Department of Chemistry

Our laboratory investigates the chemical, physical, and structural properties of proteins and nucleic acids using a variety of spectroscopic and biochemical techniques, in addition to x-ray crystallography.  We are interested in exploring how the structure and specific intermolecular interactions of macromolecules affects their biochemical activities. 

Specific Research Projects

snoRNAs and their cognate proteins

Small nucleolar RNAs (snoRNAs) are small (~30 nt) RNAs derived from introns excised from transcripts of protein-encoding genes.  snoRNAs are essential in pre-ribosomal RNA processing by specifically guiding O2′-methylation of ribosomal RNA.  These modifications are critical for biogenesis of ribosomes.  A number of nucleolar proteins specifically recognize snoRNAs and form a complex which is responsible for the methylation activity.  I have crystallized one of these snoRNA binding-proteins and am currently solving the structure.  Future studies will involve biochemical and biophysical characterization of protein-snoRNA complexes, and attempts to crystallize snoRNA-protein complexes.  This project involves a collaboration with the laboratory of Prof. E. Stuart Maxwell in the Biochemistry Dept. at NCSU. 

Fig. 1 Crystal structure of the L7 snoRNA-binding protein from Methanococcus jannaschii

Ribonucleotide Reductases

The ribonucleotide reductase family of metaloenzymes catalyze the conversion of ribonucleotides to deoxyribonucleotides, a crucial step in DNA biosynthesis and repair.  This family of enzymes is ubiquitous among the three kingdoms of cellular organisms, and a number of DNA-viruses produce their own ribonucleotide reductases during infections.  Consequently, these enzymes are potential drug-targets for anti-viral, anti-bacterial, and anti-tumor therapies.  In collaboration with Hector H. Hernandez in Cathy Drennan’s laboratory in the MIT Chemistry Department, I have cloned a number of ribonucleotide reductases and their associated proteins from several species of bacteria and thermophilic Archaeal organisms.  Our current goals are to optimize expression of these protein, characterize the biochemical activities, and initiate biophysical and structural studies. 

RNA Editing, Adenosine Deaminases, and Z-RNA

RNA editing is the process of modifying the mRNA message by changing its coding capacity.  The type of RNA-editing which I am interested is adenosine deamination, a process where a specific adenosine residues of an mRNA molecule are deaminated to produce the nucleotide inosine.  Subsequently inosine functions and codes as if it were guanosine, and consequently changes the genetically-encoded message.  The class of proteins responsible for adenosine deamination are known as ADARs (adenosine deaminases which act on double-stranded RNAs).  There are three known adenosine deaminases, and two specific neuronal receptors which require RNA-editing for proper physiological functioning.  It is poorly understood how the ADAR proteins recognize their mRNA substrates and specifically deaminate particular adenosines.   Research in our lab will investigate the biochemical, biophysical, and structural properties of the ADAR1 adenosine deaminase in an effort to understand the structural basis of substrate recognition.  Additionally, biochemical and structural studies on the ADAR1 catalytic deaminase domain will be pursued in order to investigate the chemistry of deamination.

Fig. 2 View down the recognition helix of the hADAR1 Za domain bound to Z-(dCrG)₃.

Representative Publications

1.  Schwartz, T., Lowenhaupt, K., Kim, Y.-G., Li, L., Brown, BA, II, Herbert, A., and Rich, A. (1999) Proteolytic dissection of Zab, the Z-DNA binding domain of human ADAR1. Journal of Biological Chemistry 274, 2899–2906. 

2.  Brown, BA, II, Lowenhaupt, K., Wilbert, C.M., Hanlon, E.B., and Rich, A. (2000) The Za domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA. Proceedings of the National Academy of Science, USA 97,13532–13536. 

3.  Brown, BA, II and Rich, A. (2001) The left-handed double helical nucleic acids. Acta Biochimica Polonica 48, 295–312. 

4.   Brown, BA, II, Athanasiadis, A., Hanlon, G., Wilbert, C.M, Lowenhaupt, K., and Rich, A.  (2002) Crystallization of the Za domain of human ADAR1 complexed with a chimeric oligonucleotide in the left-handed Z-conformation. Acta Crystallographica, Section D58, 120–123.