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  • synthetase
  • This invention provides methods and compositions for incorporation of an unnatural amino acid into a peptide using an orthogonal aminoacyl tRNA synthetase/tRNA pair. (patents.com)
  • In the present study, to assess their potential as secondary metabolite producers, we sequenced the whole genomes of the five type strains and searched for the presence of their non-ribosomal peptide synthetase (NRPS) and type-I polyketide synthase (PKS) gene clusters. (biomedcentral.com)
  • Evidence for distinct coding properties in tRNA acceptor stems and anticodons, and experimental demonstration that the two synthetase family ATP binding sites can indeed be coded by opposite strands of the same gene supplement these biochemical and bioinformatic data, establishing a solid basis for key intermediates on a path from simple, stereochemically coded, reciprocally catalytic peptide/RNA complexes through the earliest peptide catalysts to contemporary aminoacyl-tRNA synthetases. (mdpi.com)
  • amino
  • The mainframe structure of CDPs is a CDP scaffold generated by the condensation of two α-amino acids. (mdpi.com)
  • The nomenclature of CDPs is indicated by the three letter code for each of the two amino acids, plus a prefix to designate the absolute configuration, e.g., cyclo( l -Xaa- l -Yaa). (mdpi.com)
  • CDPs can be configured as both cis and trans isoforms, but cis configurations are predominant [ 3 ].Various amino acid modifications confer diversified chemical and biological functions. (mdpi.com)
  • wherein the O-RS preferentially aminoacylates the O-tRNA with an amino acid or unnatural amino acid. (patents.com)
  • 6. The composition of claim 1, wherein the O-RS comprises an amino acid sequence selected from the group consisting of: SEQ ID NO: 2, and a conservative substitution thereof. (patents.com)
  • 7. The composition of claim 1, wherein the unnatural amino acid comprises: a tryptophan analog or 5-hydroxy-L-tryptophan (5-HTPP). (patents.com)
  • 8. The composition of claim 1, wherein the O-RS comprises one or more improved or enhanced enzymatic properties, selected from the group consisting of: Km and Kcat, for the unnatural amino acid as compared to a natural amino acid. (patents.com)
  • However, there are numerous unnatural, nonproteinogenic amino acids that may be equally good, or even better, at folding and binding. (pnas.org)
  • We describe how, in a single experiment, multiple nonproteinogenic amino acids can be trialed at all positions in a peptide sequence, with thousands of modifications tested in parallel. (pnas.org)
  • High-resolution structure-activity analysis of polypeptides requires amino acid structures that are not present in the universal genetic code. (pnas.org)
  • Examination of peptide and protein interactions with this resolution has been limited by the need to individually synthesize and test peptides containing nonproteinogenic amino acids. (pnas.org)
  • We describe a method to scan entire peptide sequences with multiple nonproteinogenic amino acids and, in parallel, determine the thermodynamics of binding to a partner protein. (pnas.org)
  • By coupling genetic code reprogramming to deep mutational scanning, any number of amino acids can be exhaustively substituted into peptides, and single experiments can return all free energy changes of binding. (pnas.org)
  • We validate this approach by scanning two model protein-binding peptides with 21 diverse nonproteinogenic amino acids. (pnas.org)
  • This permits rapid interrogation of interaction interfaces, as well as optimization of affinity, fine-tuning of physical properties, and systematic assessment of nonproteinogenic amino acids in binding and folding. (pnas.org)
  • that is, testing all proteinogenic amino acids at all positions in a sequence and returning all effects on folding ( 3 ⇓ - 5 ), binding ( 2 , 5 ⇓ ⇓ - 8 ), or function ( 9 ). (pnas.org)
  • Extensive structure-activity maps are produced, but these methods are currently limited to the chemistry accessible within the universal genetic code-the 20 proteinogenic amino acids. (pnas.org)
  • However, extending mutagenesis to include nonproteinogenic amino acids offers many advantages. (pnas.org)
  • Certain nonproteinogenic amino acids can also improve the otherwise poor in vivo stability of short peptides and/or reduce the excessive polarity that prevents peptides crossing cell membranes ( 12 , 13 ). (pnas.org)
  • Indeed, nonproteinogenic amino acids are abundant in peptide natural products ( 14 ) and peptides modified for in vivo use ( 10 , 11 ). (pnas.org)
  • assay
  • The objective of this research project is to develop an electrochemical nucleic acid hybridization assay that is sensitive (picomole to femtomole detection level), stable with storage (6 months), portable, and easy to use in a simple assay format. (epa.gov)
  • antisense
  • These properties have led to a diverse set of applications for PNA, which includes antisense/antigene inhibition of gene expression, various DNA/RNA detection assays, nucleic acid labeling and purification technologies, and programmed assembly of nanoscale materials. (schoolbag.info)
  • NRPS
