Described herein is the preparation of new bisacylated tRNAs and their participation in protein synthesis. It has been reported that Thermus thermophilus phenylalanyl-tRNA synthetase can introduce two phenylalanine moieties onto the 3'-terminal adenosine of its cognate tRNA. It is also possible to prepare bisactivated tRNAs in vitro; these participate in protein synthesis [Wang, B.; Zhou, J.; Lodder, M.; Anderson, R. D.; Hecht, S. M. J Biol. Chem. 2006, 281, 138651. Presently, the chemical strategy used for the synthesis of the key intermediate bisacylated pdCpAs is described. Bis-S-alanyl- and bis-S-methionyl-pdCpAs were prepared initially. Further, S-threonine, S-allo-threonine, S-homoserine, and (S)-(+)-2-amino-3-hydroxy-3-methylbutyric acid were coupled with the dinucleotide to define preparative methods applicable to more complex amino acids bearing additional functionality in the form of an OH group. (c) 2007 Elsevier Ltd. All rights reserved.

While all studies of protein synthesis to date have employed monoaminoacylated transfer RNAs, there have been reports that bisphenylalanyl-tRNA is formed by Thermus thermophilus phenylalanyl-tRNA synthetase. Such tandemly activated tRNAs have now been prepared by chemicoenzymatic techniques and are shown to function in both prokaryotic and mammalian protein synthesizing systems. They exhibit characteristics consistent with their possible utility under extreme conditions in natural systems and have important potential advantages for protein elaboration in cell free systems. Mechanistically, the bisaminoacylated tRNAs bind to the ribosomal A-site and utilize the aminoacyl moiety attached to the 3'-position of the terminal adenosine for addition to the growing polypeptide chain. Following translocation to the P-site and transfer of the formed peptidyl moiety, the donor tRNA dissociates from the ribosome as a monoaminoacylated tRNA capable of functioning in a subsequent polypeptide elongation step.

The elaboration of misacylated transfer RNAs by T4 RNA ligase-mediated condensation of an aminoacylated pdCpA derivative and a tRNA (transcript) missing the two 3′-terminal nucleotides requires that the aminoacyl moiety of the dinucleotide be stabilized during the ligation reaction. This can be done conveniently by the use of a simple 4-pentenoyl group attached to Nα of the amino acid. The pentenoyl amide can be deblocked readily with aqueous iodine, presumably via an iodolactone intermediate. This protecting group can be used in conjunction with side chain protecting group for amino acids having side chain functionality, thus permitting the elaboration of proteins bearing side chain protecting groups that can be removed in a subsequent step (e.g., caged proteins). In addition, an aminated analogue of the pentenoyl protecting group, the unnatural amino acid allylglycine, can be employed as part of the peptide backbone to afford a protein cleavable by iodine.

The design and synthesis of a novel iodine-labile serine protease inhibitor was realized by the use of an ecotin analogue containing allylglycine at position 84 in lieu of methionine. Allylglycine-containing ecotins were synthesized by in vitro translation of the ecotin gene containing an engineered nonsense codon (TAG) at the positions of interest. A misacylated suppressor tRNA activated with the unnatural amino acid allylglycine was employed for the suppression of the nonsense codons in a cell-free protein biosynthesizing system, permitting the elaboration of ecotin analogues containing allyglycine at the desired sites. The derived ecotin analogues were capable of inhibiting bovine trypsin with inhibitory constants (K(i)s) comparable to that of wild-type ecotin. Iodine treatment of ecotin analogue Met84(A)Gly resulted in the deactivation of ecotin, caused by peptide backbone cleavage at its P1 reactive site. Upon iodine treatment, active trypsin could be released from the protein complex with ecotin analogue Met84(A)Gly. This constitutes a novel strategy for modulation of serine protease activity and more generally for alteration of protein-protein interaction by a simple chemical reagent.

N-Substituted 2-amino-4-pentenoic acid derivatives employed for the protection of racemic amino acids were shown to be capable of permitting the chromatographic separation of R and S isomers. When Nα was disubstituted with benzyl and phenylfluorenyl groups, the racemic amino acids could be separated with facility on open silica gel columns. Further, the optically pure N-protected amino acids so derived could be used for the preparation of misacylated suppressor transfer RNAs.

