Contact:
jbonanno@nysbc.org, jb383@columbia.edu
Bio:
Dr. Bonanno joined the Wolczanski group after finishing his B.A. in chemistry at Alfred University. Following five years of pursuing organometallics of tantalum with Dr. Wolczanski, he joined Dr. Gerard Parkin at Columbia University in 1995 to study titanium alkyl, amido, and hydrido complexes. While in the Parkin group, he assisted Ged in the solution of numerous group crystal structures.
In an effort to expand his horizons, Dr. Bonanno joined the teams of Professors Stephen Burley and John Kuriyan in 1996 at The Rockefeller University as a structural biologist. Dr. Burley acted as a mentor and trained him on the finer points of the protein _expression, purification, crystallization and structure determination. Although the primary focus of Dr. Burley’s research was transcription and translation factors, he also obtained significant funding as the lead PI of the New York Structural Genomics Research Consortium (NYSGRC, comprised of researchers from five New York area institutions) from the NIH NIGMS pilot phase of the Protein Structure Initiative (PSI) to pursue the systematic high-throughput study of pan-genomic protein structure. Dr. Bonanno contributed to this effort as a crystallographer and organizer. When Dr. Burley left The Rockefeller University to become the chief scientific officer of Structural GenomiX, Inc, San Diego, he appointed Dr. Bonanno to lead his lab and grants for one year during the shutdown. Dr. Bonanno then joined Structural GenomiX in 2003 as a crystallographer and project leader for the newly transferred grant effort, renamed NYSGXRC.
After over two years of research at Structural GenomiX and following the successful culmination of the five year NYSGXRC grant, Dr. Burley, Dr. Bonanno, and their New York collaborators submitted a competing renewal for an additional five years of participation in the production phase of the NIGMS PSI. Dr. Bonanno left Structural GenomiX (now SGX Pharmaceuticals) once again bound for New York City to rejoin the PSI as the New York coordinator for the NYSGXRC and as the deputy director of the newly formed New York Center on Membrane Protein Structure (NYCOMPS) led by Professor Wayne Hendrickson.
Dr. Bonanno is an author on over 30 scientific publications including peer reviewed papers, reviews, and book chapters; he holds positions as the Director of Protein Production at the New York Structural Biology Center and as associate research scientist at Columbia University College of Physicians and Surgeons.
Publications:
Molecular Biophysics
1. Jayaraman, S; Kumaran, D.; Bonanno, J.B.; Burley, S.K.; and Swaminathan, S. “Crystal Structure of a Putative HTH-Type Transcriptional Regulator yxaF from Bacillus subtilis,” Proteins, 2006, in the press.
2. Jayaraman, S.; Rajashankar, K.R.; Solorzano, V.; Kniewel, R.; Lima, C.D.; Bonanno, J.B.; Burley, S.K.; and Swaminathan, S. “Crystal Structures of two putative phosphoheptose isomerases,” Proteins, 2006, in the press.
3. Bonanno, J.B.; Almo, S.C.; Bresnick, A.; Chance, M.R.; Fiser, A.; Swaminathan, S.; Jiang, J.; Studier, F. W.; Shapiro, L.; Lima, C.D.; Gaasterland, T.M.; Sali, A.; Bain, K.; Feil, I.; Gao, X.; Lorimer, D.; Ramos, A.; Sauder, J.M.; Wasserman, S.; Emtage, S.; D’Amico, K.; Burley, S.K. “A Large Scale Center for the NIH Protein Structure Initiative,” J. Struct. Funct. Genomics, 2005, 6(2-3), 225-232.
4. Gao, X.; Bain, K.; Bonanno, J.B.; Buchanan, M.; Henderson, D.; Lorimer, D.; Marsh, C.; Reynes, J.A.; Sauder, J.M.; Schwinn, K.; Thai, C.; Burley, S.K. “High-Throughput Limited Proteolysis/Mass Spectrometry for Protein Domain Elucidation,” J. Struct. Funct. Genomics, 2005, 6(2-3), 129-134.
5. Sickmier, E.A.; Brekasis, D.; Paranawithana, S.; Bonanno, J.B.; Paget, M.S.; Burley, S.K.; Kielkopf, C.L. “X-Ray Structure of a Rex-Family Repressor/NADH Complex Insights into the Mechanism of Redox Sensing,” Structure, 2005, 13(1), 43-54.
