abstract: The biological and chemical diversity of protein structure and function can be greatly expanded by position-specific incorporation of non-natural amino acids bearing a variety of functional groups. Non-cognate amino acids can be incorporated into proteins at specific sites by using orthogonal aminoacyl-tRNA synthetase/tRNA pairs in conjunction with nonsense, rare, or 4-bp codons. There has been considerable progress in developing new types of amino acids, in identifying novel methods of tRNA aminoacylation, and in expanding the genetic code to direct their position. Chemical aminoacylation of tRNAs is accomplished by acylation and ligation of a dinucleotide (pdCpA) to the 3'-terminus of truncated tRNA. This strategy allows the incorporation of a wide range of natural and unnatural amino acids into pre-determined sites, thereby facilitating the study of structure-function relationships in proteins and allowing the investigation of their biological, biochemical and biophysical properties. Described in Chapter 1 is the current methodology for synthesizing aminoacylated suppressor tRNAs. Aminoacylated suppressor tRNACUAs are typically prepared by linking pre-aminoacylated dinucleotides (aminoacyl-pdCpAs) to 74 nucleotide (nt) truncated tRNAs (tRNA-COH) via a T4 RNA ligase mediated reaction. Alternatively, there is another route outlined in Chapter 1 that utilizes a different pre-aminoacylated dinucleotide, AppA. This dinucleotide has been shown to be a suitable substrate for T4 RNA ligase mediated coupling with abbreviated tRNA-COHs for production of 76 nt aminoacyl-tRNACUAs. The synthesized suppressor tRNAs have been shown to participate in protein synthesis in vitro, in an S30 (E. coli) coupled transcription-translation system in which there is a UAG codon in the mRNA at the position corresponding to Val10. Chapter 2 describes the synthesis of two non-proteinogenic amino acids, L-thiothreonine and L-allo-thiothreonine, and their incorporation into predetermined positions of a catalytically competent dihydrofolate reductase (DHFR) analogue lacking cysteine. Here, the elaborated proteins were site-specifically derivitized with a fluorophore at the thiothreonine residue. The synthesis and incorporation of phosphorotyrosine derivatives into DHFR is illustrated in Chapter 3. Three different phosphorylated tyrosine derivatives were prepared: bis-nitrobenzylphosphoro-L-tyrosine, nitrobenzylphosphoro-L-tyrosine, and phosphoro-L-tyrosine. Their ability to participate in a protein synthesis system was also evaluated. / Dissertation/Thesis / Ph.D. Chemistry 2013

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Στην παρούσα διατριβή παρουσιάζεται μια νέα μεθοδολογία σύνθεσης μη-πρωτεϊνικών αμινοξέων (ΜΠΑ) κατάλληλων για εφαρμογές στην πεπτιδική σύνθεση με χρήση του ασπαραγινικού οξέος ως χειρόμορφου εκμαγείου. Η μεθοδολογία αυτή βασίζεται στην επιτυχή και σε καλές αποδόσεις σύνθεση της β-αλδεΰδης του Ν-τριτυλοασπαραγινικού τριτ-βουτυλεστέρα, η οποία αποτελεί την ένωση «κλειδί». Αυτή στη συνέχεια έδωσε μια ποικιλία νέων ΜΠΑ μέσω αντιδράσεων Wittig, Horner-Emmons ή με επίδραση οργανοψευδραργυρικών αντιδραστηρίων. Ανάλογες μελέτες με σκοπό την σύνθεση των αντίστοιχων ομολόγων τους με έναν άνθρακα λιγότερο ή περισσότερο στην πλευρική αλυσίδα, ξεκινώντας από σερίνη ή γλουταμινικό οξύ δεν απέδωσαν τα αναμενόμενα αποτελέσματα ή ήταν ανεπιτυχείς. / In the present dissertation a new methodology is reported for the synthesis of novel non-proteinogenic amino acids (NPAAs) suitable for applications in solid phase peptide synthesis. This methodology involves aspartic acid as chiral template and relies on the successful and in good yields pepraration of the key N-tritylaspartic tert-butyl ester’s β-aldehyde, which when followed by Wittig, Horner-Emmons or Grignard type reactions may result in a variety of new NPAAs. Furthermore unsuccessful attempts towards the application of the present methodology for the synthesis of NPAA homologues bearing one carbon atom less or more in the side chain by using as chiral templates serine or glutamic acid, respectively, are also reported.