Structural Proteomics: annotating the genome using 3D structure
EMSL Project ID
2583
Abstract
Most genomes are annotated based on sequence homology but there are many proteins encoded in the genome where the sequence do not have homology to other proteins with known functions and these are presently annotated as 'hypothetical proteins'. A protein's biochemical function is often dictated by its 3 dimensional shape. A major goal of structural proteomics is to determine the structure of all the proteins in a genome. We hope that the structures of these hypothetical proteins would yield valuable clues as to the function of the proteins. The wealth of structural informations that would come from the structural proteomics project could also enrich our understanding of protein folding and the evolutionary relationship between genomes. Current experimental methods in determining structure are x-ray crystallography and NMR spectroscopy. Inspite of NMR spectroscopy's protein size limitation, NMR spectroscopy play a significant contribution to structural proteomics (Yee et al.). We have used NMR spectroscopy as part of our structural proteomics efforts. We want to determine the structures of hypothetical proteins and proteins with known functions but no sequence homology to known structures. In continuation of our structural proteomics project, we have screened proteins that appear to be well folded and amenable for structure determination using NMR spectroscopy. Our recent efforts were concentrated on yeast proteins as representative of eukaryotic systems. Attached are the 15N-HSQC spectra of three of these proteins.YIL008w, also known as urm1_yeast, is a hypothetical protein. Yeast cells that had deletion mutation on this gene were observed to be viable but this gene is highly conserved among higher eukaryotes like mouse, rice, and human. YKL086w is also a hypothetical protein conserved among fly, mouse, and human. 3D structure of these hypothetical proteins could give us some clue as to its functions. YKL167c is a structural constituent of the ribosome, it is suggested to be involve in yeast protein biosynthesis. Deletion mutation of this gene showed that the cells are viable although they are cold sensitive and respiration deficient. 3D structure of this protein could shed some light on the possible mechanism of action of this protein. This research is part of the Northeast Structural Genomics Consortium (NESG), an NIH-funded Center for structural genomics, and the Ontario program in Structural Proteomics. Project Update: Please see the attached table. Latest publications which made use of EMSL spectrometers: Yee, A., Chang, X., Pineda, A., Wu, B., Semesi, A., Le, B., Ramelot, T., Lee, G., Bhattarcharya, S., et al., NMR approach to structural proteomics. PNAS 99, 1825-30 (2002). Pineda-Lucena, A., Yi, G., Chang, X., Cort, J., Kennedy, M., Edwards, A., & Arrowsmith, C. Solution structure of the hypothetical protein Mth0637 from Methanobacterium thermoautotrophicum. J. Biomol. NMR (2002), accepted. Pineda-Lucena, A., Liao, J., Wu, B., Yee, A., Cort, J., Kennedy, M., Edwards, A., & Arrowsmith, C. NMR structure of the hypothetical protein encoded by the YjbJ gene from Escherichia coli. Proteins: Structure, Function and Genetics (2002), accepted. J.R. Cort, A.Yee, A.M. Edwards, C.H. Arrowsmith and M.A. Kennedy, Structure-based classification of hypothetical protein MTH538 from Methanobacterium thermoautotrophicum J. Mol. Biol. 302, 189-203 (2000). D. Christendat, A Yee, A. Dharamsi, Y. Kluger, A. Savchenko, J. R.Cort, V. Booth, C. D. Mackereth, V. Saridakis, I. Ekiel, G. Kozlov, K. L. Maxwell, N. Wu, L. P. McIntosh, K. Gehring, M. A. Kennedy, A. R. Davidson, E. F. Pai, M. Gerstein, A. M. Edwards and C. H. Arrowsmith, Structural Proteomics of an archaeon. Nature Struct. Biol., 7, 903-909 (2000).
Project Details
Project type
Capability Research
Start Date
2002-10-30
End Date
2003-10-23
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members