6. Ray, S.S.; Bonanno, J.B.; Chen, H.; Wu, S.; Tomasz, A.; Burley, S.K. “X-ray Structure of a Methanococcus jannaschii DNA-Binding Protein: Implications for Antibiotic Resistance in Staphylococcus aureus,” Proteins, 2003, 50, 170-173.
7. Burley, S.K.; Bonanno, J.B. “Structural Genomics,” Methods Biochem. Anal., 2003, 44, 591-612.
8. Pilloff, D.; Dabovic, K.; Romanowski, M.J.; Bonanno, J.B.; Doherty, M.; Burley, S.K.; Leyh, T.S. “The kinetic mechanism of phosphomevalonate kinase,” J. Biol. Chem., 2003, 278(7), 4510-4515.
9. Burley, S.K.; Bonanno, J.B. “Structuring the Universe of Proteins,” Ann. Rev. Genomics and Hum. Gen., 2002, 3, 243-262.
10. Ray, S.S.; Bonanno, J.B.; Rajashankar, K.R.; Pinho, M.G.; He, G.; De Lancastre, H.; Tomasz, A.; Burley, S.K. “Co-Crystal Structures of Diaminopimelate Decarboxylase: Mechanism, evolution, and inhibition of an antibiotic resistance factor,” Structure, 2002, 10, 1499-1508.
11. Burley, S.K.; Bonanno, J.B. “Structural genomics of proteins contributing to conserved biochemical pathways and processes,” Curr. Opin. Struct. Biol., 2002, 12(3), 383-391.
12. Deaconescu, A.M.; Roll-Mecak, A.; Bonanno, J.B.; Gerchman, S.E.; Kycia, H.; Studier, F.W.; Burley, S.K. “X-ray Structure of S. cerevisiae Homologous Miochondrial Matrix Factor 1 (Hmf1),” Proteins, 2002, 48(2), 431-436.
13. Romanowski, M.J.; Bonanno, J.B.; Burley, S.K. “Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily,” Proteins, 2002, 47(4), 568-571.
14. Romanowski, M.J.; Bonanno, J.B.; Burley, S.K. “Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold,” Proteins, 2002, 47(4), 563-567.
15. Chance, M.R.; Bresnick, A.R.; Burley, S.K.; Jiang, J.S.; Lima, C.D.; Sali, A.; Almo, S.C.; Bonanno, J.B.; Buglino, J.A.; Boulton, S.; Chen, H.; Eswar, N.; He, G.; Huang, R.; Ilyin, V.; McMahan, L.; Pieper, U.; Ray, S.; Vidal, M.; Wang, L.K. “Structural genomics: a pipeline for providing structures for the biologist,” Protein Sci. 2002, Apr., 11(4), 723-738.
16. Bonanno, J.B.; Edo, C.; Narayanan E.; Pieper, U.; Romanowski, M.J.; Ilyin, V.; Gerchman, S.E.; Kycia, H.; Studier, F.W.; Sali, A.; Burley, S.K. “Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis,” Proc. Nat. Acad. Sci. 2001, Nov. 6, 98(23), 12896-12901.
17. Bonanno, J.B. “Quick Guide: Structural genomics,” Curr. Biol. 1999, Dec., 9(23), R871-R872.
18. Burley, S.K.; Almo, S.C.; Bonanno, J.B.; Capel, M.; Chance, M.R.; Gaasterland, T.; Lin, D.; Sali, A.; Studier, F.W.; Swaminathan, S. “Structural genomics: beyond the human genome project,” Nat. Genet. 1999, Oct., 23(2), 151-157.
19. Deo, R.C.; Bonanno, J.B.; Sonenberg, N.; Burley, S.K. “Recognition of polyadenylate RNA by the poly(A)-binding protein,” Cell 1999, Sep. 17; 98(6), 835-845.
Chemistry
20. Lee, H.; Bonanno, J.B.; Bridgewater, B.M.; Churchill, D.G.; Parkin, G. “Ansa–Titanocene Pyrrolyl Complexes: The Synthesis and Structural Characterization of [Me2Si(C5Me4)2]Ti(NC4H4)X (X = H, Me, Cl and NC4H4) and [Me2Si(C5Me4)(C5Me3CH2)]Ti(NC4H4),” Polyhedron 2005, 24, 1356-1365.
