ArticleBiochemistry2014
Amino acid signature enables proteins to recognize modified tRNA.
Article in Biochemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 28 citations in OpenAlex.
- tRNA modifications in viral replication.The Journal of biological chemistry · 2026Review
- Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells.Communications biology · 2023Article
- Bacteriophage Infection of the Marine BacteriumMicroorganisms · 2023Article
- Design of 8-mer Peptides that BlockbioRxiv : the preprint server for biology · 2023Article
- Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides.PNAS nexus · 2022Article
- Article
- De novo design of peptides that coassemble into β sheet-based nanofibrils.Science advances · 2021Article
- Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding.Computational and structural biotechnology journal · 2020Article
- Extended Concerted Rotation Technique Enhances the Sampling Efficiency of the Computational Peptide-Design Algorithm.Journal of chemical theory and computation · 2017Article
- Simulation study of the ability of a computationally-designed peptide to recognize target tRNAProtein science : a publication of the Protein Society · 2016Article
- Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned λ N peptide binds boxB RNA.Journal of computational chemistry · 2016Article
- Exploiting tRNAs to Boost Virulence.Life (Basel, Switzerland) · 2016Review
- Unreported intrinsic disorder in proteins: Building connections to the literature on IDPs.Intrinsically disordered proteins · 2014Article
- The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity.The EnzymesReview
- tRNA wobble modifications and protein homeostasis.Translation (Austin, Tex.)Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Human tRNA(Lys3)UUU is the primer for HIV replication. The HIV-1 nucleocapsid protein, NCp7, facilitates htRNA(Lys3)UUU recruitment from the host cell by binding to and remodeling the tRNA structure. Human tRNA(Lys3)UUU is post-transcriptionally modified, but until recently, the importance of those modifications in tRNA recognition by NCp7 was unknown. Modifications such as the 5-methoxycarbonylmethyl-2-thiouridine at anticodon wobble position-34 and 2-methylthio-N(6)-threonylcarbamoyladenosine, adjacent to the anticodon at position-37, are important to the recognition of htRNA(Lys3)UUU by NCp7. Several short peptides selected from phage display libraries were found to also preferentially recognize these modifications. Evolutionary algorithms (Monte Carlo and self-consistent mean field) and assisted model building with energy refinement were used to optimize the peptide sequence in silico, while fluorescence assays were developed and conducted to verify the in silico results and elucidate a 15-amino acid signature sequence (R-W-Q/N-H-X2-F-Pho-X-G/A-W-R-X2-G, where X can be most amino acids, and Pho is hydrophobic) that recognized the tRNA's fully modified anticodon stem and loop domain, hASL(Lys3)UUU. Peptides of this sequence specifically recognized and bound modified htRNA(Lys3)UUU with an affinity 10-fold higher than that of the starting sequence. Thus, this approach provides an effective means of predicting sequences of RNA binding peptides that have better binding properties. Such peptides can be used in cell and molecular biology as well as biochemistry to explore RNA binding proteins and to inhibit those protein functions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.