Miami University Department of Chemistry and Biochemistry

Michael A. Kennedy

Ohio Eminent Scholar in Structural Biology
Full Professor, Dept. of Chemistry and Biochemistry


EDUCATION/TRAINING
INSTITUTION AND LOCATION	DEGREE	YEAR	FIELD OF STUDY
Muskingum College	B.S.	1984	Chemistry
University of South Carolina	Ph.D.	1989	Chemistry

Additional Training in Protein X-ray Crystallography at Synchrotron Facilities:
Brookhaven National Laboratory, RapidData2002 Course, April 21-26, 2002, Protein Crystallography
Cold Spring Harbor, Macromolecular Crystallography Course, October 8-9, 2002, Protein Crystallography
BESSY, Berlin, Germany, Protein Crystallography Workshop, October 16-29, 2002, Protein Crystallography.

RESEARCH AND PROFESSIONAL EXPERIENCE:

Professional Experience:
1989 - 1990	Postdoctoral Scientist, University of California, San Diego, LaJolla, California
1990 - 1993	Postdoctoral Scientist, Battelle Pacific Northwest Laboratory, Richland, Washington, University of Washington, Seattle, Washington
1993 - 2000	Senior Research Scientist, Level 3, EMSL, Macromolecular Structure & Dynamics, Battelle, Pacific Northwest National Laboratory, Richland, Washington
2000 - 2001	Senior Research Scientist, Level 4, EMSL, Macromolecular Structure & Dynamics, Battelle, Pacific Northwest National Laboratory, Richland, Washington
2001 - 2006	Staff Scientist, Level 5, EMSL, Macromolecular Structure & Dynamics, Battelle, Pacific Northwest National Laboratory, Richland, Washington
2006 -	Ohio Eminent Scholar in Structural Biology, Miami University, Oxford, Ohio
2006-	Full Professor, Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio

Ad Hoc reviewer for Journals:
Journal of Structural and Functional Genomics, Journal of the American Chemistry Society, Journal of Magnetic Resonance, Biochemistry, Journal of Molecular Biology, Nucleic Acids Research, FEBS Letters, Concepts in Magnetic Resonance, Magnetic Resonance in Chemistry, Protein Science, Proteins: Structure, Function & Genetics, Nature Methods

Ad Hoc reviewer for funding agencies:
Canadian Institutes for Health Research Genomics Review Panel: Genomics Research Program (March, 2001).NIH Special Emphasis Panel Study Section for Structural Genomics (March 13, 2000)
NIH Special Emphasis Panel Study Section for Structural Genomics (Nov. 31-Dec. 1, 2000)
NIH Special Emphasis Panel Study Section for Structural Genomics (June 27-28, 2001)
Ad Hoc reviewer for the Department of Energy Office of Biological and Environmental Research
NIH P41 Site Visit Team, (Madison, Wisconsin, July 22-25, 2004)
National Science Foundation, Review of the Protein Data Bank, Piscataway, NJ, March, 2005.
NIH Protein Structure Initiative Special Technology Centers Review, Washington DC, April, 2005
DOE Structural Biology Center Site Visit Team, APS, Argonne National Lab, May, 2006.

Other Professional Services:
Organized 1^st EMSL Workshop on Structural Genomics, June 25-26, 1999, Richland, WA.
Organized 2^nd EMSL Workshop on Structural Genomics, July 28-29, 2000, Richland, WA.
Invited to participate in DOE workshop “Beyond the Genome Sequence: Protein Structure, Function and
interactions” Washington DC, June 10-11, 1999.
Invited to participate in DOE workshop “Facilities for Genomes to Life” Oakland, CA June 22, 2002.
Invited to participate in DOE workshop “Facilities for Genomes to Life” Chicago, IL August 16-17, 2002.
Invited Session Chair at International Structural Genomics Organization Workshop on NMR in Structural
Genomics, Madison, Wisconsin, June 2002.
Invited Session Chair of 13^th Albany Conversation, Albany, New York June 17-21, 2003.
Co-Organized EMSL 2004 User’s Meeting with theme, “Bridging Technologies for Structural Biology”

