arbely.jpg
Ph.D.: The Hebrew University of Jerusalem, Israel
Post-doctorate: MRC Center for Protein Engineering and Laboratory of Molecular Biology, Cambridge, UK
Position: Senior Lecturer
Department of Chemistry
E-mail: arbely@bgu.ac.il
Webpage: www.bgu.ac.il/~arbely

 

Expanding the Repertoire of Ribosomally-Synthesized Proteins

 

 

  

  • Background

The translation mechanism has been evolved over hundreds of millions of years to translate 64 triple-nucleotide codons, each encoding either one of the common 20 amino acids, or the termination of translation. Yet, this machinery is far from exploiting its full potential – proteins with expanded chemistry can be ribosomally synthesized by site-specific incorporation of non-proteinogenic amino acids, using the amber stop codon (UAG) and an orthogonal aminoacyl-tRNA synthetase/tRNA pair. The chemical and structural diversity of such proteins can be expanded even further by exploiting the unique chemistry of bacteriocins - ribosomally synthesized peptides, transformed into biologically active compounds by a series of unique structural and chemical post-translational modifications. Our laboratory is interested in developing and applying different methods for ribosomal expression of chemically and structurally-modified proteins for basic biochemical or biophysical research and as a platform for developing peptide-based, bioactive molecules in general and particularly for novel antibiotics.

  • Current research

1. Developing and applying methods for in-vivo incorporation of non-proteinogenic amino acids. Genetic code engineering allows the site-specific incorporation of tailor-made amino acids into recombinant proteins. Equipped with a unique biophysical or chemical property, such amino acids may aid in studying the structure and cellular function of proteins. For example, the incorporation of modified amino acids carrying a naturally occurring post-translational modification such as acetylation or phosphorylation. Using genetic code engineering and directed evolution, we aim to develop and apply novel methods for in vivo and in vitro studies of post-translationally modified proteins. Specifically, we are interested in studying the effect of acetylation on the structure, subcellular localization and DNA binding affinity of transcription factors such as NF-B and p53. In recent years a direct link was found between acetylation and cellular metabolism. In light of the high frequency of metabolic disorders associated with diseases ranging from cancer to obesity, we aim at understanding how cellular metabolism and acetylation level are correlated with acetylation and transcription activity of key transcription factors.

2. Bacteriocin engineering and DNA directed peptide synthesis. Bacteriocins are ribosomally-synthesized and heavily posttranslationally modified bioactive (usually antimicrobial) peptides. In general, the biosynthesis of bacteriocins includes a series of chemical and structural modifications of the C-terminal part of a ribosomally synthesized precursor peptide. Typically, the enzymes that catalyze the biosynthetic transformations are directed by the N-terminal part of the precursor peptide, which is usually cleaved off, leaving behind the modified and bioactive version of the C-terminal peptide. Consequently, the biosynthetic enzymes show a high level of promiscuity allowing the biosynthesis of different natural products using the same biosynthetic pathway. Our laboratory is studying the biosynthetic pathways of different bacteriocins aiming at exploiting the high level of promiscuity for the production of DNA encoded libraries of cyclized and chemically modified peptides.

 

  • Selected publications

Arbely E. and Arkin I.T. (2004). Experimental Measurement of The Strength of a Cα- H…O Bond in a Lipid Bilayer. J. Am. Chem. Soc. 126:5362-5363.

Arkin I.T., Xu H., Jensen M.O., Arbely E., Bennett E.R., Bowers K.J., Chow E., Dror R.O., Eastwood M.P., Flitman-Tene R., Gregersen B.A., Klepeis J.L., Kolossváry I., Shan Y. and Shaw D.E. (2007). Mechanism of Na+/H+ Antiporting. Science 317:799-803.

Arbely E., Rutherford J.T., Sharpe D.T., Ferguson N. and Fersht A.R. (2009). Downhill versus Barrier-Limited Folding of BBL 1: Energetic and Structural Perturbation Effects upon Protonation of a Histidine of Unusually Low pKa. J. Mol. Bio. 387:986-992.

Arbely E., Rutherford J.T., Neuweiler H., Sharpe D.T., Ferguson N. and Fersht A.R. (2010). Carboxyl pKa-Values and Acid Denaturation of BBL. J. Mol. Bio. 403:313-327.

Arbely E., Natan E., Brandt T., Allen M.D., Veprintsev D.B., Robinson C.V., Chin J. W., Joerger A.C. and Fersht A.R. (2011). Acetylation of Lysine 120 of p53 endows DNA binding specificity at effective physiological salt concentration. Proc. Natl. Acad. Sci. USA. 108:8251-8256.

Arbely E., Torres-Kolbus J., Deiters, A., Chin J.W. (2012). Photocontrol of tyrosine phosphorylation in mammalian cells via genetic encoding of photocaged tyrosine. J. Am. Chem. Soc. 134:11912-11915.