  • In the E. coli enterobactin NRPS system, the EntE adenylation domain catalyzes the transfer of a molecule of 2,3-dihydroxybenzoic acid to the pantetheine cofactor of EntB. (rcsb.org)
  • In this paper, we present a novel peptide fingerprint based on monomer composition (MCFP) of NRPs. (springer.com)
  • One monomer can display more than two peptidic bonds, and non peptidic bonds are also observed in NRPs leading to peptides with cycles and/or branches. (springer.com)
  • Catalysis
  • Monro R. E. Catalysis of peptide bond formation by 50S ribosomal subunits from Escherichia coli. (ximicat.com)
  • They proposed that this complementarity, and specifically a repeating hydrogen bond between ribose 2'OH groups and outward-pointing carbonyl oxygen atoms, suggested a basis for reciprocal pre-biotic autocatalysis, in which screw dislocations between the two partners could serve, respectively, as rudimentary active-sites for catalysis of subsequent polymerization of peptides by RNA and RNA by peptides ( Figure 2 ) [ 1 , 2 ]. (mdpi.com)
  • derivatives
  • In the present communication, we have conjugated five different MTD peptides, penetratin, tat peptide, transportan-27, and two of its truncated derivatives, transportan-21 and transportan-22, to a 16mer PNA targeted to the TAR region of the HIV-1 genome. (pubmedcentralcanada.ca)
  • The present invention provides a novel class of peptide nucleic acid derivatives, which show good cell penetration and strong binding affinity for nucleic acid. (justia.com)
  • small molecules
  • We are currently looking into designing small molecules such as specific peptide nucleic acids , which are stable and can be easily delivered to block the cancer-driven RNA editing process, said Prof Tan, who is also from the Duke-NUS Medical School and Genome Institute of Singapore (GIS). (thefreedictionary.com)
  • synthetases
  • CDP synthases (CDPSs) and non-ribosomal peptide synthetases (NRPSs) catalyze the biosynthesis of the CDP core structure, which is further modified by tailoring enzymes often associated with CDP biosynthetic gene clusters. (mdpi.com)
  • POLYNUCLEOTIDE
  • 5. The composition of claim 1, wherein the O-RS is encoded by a nucleic acid comprising a polynucleotide sequence selected from the group consisting of: SEQ ID NO: 1, a conservative variation thereof, and a complementary polynucleotide sequence thereof. (patents.com)
  • backbone
  • Peptide nucleic acid (PNA) is a chimeric molecule that consists of hydrogen-bonding purine and pyrimidine heterocycles attached to a pseudopeptide backbone. (schoolbag.info)
  • However, one of the most radical structural modifications of DNA to appear in the literature is peptide nucleic acid (PNA, Fig. 1), in which the sugar-phosphate backbone is abolished entirely in favor of a pseudopeptide. (schoolbag.info)
  • A synthetic nucleic acid analog in which natural nucleotide bases are linked to a peptide-like backbone instead of the sugar-phosphate backbone found in DNA and RNA. (thefreedictionary.com)
  • We predicted the chemical backbone structures of non-ribosomal peptides and polyketides synthesized by these gene clusters, based on module number and domain organization of NRPSs and PKSs. (biomedcentral.com)
  • vitro
  • These results indicate that anti-HIV-1 PNA conjugated with MTD peptides are not only inhibitory to HIV-1 replication in vitro but are also potent virucidal agents which render HIV-1 virions non-infectious upon brief exposure. (pubmedcentralcanada.ca)
  • Antibody
  • MitoTracker® Red CMXRos, SYTOX® Green nucleic acid stain, biotin-XX goat anti-mouse IgG antibody and Cascade Blue® NeutrAvidin biotin-binding protein. (thermofisher.com)
  • A prometaphase muntjac skin fibroblast stained with Alexa Fluor® 350 phalloidin, an anti-a-tubulin antibody and an anti-cdc6 peptide antibody. (thermofisher.com)
  • gene
  • We determined that a 10-nucleotide oligomer of peptide nucleic acid (PNA) targeting the start codon region of an essential gene acpP is able to cause complete growth inhibition of E. amylovora . (frontiersin.org)
  • vivo
  • Studies selected were original articles publishing results on the effect of different peptides on osteoblasts and osteoprogenitor cells as well as in vivo studies on bone healing. (biomedcentral.com)
  • conjugates
  • The conjugates with penetratin, transportan-21 and tat-peptides were most effective as an anti-HIV virucidal agents with IC 50 values in the range of 28-37 nM while IC 50 for inhibition of HIV-1 replication was lowest with PNA TAR -transportan-27 (0.4 μM) followed by PNA TAR -tat (0.72 μM) and PNA TAR -penetratin (0.8 μM). (pubmedcentralcanada.ca)
  • analog
  • Earlier, we have shown that an anti-TAR polyamide nucleotide analog (PNA TAR ) conjugated to a membrane transducing (MTD) peptide, transportan, is efficiently taken up by the cells and displays potent antiviral and virucidal activity [B. Chaubey, S. Tripathi, S. Ganguly, D. Harris, R. A. Casale and V. N. Pandey (2005) Virology , 331, 418- (pubmedcentralcanada.ca)
  • compounds
  • Non-ribosomal peptides, polyketides and their hybrid compounds often show pharmaceutically useful bioactivities, many of which have been developed into various drugs, such as antibiotics, anticancer agents and immunosuppressants. (biomedcentral.com)