HONORS AND AWARDS:
2006	Ohio Eminent Scholar in Structural Biology – Miami University, Oxford, Ohio
2002	Outstanding Team Performance Award– Pacific Northwest National Laboratory, “The 900 MHz NMR Team”
1999	Outstanding Performance Award – Pacific Northwest National Laboratory, “Organization of EMSL Structural Genomics Meeting”
1991-1993	Distinguished Alexander Hollaender Postoctoral Fellow - DOE
1990	Northwest College and University Association for Science Fellow - DOE
1990	Miller Research Fellow - Alternate - U. California, Berkeley
1989	Guy Lipscomb Award for Outstanding Research in Chemistry – U. South Carolina

PUBLICATIONS: (94 since 1989)
1)   Marchetti, P. S.; Bank, S.; Bell, T. W.; Kennedy, M. A.; and Ellis, P. D., Cadium-113 NMR Spectroscopy. Long Bond Interactions and Chemical Shielding in the Cadmium Complex of an Unsaturated Nitrogen Analogue of 18-Crown-6. Journal of American Chemical Society 1989, 111, 2063-2066.
2)   Kennedy, M. A.; and Ellis, P. D., ¹¹³Cd Nuclear Magnetic Resonance Spectroscopy of Cd^2+-Substituted Heme and Myoglobin. Journal of American Chemical Society, 1989, 111, 3195-3203.
3)   Kennedy, M. A.; and Ellis, P. D., The Single Crystal NMR Experiment: An Experimentalist's Guide. Part I: Experimental Aspects and Symmetry Considerations. Concepts in Magnetic Resonance 1989, 1, 35-47.
4)   Kennedy, M. A.; and Ellis, P. D., The Single Crystal NMR Experiment: An Experimentalist's Guide. Part II: Data Analysis and Assignment of Symmetry Related Tensors. Concepts in Magnetic Resonance 1989, 1, 109-129.
5)   Rivera, E.; Kennedy, M. A.; Ellis, P. D., ¹¹³Cd NMR of Cd^2+-Substituted Carboxypeptidase. A perspective from ¹¹³Cd Shielding Tensors. Advances in Magnetic Resonance 1989, 13, 257-273.
6)   Kennedy, M. A.; Ellis, P. D.; and Jakobsen, H. J., 113Cd Shielding Tensors of Cadmium Compounds. 6. Single-Crystal NMR Study of CdCl2*18-crown-6 Complex”, Inorganic Chemistry 1990, 29, 550-552.
7)   Kennedy, M. A.; Sessler, J. L.; Murai, T.; Ellis, P. D., 113Cd Shielding Tensors of the Cadmium Complex of Texaphyrin, a novel Expanded Porphyrin and Its Pyridine and Benzimidazole Adducts. Inorganic Chemistry 1990, 29, 1050-1054.
8)   Rivera, E.; Kennedy, M. A.; Adams, R. D.; and Ellis, P. D., Cadmium-113 Shielding Tensors of Cadmium Compounds. 7. Structure and¹¹³Cd NMR Study of poly-bis(aetato)bis(imidazole) Cd(II): A Model Compound for Carboxypeptidase-A and Thermolysin. Journal of American Chemical Society 1990, 112, 1400-1407.
9) Kennedy, M. A.; and P. D. Ellis, 113Cd Shielding Tensors of Cadmium Compounds. 5. Single Crystal Studies of the Dimer of Diaquobis(2-hydroxybenzoato)cadmium(II) and Tetrakis(4-picoline)(nitrato-O,O’)(nitrato-O) cadmium(II). Inorganic Chemistry, 1990, 29, 541-549.
10) Kennedy, M. A.; Vold, R. R.; and Vold, R. L., A Solid-State Deuterium NMR Study of Internal Rotation in p-Nitroaniline. Journal of Magnetic Resonance 1991, 91, 301-315.
11) Kennedy, M. A.; Vold, R. L. and Vold, R. R., Stepped Frequency NMR Spectroscopy. Journal of Magnetic Resonance, 1991, 92, 320-331.
12) Wang, A. C.; Kennedy, M. A.; Reid, B. R.; Drobny, G. P., A Solid-State H-2 NMR Relaxation Study of a 12-Base Pair Rna Duplex. Journal of the American Chemical Society 1992, 114, (16), 6583-6585.
