My research is directed toward understanding structures of protein-RNA complexes in order to learn how protein nucleic acid interactions lead to specific chemical or cellular functions. The research emphasizes structure determination by X-ray crystallography but also uses many aspects of molecular biology, biochemistry, and biophysics. Currently, we are pursuing these areas of interest: (1) structure mechanism of splicing endonucleases and (2) structural mechanism of ribosome and spliceosome biogenesis by ribonucleoprotein particles.
Introns interrupt the continuity of genes including the tRNA genes of many organisms. In Eucarya and Archaea, splicing of tRNA introns requires the function of protein-based enzymes. The first step of the reaction is catalyzed by a site-specific endonuclease capable of recognizing and excising the introns. Yeast and archaeal tRNA-splicing endonucleases contain the same catalytic triad but recognize the two exon-intron junctions through different secondary structures in the precursor tRNA molecules. A complete understanding of these two different recognition mechanisms requires structural details of the pre-tRNAs, the endonucleases, and their interactions. We are currently working with the hypothesis that both archaeal and eukaryal endonucleases can induce a similar RNA-isomerization required for the reaction of phosphodiester bond breakage by binding specifically to their cognate RNA targets.
Ribosome and spliceosome are megadalton macromolecular complexes required for protein synthesis. Ribosome catalyzes the formation of peptide bond of every protein while spliceosome removes intervening sequences from RNA transcripts that direct protein synthesis. Both enzymes contain essential RNA subunits that are processed and chemically modified by another class of ribonucleoprotein particles called small nucleolar ribonucleoprotein particles (snoRNPs). The maturation process mediated by snoRNPs is complicated and involves many protein-protein, protein-RNA, and RNA-RNA interactions. We employ X-ray crystallographic techniques to visualize the three dimensional structures of these complexes along their functional pathways including substrate-bound and reaction intermediate complexes.
Wang, R., Preamplume, G., Terns, M. P., Terns, R. M. & Li, H. Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Structure2011, 19(2):257
Zhou J, Liang B, Li H. Structural and Functional Evidence of High Specificity of Cbf5 for ACA Trinucleotide. RNA2011, 17(2):244-250
Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H. Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle. Molecular Cell2010, 39(6):939-49
Zhou J, Liang B, Li H. Functional and structural impact of target uridine substitutions on the H/ACA ribonucleoprotein particle pseudouridine synthase. Biochemistry2010, 49(29):6276-81
Zhou J, Lv C, Liang B, Chen M, Yang W, Li H. Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study. Journal of Molecular Biology2010, 401(5):690-5