Computational Aminoacyl-tRNA Synthetase Library Design for Photocaged Tyrosine

@article{Baumann2019ComputationalAS,
  title={Computational Aminoacyl-tRNA Synthetase Library Design for Photocaged Tyrosine},
  author={Tobias Baumann and Matthias Hauf and Florian Richter and Suki Albers and Andreas M{\"o}glich and Zoya Ignatova and Nediljko Budisa},
  journal={International Journal of Molecular Sciences},
  year={2019},
  volume={20}
}
Engineering aminoacyl-tRNA synthetases (aaRSs) provides access to the ribosomal incorporation of noncanonical amino acids via genetic code expansion. Conventional targeted mutagenesis libraries with 5–7 positions randomized cover only marginal fractions of the vast sequence space formed by up to 30 active site residues. This frequently results in selection of weakly active enzymes. To overcome this limitation, we use computational enzyme design to generate a focused library of aaRS variants… Expand
8 Citations
Expanding the Scope of Orthogonal Translation with Pyrrolysyl-tRNA Synthetases Dedicated to Aromatic Amino Acids
TLDR
This study revealed the engineering of both first shell and distant residues to modify substrate specificity as an important strategy to further expand the substrate scope of orthogonal translation by a semi-rational approach; redesigning the MmPylRS efficiency. Expand
Engineering aminoacyl-tRNA synthetases for use in synthetic biology.
TLDR
The importance of orthogonality in GCE is discussed, laboratory techniques employed to create designer aaRSs and tRNAs are discussed, and an overview of Orthogonal aa RS•tRNA pairs for GCE purposes are provided. Expand
Overcoming near-cognate suppression in a Release Factor 1-deficient host with an improved nitro-tyrosine tRNA synthetase.
TLDR
This work establishes Rosetta-guided design and incremental aaRS improvement as a viable and accessible path to improve GCE systems challenged by truncation and/or near-cognate suppression issues and expands the ability to study the role protein nitration plays in disease development through producing homogenous, truncation-free nitroTyr-containing protein. Expand
An Orthogonal Tyrosyl-tRNA Synthetase/tRNA Pair from a Thermophilic Bacterium for an Expanded Eukaryotic Genetic Code.
TLDR
A new class of tyrosyl-tRNA synthetase/tRNATyr pair from thermophilic bacterium Geobacillus stearothermophilus is characterized, which can charge a diverse set of ncAAs with a comparable cellular efficiency, better specificity and lower background, as compared to its E.coli homolog. Expand
A rationally designed orthogonal synthetase for genetically encoded fluorescent amino acids
TLDR
The rational generation of a novel orthogonal aminoacyl-tRNA synthetase based on the E. coli tyrosine synthetases that is capable of encoding the f-ncAA tyr-coumarin in HEK-293T cells is described. Expand
Integration of Machine Learning Improves the Prediction Accuracy of Molecular Modelling for M. jannaschii Tyrosyl-tRNA Synthetase Substrate Specificity
TLDR
A novel workflow through integration of molecular modeling and data-driven machine learning method to generate mutant libraries with high enrichment ratio for recognition of specific substrate and it is found D158G/P is the critical residue which influences the backbone disruption of helix with residue 158-163. Expand
Combating Antimicrobial Resistance With New-To-Nature Lanthipeptides Created by Genetic Code Expansion
TLDR
It is anticipated that Synthetic Biology, using engineered lantibiotics and even more complex scaffolds will be a promising tool to address an urgent problem of antibiotic resistance, especially in a class of multi-drug resistant microbes known as superbugs. Expand
Current computational methods for enzyme design
Computational enzyme design has made great strides over the last five years. Traditional methods of enzyme design require synthesis and evaluation of many mutations. Computational enzyme design has...

References

SHOWING 1-10 OF 76 REFERENCES
Continuous directed evolution of aminoacyl-tRNA synthetases
TLDR
Phage-assisted continuous evolution selections are designed to rapidly produce highly active and selective orthogonal AARSs with high activity and amino acid specificity and the capability of PACE is established to efficiently evolve orthogsonal Aarss withHigh activity and Amino acid specificity. Expand
Structural diversity and protein engineering of the aminoacyl-tRNA synthetases.
TLDR
A suggested general approach to rational design is presented, which should yield insight into the identities of the protein-RNA motifs at the heart of the genetic code, while also offering a basis for improving the catalytic properties of engineered tRNA synthetases emerging from genetic selections. Expand
Polyspecific pyrrolysyl-tRNA synthetases from directed evolution
TLDR
Structural and biochemical data reveal the molecular basis of polyspecificity in AcKRS and in a PylRS variant that displays both enhanced activity and substrate promiscuity over a chemical library of 313 ncAAs and suggest that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids. Expand
Reassignment of sense codons: Designing and docking of proline analogs for Escherichia coli prolyl-tRNA synthetase to expand the genetic code
Amino acyl-tRNA synthetases (AARSs) play a vital role in protein synthesis by catalyzing the aminoacylation of tRNA with its cognate amino acid. More recently, the endogenous AARS has been reportedExpand
Performance Analysis of Orthogonal Pairs Designed for an Expanded Eukaryotic Genetic Code
TLDR
This study provides a comprehensive scrutiny of o-pairs developed for the site-specific incorporation of reactive ncAAs in S. cerevisiae and suggests that future development of o'pairs as efficient biotechnological tools will greatly benefit from sound characterization in vivo and in vitro in parallel to monitoring intracellular ncAA levels. Expand
An in silico approach to evaluate the polyspecificity of methionyl-tRNA synthetases.
TLDR
This work analyzed the polyspecificity of the methionyl-tRNA synthetases (MetRSs) towards multiple reported and virtually generated methionine analogs and predicted the substrate selectivity of the MetRS and the key residues responsible for the recognition of methionin analogs. Expand
Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids
TLDR
An in vivo evolution approach in a genomically recoded Escherichia coli strain for the selection of orthogonal translation systems capable of multi-site nsAA incorporation should accelerate and expand the ability to produce functionalized proteins and sequence-defined polymers with diverse chemistries. Expand
Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-l-tyrosine
TLDR
The clash opportunity progressive (COP) computational method for designing a mutant aaRS to preferentially take up the analog compared with the natural amino acids is described and applied to the design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase. Expand
Importance of single molecular determinants in the fidelity of expanded genetic codes
TLDR
The view is that the central claims of fidelity reported in several NAA systems remain unproven and unprecedented and reinforce the long-established central dogma regarding the molecular basis by which these enzymes contribute to the fidelity of translation. Expand
A Mutant Escherichia coli Tyrosyl-tRNA Synthetase Utilizes the Unnatural Amino Acid Azatyrosine More Efficiently than Tyrosine*
TLDR
Kinetic analysis of aminoacyl-tRNA formation by the wild-type and mutated F130S TyrRS enzymes showed that the specificity for azatyrosine, measured by the ratios ofk cat/K m for tyrosine and the analogue, increased from 17 to 36 as a result of the F 130S mutation. Expand
...
1
2
3
4
5
...