Aspartates 25 and 125, the active site residues of HIV-1 protease, participate functionally in proteolysis by what is believed to be a general acid-general base mechanism. However, the structural role that these residues may play in the formation and maintenance of the neighboring S1/S1' substrate binding pockets remains largely unstudied. Because the active site aspartic acids are essential for catalysis, alteration of these residues to any other naturally occurring amino acid by conventional site-directed mutagenesis renders the protease inactive, and hence impossible to characterize functionally. To investigate whether Asp-25 and Asp-125 may also play a structural role that influences substrate processing, a series of active site protease mutants has been produced in a cell-free protein synthesizing system via readthrough of mRNA nonsense (UAG) codons by chemically misacylated suppressor tRNAs. The suppressor tRNAs were activated with the unnatural aspartic acid analogues erythro-beta-methylaspartic acid, threo-beta-methylaspartic acid, or beta,beta-dimethylaspartic acid. On the basis of the specific activity measurements of the mutants that were produced, the introduction of the beta-methyl moiety was found to alter protease function to varying extents depending upon its orientation. While a beta-methyl group in the erythro orientation was the least deleterious to the specific activity of the protease, a beta-methyl group in the threo orientation, present in the modified proteins containing threo-beta-methylaspartate and beta,beta-dimethylaspartate, resulted in specific activities between 0 and 45% of that of the wild type depending upon the substrate and the substituted active site position. Titration studies of pH versus specific activity and inactivation studies, using an aspartyl protease specific suicide inhibitor, demonstrated that the mutant proteases maintained bell-shaped pH profiles, as well as suicide-inhibitor susceptibilities that are characteristic of aspartyl proteases. A molecular dynamics simulation of the beta-substituted aspartates in position 25 of HIV-1 protease indicated that the threo-beta-methyl moiety may partially obstruct the adjacent S1' binding pocket, and also cause reorganization within the pocket, especially with regard to residues Val-82 and Ile-84. This finding, in conjunction with the biochemical studies, suggests that the active site aspartate residues are in proximity to the S1/S1' binding pocket and may be spatially influenced by the residues presented in these pockets upon substrate binding. It thus seems possible that the catalytic residues cooperatively interact with the residues that constitute the S1/S1' binding pockets and can be repositioned during substrate binding to orient the active site carboxylates with respect to the scissile amide bond, a process that likely affects the facility of proteolysis.

A novel strategy has been developed to generate trypsin from trypsinogen without proteolytic processing. The unnatural amino acid allylglycine was incorporated into a trypsinogen variant to permit cleavage specifically at Ile-16, the prototypical activation site, and generate the active protease, trypsin. A suppressor tRNA, activated with allylglycine, was used to synthesize the allylglycine trypsinogen variant by in vitro translation of an mRNA transcript that placed the UAG stop codon immediately prior to the authentic trypsin coding region. Iodine treatment of the variant trypsinogen resulted in trypsin that was fully active and kinetically indistinguishable from wild type recombinant trypsin. Using single substrates, the iodine treated variant exhibited a catalytic profile essentially identical to that of wild type recombinant rat trypsin (kcat/KM=3.7±0.5 vs 3.7±0.8μM−1s−1, respectively). Furthermore, the specificity profiles generated from substrate combinatorial libraries are indistinguishable. These results illustrate that (1) iodine activated allylglycine trypsinogen is virtually identical to enteropeptidase activated recombinant trypsinogen and (2) this novel technique is a feasible alternative to achieve site specific cleavage of serine protease zymogens.

Several derivatives of aspartic acid were protected on Nαas their NVOC derivatives, and on the side chain carboxylates as nitroveratryl esters. Following activation as the cyanomethyl esters, these fully protected aspartate derivatives were converted to the respective pdCpA esters. The protected aspartyl-pdCpA esters were then utilized as substrates for T4 RNA ligase in the presence of in vitro transcripts of tRNA lacking the pCpA dinucleotide normally found at the 3'-end. In this fashion, several misacylated tRNAs were prepared; following photolytic deprotection, these were employed successfully for incorporation into proteins at predetermined positions.Key words: aminoacylated nucleotides, amino acid protection, protein synthesis, tRNA activation.

