The long term goals of this research include altering the 23S RNA in ribosomes to enable the in vitro preparation of proteins containing a broad variety of unnatural amino acids other than alpha-L-amino acids in quantities sufficient for routine biochemical studies. This will be done employing a novel selection strategy that uses modified derivatives of puromycin, a structural mimic of the 3'-end of aminoacyl-tRNA which terminates (cellular) protein synthesis in prokaryotes, resulting in cell death. By screening a large library of modified ribosomes, each of which has been expressed in E. coli following cell transformation with a (modified) plasmid-born 23S ribosomal RNA, for sensitivity to puromycin analogues containing a specific, structurally modified amino acid, it is possible to identify ribosomes potentially capable of recognizing (and incorporating) those same amino acids attached to transfer RNAs. The enhanced incorporation of beta amino acids has been achieved in this fashion. For the five-year period of requested support, the 23S rRNA constituent of ribosomes will be altered to permit the incorporation into proteins of several types of modified amino acids that native ribosomes cannot incorporate. This includes a variety of beta amino acids, which will allow definition of the specific positions/stereochemistry of substituents tolerated by the modified ribosomes. Also studied will be the ability of the beta amino acids to stabilize secondary structures in proteins.

Public Health Relevance

The present project will provide access to modified ribosomes capable of incorporating very unusual structurally modified amino acids into proteins, and will do so using an innovative new strategy. It will also enable novel insights into the molecular mechanism of ribosomally mediated protein synthesis, and possibly into ways to change the mechanism. It will permit novel biomaterials to be prepared, having broad application to the analysis and treatment of diseases, including cancer and conditions associated with aging.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Synthetic and Biological Chemistry B Study Section (SBCB)
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Gerratana, Barbara
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Arizona State University-Tempe Campus
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United States
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Chen, Shengxi; Maini, Rumit; Bai, Xiaoguang et al. (2017) Incorporation of Phosphorylated Tyrosine into Proteins: In Vitro Translation and Study of Phosphorylated I?B-? and Its Interaction with NF-?B. J Am Chem Soc 139:14098-14108
Bai, Xiaoguang; Talukder, Poulami; Daskalova, Sasha M et al. (2017) Enhanced Binding Affinity for an i-Motif DNA Substrate Exhibited by a Protein Containing Nucleobase Amino Acids. J Am Chem Soc 139:4611-4614
Chowdhury, Sandipan Roy; Chauhan, Pradeep S; Dedkova, Larisa M et al. (2016) Synthesis and Evaluation of a Library of Fluorescent Dipeptidomimetic Analogues as Substrates for Modified Bacterial Ribosomes. Biochemistry 55:2427-40
Talukder, Poulami; Dedkova, Larisa M; Ellington, Andrew D et al. (2016) Synthesis of alanyl nucleobase amino acids and their incorporation into proteins. Bioorg Med Chem 24:4177-4187
Gerasimova, Yulia V; Yakovchuk, Petro; Dedkova, Larisa M et al. (2015) Expedited quantification of mutant ribosomal RNA by binary deoxyribozyme (BiDz) sensors. RNA 21:1834-43
Chowdhury, Sandipan Roy; Maini, Rumit; Dedkova, Larisa M et al. (2015) Synthesis of fluorescent dipeptidomimetics and their ribosomal incorporation into green fluorescent protein. Bioorg Med Chem Lett 25:4715-8
Maini, Rumit; Dedkova, Larisa M; Paul, Rakesh et al. (2015) Ribosome-Mediated Incorporation of Dipeptides and Dipeptide Analogues into Proteins in Vitro. J Am Chem Soc 137:11206-9
Maini, Rumit; Chowdhury, Sandipan Roy; Dedkova, Larisa M et al. (2015) Protein Synthesis with Ribosomes Selected for the Incorporation of ?-Amino Acids. Biochemistry 54:3694-706