Dr. Adrian K. Arakaki
Research Scientist II
Adrian Arakaki
-
Contact information:
- Center for the Study of Systems Biology
- 250 14th Street NW, Room 140
- Atlanta GA, 30318, Mail Code:0590
- Tel :(404) 407-8977
- Fax: 404-385-7478
- Email:
Research Interests
- Protein structure prediction.
- Protein function prediction.
- Evolution of protein function.
- Cancer Metabolism.
List of publications:
[28] | Arakaki A.K., Mezencev R., Bowen N.J., Huang Y., McDonald J.F. and Skolnick J. (2008) "Identification of metabolites with anticancer properties by Computational Metabolomics" Molecular Cancer 7, 57 (Highly accessed). |
| [27] | Thomas S.H., Wagner R.D., Arakaki A.K., Skolnick J., Kirby J.R., Shimkets L.J., Sanford R.A. and Loffler F.E. "The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria" PLoS ONE 3, e2103. |
| [26] | Musumeci M.A., Arakaki A.K., Rial D.V., Catalano-Dupuy D.L. and Ceccarelli E.A. (2008) "Modulation of the enzymatic efficiency of ferredoxin-NADP(H) reductase by the amino acid volume around the catalytic site" FEBS Journal 275, 1350-1366. |
| [25] | Martinez R.J., Beazley M.J., Taillefert M., Arakaki A.K., Skolnick J. and Sobecky P.A. "Aerobic Uranium (VI) Bioprecipitation by Metal Resistant Bacteria Isolated from Radionuclide- and Metal-Contaminated Subsurface Soils" Environmental Microbiology 9, 3122-3133. |
| [24] | Arakaki A.K., Tian W. and Skolnick J. (2006) "High precision multi-genome scale reannotation of enzyme function by EFICAz" BMC Genomics 7:315. |
| [23] | Rial D.V., Arakaki A.K., Almara A.M., Orellano E.G. and Ceccarelli E.A. (2006) "Chloroplast Hsp70s are not involved in the import of ferredoxin-NADP+ reductase precursor" Physiologia Plantarum, 128, 618-632. |
| [22] | Zhang Y., Hubner I.A., Arakaki A.K., Shakhnovich E. and Skolnick J. (2005) "On the origin and highly likely completeness of single-domain protein structures" PNAS 103, 2605-2610. |
| [21] | Zhang Y., Arakaki A.K. and Skolnick J. (2005) "TASSER: an automated method for the prediction of protein tertiary structures in CASP6" Proteins, 61, 91-98. |
| [20] | Szilágýi A., Grimm V., Arakaki A.K. and Skolnick J. (2005) "Prediction of physical protein-protein interactions" Physical Biology 2, S1-S16. |
| [19] | Tian W., Arakaki A.K. and Skolnick J. (2004) "EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference" Nucleic Acids Research 32, 6226-6239. |
| [18] | Ceccarelli E.A., Arakaki A.K., Cortez N. and Carrillo N. (2004) "Functional plasticity and catalytic efficiency in plant and bacterial ferredoxin-NADP(H) reductases" Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology 1698, 155-165. |
| [17] | Arakaki A.K., Zhang Y., and Skolnick J. (2004) "Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment" Bioinformatics 20, 1087-1096. |
| [16] | Skolnick J., Zhang Y., Arakaki A.K., Kolinski A., Boniecki M., Szilágýi A. and Kihara D. (2003) "TOUCHSTONE: a unified approach to protein structure prediction" Proteins, 54, 469-479. |
| [15] | Lu L., Arakaki A.K., Lu H. and Skolnick J. (2003) "Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome" Genome Research, 13(6A), 1146-1154. |
| [14] | Arakaki A.K., Orellano E.G., Calcaterra N.B., Ottado J. and Ceccarelli E.A. (2001) "Involvement of the flavin si-face tyrosine on the structure and function of ferredoxin-NADP+ reductases" Journal of Biological Chemistry 276, 44419-44426. |
| [13] | Rial D.V., Arakaki A.K. and Ceccarelli E.A. (2000) "Interaction of the targeting sequence of chloroplast precursors with Hsp70 molecular chaperones" European Journal of Biochemistry 267, 6239-6248. |
