overall, our work provides the first mechanistic insight into the ancient mechanism that helps living cells ensure the stereochemistry of protein synthesis.
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Affiliation(s)
- Sergey V Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Nelli F Khabibullina
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Elisabeth Mairhofer
- Institute of Organic Chemistry at Leopold Franzens University, A-6020 Innsbruck, Austria
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Ronald Micura
- Institute of Organic Chemistry at Leopold Franzens University, A-6020 Innsbruck, Austria
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA
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Richardson SL, Dods KK, Abrigo NA, Iqbal ES, Hartman MC. In vitro genetic code reprogramming and expansion to study protein function and discover macrocyclic peptide ligands. Curr Opin Chem Biol 2018; 46:172-179. [PMID: 30077877 DOI: 10.1016/j.cbpa.2018.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 05/02/2018] [Accepted: 07/13/2018] [Indexed: 01/26/2023]
Abstract
The ability to introduce non-canonical amino acids into peptides and proteins is facilitated by working within in vitro translation systems. Non-canonical amino acids can be introduced into these systems using sense codon reprogramming, stop codon suppression, and by breaking codon degeneracy. Here, we review how these techniques have been used to create proteins with novel properties and how they facilitate sophisticated studies of protein function. We also discuss how researchers are using in vitro translation experiments with non-canonical amino acids to explore the tolerance of the translation apparatus to artificial building blocks. Finally, we give several examples of how non-canonical amino acids can be combined with mRNA-displayed peptide libraries for the creation of protease-stable, macrocyclic peptide libraries for ligand discovery.
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Affiliation(s)
- Stacie L Richardson
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Kara K Dods
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Nicolas A Abrigo
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Emil S Iqbal
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Matthew Ct Hartman
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA.
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Rybak MY, Kovalenko OP, Tukalo MA. The Dual Role of the 2'-OH Group of A76 tRNA Tyr in the Prevention of d-tyrosine Mistranslation. J Mol Biol 2018; 430:2670-2676. [PMID: 29953888 DOI: 10.1016/j.jmb.2018.06.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 06/17/2018] [Accepted: 06/19/2018] [Indexed: 02/02/2023]
Abstract
Aminoacyl-tRNA-synthetases are crucial enzymes for initiation step of translation. Possessing editing activity, they protect living cells from misincorporation of non-cognate and non-proteinogenic amino acids into proteins. Tyrosyl-tRNA synthetase (TyrRS) does not have such editing properties, but it shares weak stereospecificity in recognition of d-/l-tyrosine (Tyr). Nevertheless, an additional enzyme, d-aminoacyl-tRNA-deacylase (DTD), exists to overcome these deficiencies. The precise catalytic role of hydroxyl groups of the tRNATyr A76 in the catalysis by TyrRS and DTD remained unknown. To address this issue, [32P]-labeled tRNATyr substrates have been tested in aminoacylation and deacylation assays. TyrRS demonstrates similar activity in charging the 2' and 3'-OH groups of A76 with l-Tyr. This synthetase can effectively use both OH groups as primary sites for aminoacylation with l-Tyr, but demonstrates severe preference toward 2'-OH, in charging with d-Tyr. In both cases, the catalysis is not substrate-assisted: neither the 2'-OH nor the 3'-OH group assists catalysis. In contrast, DTD catalyzes deacylation of d-Tyr-tRNATyr specifically from the 3'-OH group, while the 2'-OH assists in this hydrolysis.
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Affiliation(s)
- Mariia Yu Rybak
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Str., 03143 Kyiv, Ukraine.
| | - Oksana P Kovalenko
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Str., 03143 Kyiv, Ukraine
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Str., 03143 Kyiv, Ukraine
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Grube CD, Roy H. A continuous assay for monitoring the synthetic and proofreading activities of multiple aminoacyl-tRNA synthetases for high-throughput drug discovery. RNA Biol 2017; 15:659-666. [PMID: 29168435 PMCID: PMC6103669 DOI: 10.1080/15476286.2017.1397262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyze the aminoacylation of tRNAs to produce the aminoacyl-tRNAs (aa-tRNAs) required by ribosomes for translation of the genetic message into proteins. To ensure the accuracy of tRNA aminoacylation, and consequently the fidelity of protein synthesis, some aaRSs exhibit a proofreading (editing) site, distinct from the aa-tRNA synthetic site. The aaRS editing site hydrolyzes misacylated products formed when a non-cognate amino acid is used during tRNA charging. Because aaRSs play a central role in protein biosynthesis and cellular life, these proteins represent longstanding targets for therapeutic drug development to combat infectious diseases. Most existing aaRS inhibitors target the synthetic site, and it is only recently that drugs targeting the proofreading site have been considered. In the present study, we developed a robust assay for the high-throughput screening of libraries of inhibitors targeting both the synthetic and the proofreading sites of up to four aaRSs simultaneously. Thus, this assay allows for screening of eight distinct enzyme active sites in a single experiment. aaRSs from several prominent human pathogens (i.e., Mycobacterium tuberculosis, Plasmodium falciparum, and Escherichia coli) were used for development of this assay.
