The last several years have seen a paradigm shift in biology brought about by the sequencing of the genomes of numerous organisms. The next important step in the post-genomic era is to identify the function of all the genes and gene products in a given genome. To assist in this objective, the long-term goal of the research described in this proposal is the development of protein threading algorithms which, when coupled to the appropriate active-site functional descriptors, identify both the global fold and the biochemical function of the protein. To be relevant in the post-genomic era, these methods must be applicable on a genomic scale and provide information beyond sequence-based, evolutionary approaches. Thus, the predicted structures must be at the requisite resolution to be able to identify biochemical function and binding regions in the protein. However, threading models often have significant errors in their alignments, even when the global fold is correct. Thus, techniques must be developed to improve the initial alignments generated by threading approaches. To achieve these objectives, the following specific alms are proposed to realize the goal of a predicted sequence-to-structure-to-function methodology: (1) Dr. Skolnick's current generation of threading algorithms will be further improved by enhancements in the scoring functions that evaluate sequence-structure specificity. (2) Algorithms that refine distant threading models will be further developed and generalized. Such techniques should be able to take structures whose backbone root-mean-square deviation from native is 8-10 A to the 4-6 A range necessary for active site identification. (3) An expanded, high quality library of three-dimensional, active-site functional motifs will be developed. (4) Whole genome threading followed by threading model refinement and active-site library screening will be carried out on M. genitalium, E. coli, S. cerevisiae, C. elegans and human. (5) A structure-function database of fold/function prediction of these five genomes will be constructed and will be available on a website (http://bioinformatics.danforthcenter.org).

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM048835-09
Application #
6498679
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Wehrle, Janna P
Project Start
1994-05-01
Project End
2003-01-31
Budget Start
2002-02-01
Budget End
2003-01-31
Support Year
9
Fiscal Year
2002
Total Cost
$195,000
Indirect Cost
Name
Donald Danforth Plant Science Center
Department
Type
DUNS #
City
St. Louis
State
MO
Country
United States
Zip Code
63132
Srinivasan, Bharath; Marks, Hanna; Mitra, Sreyoshi et al. (2016) Catalytic and substrate promiscuity: distinct multiple chemistries catalysed by the phosphatase domain of receptor protein tyrosine phosphatase. Biochem J 473:2165-77
Zhou, Hongyi; Skolnick, Jeffrey (2016) A knowledge-based approach for predicting gene-disease associations. Bioinformatics 32:2831-8
Skolnick, Jeffrey; Gao, Mu; Zhou, Hongyi (2016) How special is the biochemical function of native proteins? F1000Res 5:
Roy, Ambrish; Skolnick, Jeffrey (2015) LIGSIFT: an open-source tool for ligand structural alignment and virtual screening. Bioinformatics 31:539-44
Zhou, Hongyi; Gao, Mu; Skolnick, Jeffrey (2015) Comprehensive prediction of drug-protein interactions and side effects for the human proteome. Sci Rep 5:11090
Skolnick, Jeffrey; Gao, Mu; Roy, Ambrish et al. (2015) Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function. Bioorg Med Chem Lett 25:1163-70
Srinivasan, Bharath; Skolnick, Jeffrey (2015) Insights into the slow-onset tight-binding inhibition of Escherichia coli dihydrofolate reductase: detailed mechanistic characterization of pyrrolo [3,2-f] quinazoline-1,3-diamine and its derivatives as novel tight-binding inhibitors. FEBS J 282:1922-38
Srinivasan, Bharath; Tonddast-Navaei, Sam; Skolnick, Jeffrey (2015) Ligand binding studies, preliminary structure-activity relationship and detailed mechanistic characterization of 1-phenyl-6,6-dimethyl-1,3,5-triazine-2,4-diamine derivatives as inhibitors of Escherichia coli dihydrofolate reductase. Eur J Med Chem 103:600-14
Boles, Richard G; Hornung, Holly A; Moody, Alastair E et al. (2015) Hurt, tired and queasy: Specific variants in the ATPase domain of the TRAP1 mitochondrial chaperone are associated with common, chronic ""functional"" symptomatology including pain, fatigue and gastrointestinal dysmotility. Mitochondrion 23:64-70
Gao, Mu; Zhou, Hongyi; Skolnick, Jeffrey (2015) Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis. Structure 23:1362-9

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