| [12] | Piubelli L., Aliverti A., Arakaki A.K., Carrillo N., Ceccarelli E.A., Karplus P.A. and Zanetti G. (2000) "Competition between C-terminal tyrosine and nicotinamide modulates pyridine nucleotide affinity and specificity in plant ferredoxin-NADP(+) reductase" Journal of Biological Chemistry 275, 10472-10476. |
| [11] | Piubelli L., Aliverti A., Zanetti G., Arakaki A.K., Carrillo N., Ceccarelli E.A. and Karplus P.A. (1999) "Role of the C-terminal tyrosine of plant ferredoxin:NADP+ reductase in NADP+ binding affinity and pyridine nucleotide specificity" in Flavins and Flavoproteins 1999 (S. Ghisla, P. Kroneck, P. Macheroux and H. Sund, editors) Rudolf Weber, Berlin, Germany, 269-272. |
| [10] | Medina M., Gómez-Moreno C., Cammack R., Arakaki A.K., Carrillo N. and Ceccarelli E.A. (1999) "Advanced EPR spectroscopic studies of mutants of ferredoxin-NADP+ reductase from pea" in Flavins and Flavoproteins 1999 (S. Ghisla, P. Kroneck, P. Macheroux and H. Sund, editors) Rudolf Weber, Berlin, Germany, 87-90. |
| [09] | Deng Z., Aliverti A., Zanetti G., Arakaki A.K., Ottado J., Orellano E.G., Calcaterra N.B., Ceccarelli E.A., Carrillo N. and Karplus A. (1999) "A productive NADP+ binding mode of ferredoxin-NADP + reductase revealed by protein engineering and crystallographic studies" Nature Structural Biology 6, 847-853. |
| [08] | Dionisi Hebe M., Checa Susana K., Krapp Adriana R., Arakaki Adrián K., Ceccarelli Eduardo A., Carrillo Néstor and Viale Alejandro M. (1998) "Cooperation of the DnaK and GroE chaperone systems in the folding pathway of plant ferredoxin-NADP+ reductase expressed in Escherichia coli" European Journal of Biochemistry 251, 724-728. |
| [07] | Arakaki Adrián K., Ceccarelli Eduardo A. and Carrillo Néstor (1997) "Plant-type ferredoxin-NADP+ reductases: a basal structural framework and a multiplicity of functions" FASEB Journal 11, 133-140. |
| [06] | Ottado Jorgelina, Calcaterra Nora B., Arakaki Adrián K., Orellano Elena G., Carrillo Néstor and Ceccarelli Eduardo A. (1996) "On The Role Of Aromatic Amino Acids Interacting With Fad In Plant-type Ferredoxin-NADP+ Reductases" in Flavins and Flavoproteins 1997 (K.J. Stevenson, V. Massey and C.H. Williams, Jr., eds.) University of Calgary Press, Calgary, Canada, 501-504. |
| [05] | Arakaki Adrián K. and Viale Alejandro M. (1995) "Origins of Organelles in Plants and Algae As Inferred From Comparisons of Highly Conserved Chaperone Proteins" in Progress Research in Photosynthesis (P. Mathis, ed.) Kluwer, Dordrecht, 971-974. |
| [04] | Carrillo Néstor, Calcaterra Nora B., Krapp Adriana R., Arakaki Adrián K., Ottado Jorgelina, Serra Esteban, Orellano Elena G. and Ceccarelli Eduardo A. (1994) "From Photosynthesis To Nitrogen Assimilation. A perspective On Plant Ferredoxin-NADP+ Oxidoreductases" Plant Physiology. (Life Science Advances) 13, 295-303. |
| [03] | Ottado Jorgelina, Arakaki Adrián K., Calcaterra Nora B. and Ceccarelli Eduardo A. (1994) "Expression, assembly and secretion of a fully active plant ferredoxin-NADP+ reductase by Saccharomyces cerevisiae" European Journal of Biochemistry. 225, 677-685. |
| [02] | Viale Alejandro M., Arakaki Adrián K., Soncini Fernando C. and Ferreyra Raúl (1994) "Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons" International Journal of Systematic Bacteriology. 44, 527-533. |
| [01] | Viale Alejandro M. and Arakaki Adrián K. (1994) "The chaperone connection to the origins of the eukaryotic organelles" FEBS letters. 341, 146-151. |