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1.  Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence 
Science (New York, N.Y.)  1998;282(5396):2022-2028.
Comparative analysis of predicted protein sequences encoded by the genomes of Caenorhabditis elegans and Saccharomyces cerevisiae suggests that most of the core biological functions are carried out by orthologous proteins (proteins of different species that can be traced back to a common ancestor) that occur in comparable numbers. The specialized processes of signal transduction and regulatory control that are unique to the multicellular worm appear to use novel proteins, many of which re-use conserved domains. Major expansion of the number of some of these domains seen in the worm may have contributed to the advent of multicellularity. The proteins conserved in yeast and worm are likely to have orthologs throughout eukaryotes; in contrast, the proteins unique to the worm may well define metazoans.
PMCID: PMC3057080  PMID: 9851918
2.  Covalent labeling of nuclear vitamin D receptor with affinity labeling reagents containing a cross-linking probe at three different positions of the parent ligand: structural and biochemical implications 
Bioorganic chemistry  2009;37(2):57-63.
Structure-functional characterization of vitamin D receptor (VDR) requires identification of structurally distinct areas of VDR-ligand-binding domain (VDR-LBD) important for biological properties of 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). We hypothesized that covalent attachment of the ligand into VDR-LBD might alter ‘surface structure’ of that area influencing biological activity of the ligand. We compared anti-proliferative activity of three affinity alkylating derivatives of 1,25(OH)2D3 containing an alkylating probe at 1,3 and 11 positions. These compounds possessed high-affinity binding for VDR; and affinity labeled VDR-LBD. But, only the analog with probe at 3-position significantly altered growth in keratinocytes, compared with 1,25(OH)2D3. Molecular models of these analogs, docked inside VDR-LBD tentatively identified Ser237 (helix-3: 1,25(OH)2D3-1-BE), Cys288 (β-hairpin region: 1,25(OH)2D3-3-BE,) and Tyr295 (helix-6: 1,25(OH)2D3-11-BE,) as amino acids that are potentially modified by these reagents. Therefore, we conclude that the β-hairpin region (modified by 1,25(OH)2D3-3-BE) is most important for growth-inhibition by 1,25(OH)2D3, while helices 3 and 6 are less important for such activity.
doi:10.1016/j.bioorg.2009.01.001
PMCID: PMC2696187  PMID: 19223058
1α ; 25-Dihydroxyvitamin D3; vitamin D receptor; vitamin D receptor-ligand binding domain; affinity labeling derivatives of 1α; 25-dihydroxyvitamin D3; growth inhibitory property of 1α; 25-dihydroxyvitamin D3 and its affinity labeling derivatives in keratinocyes; structural elements in vitamin D receptor-ligand binding domain; molecular modeling
3.  Survey of human mitochondrial diseases using new genomic/proteomic tools 
Genome Biology  2001;2(6):research0021.1-research0021.16.
Background
We have constructed Bayesian prior-based, amino-acid sequence profiles for the complete yeast mitochondrial proteome and used them to develop methods for identifying and characterizing the context of protein mutations that give rise to human mitochondrial diseases. (Bayesian priors are conditional probabilities that allow the estimation of the likelihood of an event - such as an amino-acid substitution - on the basis of prior occurrences of similar events.) Because these profiles can assemble sets of taxonomically very diverse homologs, they enable identification of the structurally and/or functionally most critical sites in the proteins on the basis of the degree of sequence conservation. These profiles can also find distant homologs with determined three-dimensional structures that aid in the interpretation of effects of missense mutations.
Results
This survey reports such an analysis for 15 missense mutations, one insertion and three deletions involved in Leber's hereditary optic neuropathy, Leigh syndrome, mitochondrial neurogastrointestinal encephalomyopathy, Mohr-Tranebjaerg syndrome, iron-storage disorders related to Friedreich's ataxia, and hereditary spastic paraplegia. We present structural correlations for seven of the mutations.
Conclusions
Of the 19 mutations analyzed, 14 involved changes in very highly conserved parts of the affected proteins. Five out of seven structural correlations provided reasonable explanations for the malfunctions. As additional genetic and structural data become available, this methodology can be extended. It has the potential for assisting in identifying new disease-related genes. Furthermore, profiles with structural homologs can generate mechanistic hypotheses concerning the underlying biochemical processes - and why they break down as a result of the mutations.
PMCID: PMC33397  PMID: 11423010

Results 1-3 (3)