ArticleScientific reports2015
Study of the Binding Energies between Unnatural Amino Acids and Engineered Orthogonal Tyrosyl-tRNA Synthetases.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 21 citations in OpenAlex.
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- Evaluation of therapeutic potentials of selected phytochemicals against Nipah virus, a multi-dimensional in silico study.3 Biotech · 2023Article
- Evaluation of tea (Camellia sinensis L.) phytochemicals as multi-disease modulators, a multidimensional in silico strategy with the combinations of network pharmacology, pharmacophore analysis, statistics and molecular docking.Molecular diversity · 2023Article
- Biomolecular simulation based machine learning models accurately predict sites of tolerability to the unnatural amino acid acridonylalanine.Scientific reports · 2021Article
- A general strategy to red-shift green fluorescent protein-based biosensors.Nature chemical biology · 2020Article
- C7-Prenylation of Tryptophan-Containing Cyclic Dipeptides by 7-Dimethylallyl Tryptophan Synthase Significantly Increases the Anticancer and Antimicrobial Activities.Molecules (Basel, Switzerland) · 2020Article
- Overcoming Near-Cognate Suppression in a Release Factor 1-Deficient Host with an Improved Nitro-Tyrosine tRNA Synthetase.Journal of molecular biology · 2020Article
- Identification of Phytochemicals Targeting c-Met Kinase Domain using Consensus Docking and Molecular Dynamics Simulation Studies.Cell biochemistry and biophysics · 2018Article
- Recent Developments and Applications of the MMPBSA Method.Frontiers in molecular biosciences · 2017Review
- Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis.Advances in nutrition (Bethesda, Md.) · 2016Review
- Regiospecific synthesis of prenylated flavonoids by a prenyltransferase cloned from Fusarium oxysporum.Scientific reports · 2016Article
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3 authors at 1 institution in 1 country.
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Abstract
We utilized several computational approaches to evaluate the binding energies of tyrosine (Tyr) and several unnatural Tyr analogs, to several orthogonal aaRSes derived from Methanocaldococcus jannaschii and Escherichia coli tyrosyl-tRNA synthetases. The present study reveals the following: (1) AutoDock Vina and ROSETTA were able to distinguish binding energy differences for individual pairs of favorable and unfavorable aaRS-amino acid complexes, but were unable to cluster together all experimentally verified favorable complexes from unfavorable aaRS-Tyr complexes; (2) MD-MM/PBSA provided the best prediction accuracy in terms of clustering favorable and unfavorable enzyme-substrate complexes, but also required the highest computational cost; and (3) MM/PBSA based on single energy-minimized structures has a significantly lower computational cost compared to MD-MM/PBSA, but still produced sufficiently accurate predictions to cluster aaRS-amino acid interactions. Although amino acid-aaRS binding is just the first step in a complex series of processes to acylate a tRNA with its corresponding amino acid, the difference in binding energy, as shown by MD-MM/PBSA, is important for a mutant orthogonal aaRS to distinguish between a favorable unnatural amino acid (unAA) substrate from unfavorable natural amino acid substrates. Our computational study should assist further designing and engineering of orthogonal aaRSes for the genetic encoding of novel unAAs.
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