21. Bonanno, J.B.; Veige, A.S.; Wolczanski, P.T.; Lobkovski, E.B. “Amide derivatives of tantalum and a niobium-promoted ring opening of 3,5-lutidine,” Inorg. Chim. Acta 2003, 345, 173-184.
22. Trnka, T.M.; Bonanno, J.B.; Bridgewater, B.M.; Parkin, G. “Bis(permethylindenyl) Complexes of Thorium: Synthesis, Structure, and Reactivity,” Organometallics 2001, 20(15), 3255-3264.
23. Shin, J.H.; Savage, W.; Murphy, V.J.; Bonanno, J.B.; Churchill, D.G.; Parkin, G. “The syntheses, structures and reactivity of bis(tert-butylcyclopentadienyl)molybdenum derivatives: nitrogen alkylation of an h-2-acetonitrile ligand and influence of the chalcogen on the barrier to inversion of chalcogenoether adducts,” J. Chem. Soc., Dalton Trans. 2001, 11, 1732-1753.
24. Kimblin, C.; Murphy, V.J.; Hascall, T.; Bridgewater, B.M.; Bonanno, J.B.; Parkin, G. “Structural Studies of the [Tris(imidazolyl)phosphine] Metal Nitrate Complexes {[PimPri,But]M(NO3)}+ (M = Co, Cu, Zn, Cd, Hg): Comparison of Nitrate-Binding Modes in Synthetic Analogues of Carbonic Anhydrase,” Inorg. Chem. 2000, 39(5), 967-974.
25. Ghosh, P.; Wood, M.; Bonanno, J.B.; Hascall, T.; Parkin, G. “Bis(pyrazolylethyl)thioether ligation to zinc and cadmium: structural characterization of [S(CH2CH2pzMe2)2]ZnCl2, [S(CH2CH2pzMe2)2]CdI2 and [S((CH2CH2pzMe2)2]Cd(NO3)2,” Polyhedron 1999, 18(8,9), 1107-1113.
26. Lee, H.; Bonanno, J.B.; Hascall, T.; Cordaro, J.; Hahn, J.M.; Parkin, G. “[Me2Si] Ansa bridged complexes of permethyltitanocene: synthesis and structural characterization of fulvene derivatives with trialkylidenemethane character,” Dalton Trans. 1999, 9; 1365-8.
27. Ghosh, P.; Bonanno, J.B.; Parkin, G. “Synthesis and structure of [BpBut,Pri]2Co: a bis(pyrazolyl)hydroborato cobalt(II) complex with trans [Co···H-B] interactions,” Dalton Trans. 1998, 17, 2779-2782.
28. Kuchta, M.C.; Bonanno, J.B.; Parkin, G. “Monovalent Gallium Complexes Supported by Tris(3,5-di-tert-butylpyrazolyl)hydroborato Ligation: The Syntheses and Structures of [TpBut2]Ga and Its GaI3 Adduct [Tp But2]Ga·GaI3,” J. Am. Chem. Soc. 1996, 118(44), 10914-10915.
29. Bonanno, J.B.; Henry, T.P.; Neithamer, D.R.; Wolczanski, P.T.; Lobkovsky, E.B. “Aryl Amine C-N Bond Oxidative Addition to (silox)3Ta (silox = tBu3SiO),” J. Am. Chem. Soc. 1996, 118(21), 5132-5133.
30. Bonanno, J.B.; Wolczanski, P.T.; Lobkovsky, E.B. “Arsinidine, Phosphinidine, and Imide Formation via 1,2-H2-Elimination from (silox)3HTaEHPh (E = N, P, As): Structures of (silox)3Ta=EPh (E = P, As),” J. Am. Chem. Soc. 1994, 116(24), 11159-11160.
31. Schaller, C.P.; Bonanno, J.B.; Wolczanski, P.T. “Does Methane Bind to d0 (tBu3SiNH)2Zr=NSitBu3 Prior to C-H Bond Activation? An Inter vs. Intramolecular Isotope Effect Study,” J. Am. Chem. Soc. 1994, 116(9), 4133-4134.
32. Sowa, J.R., Jr.; Bonanno, J.B.; Zanotti, V.; Angelici, R.J. “Calorimetric Studies of the Heats of Protonation of the Metal in cis-M(CO)2(bidentate phosphine)2 Complexes of Chromium, Molybdenum, and Tungsten,” Inorg. Chem. 1992, 31(8), 1370-1375.