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Affiliation(s)
- Christopher D Grube
- a Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida , United States of America
| | - Hervé Roy
- a Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida , United States of America
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Abstract
The genetic code-the language used by cells to translate their genomes into proteins that perform many cellular functions-is highly conserved throughout natural life. Rewriting the genetic code could lead to new biological functions such as expanding protein chemistries with noncanonical amino acids (ncAAs) and genetically isolating synthetic organisms from natural organisms and viruses. It has long been possible to transiently produce proteins bearing ncAAs, but stabilizing an expanded genetic code for sustained function in vivo requires an integrated approach: creating recoded genomes and introducing new translation machinery that function together without compromising viability or clashing with endogenous pathways. In this review, we discuss design considerations and technologies for expanding the genetic code. The knowledge obtained by rewriting the genetic code will deepen our understanding of how genomes are designed and how the canonical genetic code evolved.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511;
| | - Marc J Lajoie
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511;
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; .,Department of Chemistry, Yale University, New Haven, Connecticut 06511
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Reynolds NM, Vargas-Rodriguez O, Söll D, Crnković A. The central role of tRNA in genetic code expansion. Biochim Biophys Acta Gen Subj 2017; 1861:3001-3008. [PMID: 28323071 DOI: 10.1016/j.bbagen.2017.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND The development of orthogonal translation systems (OTSs) for genetic code expansion (GCE) has allowed for the incorporation of a diverse array of non-canonical amino acids (ncAA) into proteins. Transfer RNA, the central molecule in the translation of the genetic message into proteins, plays a significant role in the efficiency of ncAA incorporation. SCOPE OF REVIEW Here we review the biochemical basis of OTSs for genetic code expansion. We focus on the role of tRNA and discuss strategies used to engineer tRNA for the improvement of ncAA incorporation into proteins. MAJOR CONCLUSIONS The engineering of orthogonal tRNAs for GCE has significantly improved the incorporation of ncAAs. However, there are numerous unintended consequences of orthogonal tRNA engineering that cannot be predicted ab initio. GENERAL SIGNIFICANCE Genetic code expansion has allowed for the incorporation of a great diversity of ncAAs and novel chemistries into proteins, making significant contributions to our understanding of biological molecules and interactions. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
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Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics. J Mol Graph Model 2016; 71:192-199. [PMID: 27939931 DOI: 10.1016/j.jmgm.2016.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 12/28/2022]
Abstract
The stereospecificity of aminoacyl-tRNA synthetases helps exclude d-amino acids from protein synthesis and could perhaps be engineered to allow controlled d-amino acylation of tRNA. We use molecular dynamics simulations to probe the stereospecificity of the class I tyrosyl- and glutaminyl-tRNA synthetases (TyrRS, GlnRS), including wildtype enzymes and three point mutants suggested by three different protein design methods. l/d binding free energy differences are obtained by alchemically and reversibly transforming the ligand from L to D in simulations of the protein-ligand complex. The D81Q mutation in Escherichia coli TyrRS is homologous to the D81R mutant shown earlier to have inverted stereospecificity. D81Q is predicted to lead to a rotated ligand backbone and an increased, not a decreased l-Tyr preference. The E36Q mutation in Methanococcus jannaschii TyrRS has a predicted l/d binding free energy difference ΔΔG of just 0.5±0.9kcal/mol, compared to 3.1±0.8kcal/mol for the wildtype enzyme (favoring l-Tyr). The ligand ammonium position is preserved in the d-Tyr complex, while the carboxylate is shifted. Wildtype GlnRS has a similar preference for l-glutaminyl adenylate; the R260Q mutant has an increased preference, even though Arg260 makes a large contribution to the wildtype ΔΔG value.
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Spectrophotometric assays for monitoring tRNA aminoacylation and aminoacyl-tRNA hydrolysis reactions. Methods 2016; 113:3-12. [PMID: 27780756 DOI: 10.1016/j.ymeth.2016.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/17/2016] [Accepted: 10/21/2016] [Indexed: 11/22/2022] Open
Abstract
Aminoacyl-tRNA synthetases play a central role in protein synthesis, catalyzing the attachment of amino acids to their cognate tRNAs. Here, we describe a spectrophotometric assay for tyrosyl-tRNA synthetase in which the Tyr-tRNA product is cleaved, regenerating the tRNA substrate. As tRNA is the limiting substrate in the assay, recycling it substantially increases the sensitivity of the assay while simultaneously reducing its cost. The tRNA aminoacylation reaction is monitored spectrophotometrically by coupling the production of AMP to the conversion of NAD+ to NADH. We have adapted the tyrosyl-tRNA synthetase assay to monitor: (1) aminoacylation of tRNA by l- or d-tyrosine, (2) cyclodipeptide formation by cyclodipeptide synthases, (3) hydrolysis of d-aminoacyl-tRNAs by d-tyrosyl-tRNA deacylase, and (4) post-transfer editing by aminoacyl-tRNA synthetases. All of these assays are continuous and homogenous, making them amenable for use in high-throughput screens of chemical libraries. In the case of the cyclodipeptide synthase, d-tyrosyl-tRNA deacylase, and post-transfer editing assays, the aminoacyl-tRNAs are generated in situ, avoiding the need to synthesize and purify aminoacyl-tRNA substrates prior to performing the assays. Lastly, we describe how the tyrosyl-tRNA synthetase assay can be adapted to monitor the activity of other aminoacyl-tRNA synthetases and how the approach to regenerating the tRNA substrate can be used to increase the sensitivity and decrease the cost of commercially available aminoacyl-tRNA synthetase assays.
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