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTChemically Mediated Site-Specific Cleavage of ProteinsBixun Wang, Michiel Lodder, Jia Zhou, Teaster T. Baird,, Kathlynn C. Brown, Charles S. Craik, and Sidney M. HechtView Author Information Departments of Chemistry and Biology University of Virginia, Charlottesville, Virginia 22901 Department of Pharmaceutical Chemistry University of California San Francisco, California 94143 Cite this: J. Am. Chem. Soc. 2000, 122, 30, 7402–7403Publication Date (Web):July 12, 2000Publication History Received21 January 2000Published online12 July 2000Published inissue 1 August 2000https://doi.org/10.1021/ja0002262Copyright © 2000 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views535Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (60 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Bond cleavage,Crystal cleavage,Peptides and proteins,Rodent models,Solvents Get e-Alerts

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTCaged HIV-1 Protease: Dimerization Is Independent of the Ionization State of the Active Site AspartatesGlenn F. Short, Michiel Lodder, Andrei L. Laikhter, Tuncer Arslan, and Sidney M. HechtView Author Information Departments of Chemistry and Biology University of Virginia, Charlottesville, Virginia 22901 Cite this: J. Am. Chem. Soc. 1999, 121, 2, 478–479Publication Date (Web):January 5, 1999Publication History Received2 November 1998Published online5 January 1999Published inissue 1 January 1999https://pubs.acs.org/doi/10.1021/ja9838054https://doi.org/10.1021/ja9838054rapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views314Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Allyl group,Hydrocarbons,Monomers,Oligomers,Peptides and proteins Get e-Alerts

A new strategy for studying the mechanism of translation initiation in eukaryotes has been developed. The strategy involves the use of an in vitro translation system to incorporate a non-natural fluorescent amino acid into a protein from a suppressor tRNAPheCUA misacylated with that amino acid. It is thereby possible to monitor translation initiation efficiency at an AUG codon in different contexts; this is illustrated for three constructs encoding Escherichia coli dihydrofolate reductase mRNA with different translation initiation regions. Fluorescence measurements after in vitro translation of the mRNAs in rabbit reticulocyte lysate reflected differences in the position and efficiency of translation initiation and, therefore, can be used for characterization of the translation initiation process.

The 4-pentenoyl group and a number of derivatives have been studied as protecting groups for N(alpha) of the aminoacyl moiety in misacylated tRNAs. The unsubstituted 4-pentenoyl group itself was found to function as efficiently as any of the derivatives studied. Four different N-(4-pentenoyl)aminoacyl-tRNA(CUA)s were prepared and shown to undergo deprotection readily upon admixture of aqueous iodine; the derived misacylated tRNAs all functioned well as suppressors of a nonsense codon in an in vitro protein biosynthesizing system. Also prepared were four N(alpha)-(4-pentenoyl)aspartyl-tRNA(CUA)s that were protected on the side chain carboxylate as the nitroveratryl ester. Following treatment with aqueous iodine, the misacylated suppressor tRNAs incorporated the aspartate derivatives into position 27 of dihydrofolate reductase by suppression of a UAG codon in the mRNA. The suppression yields were significantly better than those obtained when side chain protection was absent. The resulting "caged proteins" were inactive, but full catalytic potential was restored by irradiation under conditions sufficient to effect deprotection of the side chain carboxylate moiety.

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTChemical Deprotection Strategy for the Elaboration of Misacylated Transfer RNA'sMichiel Lodder, Serguei Golovine, and Sidney M. HechtView Author Information Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901 Cite this: J. Org. Chem. 1997, 62, 4, 778–779Publication Date (Web):February 21, 1997Publication History Received20 November 1996Published online21 February 1997Published inissue 1 February 1997https://pubs.acs.org/doi/10.1021/jo962170thttps://doi.org/10.1021/jo962170trapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views505Altmetric-Citations56LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Iodine,Monomers,Peptides and proteins,Protective groups,Reaction products Get e-Alerts