13) Wang, A. C.; Kennedy, M. A.; Reid, B. R.; Drobny, G. P., A Solid-State H-2 NMR-Study of Purine Motion in a 12 Base-Pair Oligoribonucleotide. Faseb Journal 1992, 6, (1), A269-A269.
14) Kennedy, M. A.; Nuutero, S. T.; Davis, J. T.; Drobny, G. P.; Reid, B. R., Mobility at the Tpa Cleavage Site in the T3a3-Containing Ahaiii and Pmei Restriction Sequences. Biochemistry 1993, 32, (31), 8022-8035.
15) Kennedy, M. A.; Nuutero, S. T.; Davis, J. T.; Drobny, G. P.; Reid, B. R., Evidence for Mobility at the Tpa Junction in Tnan-Containing DNA Oligomers. Journal of Cellular Biochemistry 1993, 264-264.
16) Kennedy, M. A., NMR and Enzymology of Modified DNA-Protein Interactions. In DNA Damage, ed.; NEW YORK ACAD SCIENCES: New York, 1994; 726, 303-305.
17) Wang, A. C.; Kennedy, M. A.; Reid, B. R.; Drobny, G. P., A Solid-State H-2-NMR Investigation of Purine Motion in a 12-Base-Pair Rna Duplex. Journal of Magnetic Resonance Series B 1994, 105, (1), 1-10.
18) Zhu, L. M.; Reid, B. R.; Kennedy, M.; Drobny, G. P., Modulation of J-Couplings by Cross-Relaxation in DNA Sugars. Journal of Magnetic Resonance Series A 1994, 111, (2), 195-202.
19) Tolman, J. R.; Flanagan, J. M.; Kennedy, M. A.; Prestegard, J. H., Nuclear Magnetic Dipole Interactions in Field-Oriented Proteins - Information for Structure Determination in Solution. Proceedings of the National Academy of Sciences of the United States of America 1995, 92, (20), 9279-9283.
20) McAteer, K.; Ellis, P. D.; Kennedy, M. A., The Effects of Sequence Context on Base Dynamics at Tpa Steps in DNA Studied by NMR. Nucleic Acids Research 1995, 23, (19), 3962-3966.
21) Lingbeck, J.; Kubinec, M. G.; Miller, J.; Reid, B. R.; Drobny, G. P.; Kennedy, M. A., Effect of adenine methylation on the structure and dynamics of TpA steps in DNA: NMR structure determination of d(CGAGGTTTAAACCTCG) (2) and its A9-methylated derivative at 750 MHz. Biochemistry 1996, 35, (3), 719-734.
22) Kennedy, M. A.; Kubinec, M. G.; Lingbeck, J. M.; McAteer, K.; Thrall, B. D.; and Ellis, P.D., 750 MHz NMR Studies of Chemically Modified DNA Structure/Dynamics: Sequence Context Effects and Protein Recognition. Bull. Magnetic Resonance 1996, 18(1/2), 77-80.
23) McAteer, K.; Lipton, A. S.; Kennedy, M. A.; Ellis, P. D., A multiphase Cd-113 NMR investigation of metalloporphyrin reorientation in cadmium-substituted myoglobin. Solid State Nuclear Magnetic Resonance 1996, 7, (3), 229-238.
24) McAteer, K.; Kennedy, M. A.; Jing, Y. Q.; Taylor, J. S. D., 750 MHZ NMR study of the structure of a DNA dodecamer duplex containing a cis-syn thymine dimer. Abstracts of Papers of the American Chemical Society 1996, 212, 6-BIOL.
25) Tolman, J. R.; Flanagan, J. M.; Kennedy, M. A.; Prestegard, J. H., NMR evidence for slow collective motions in cyanometmyoglobin. Nature Structural Biology 1997, 4, (4), 292-297.
26) Hernandez, G.; Blumenthal, D. K.; Kennedy, M. A.; Unkefer, C. J.; Trewhella, J. D., Troponin I inhibitory peptide (96-115) has an extended conformation when bound to skeletal muscle troponin C. Biochemistry 1999, 38, (21), 6911-6917.
27) Buchko, G. W.; Kennedy, M. A., Human nucleotide excision repair protein XPA: H-1 NMR and CD solution studies of a synthetic peptide fragment corresponding to the zinc-binding domain (101-141). Journal of Biomolecular Structure & Dynamics 1997, 14, (6), 677-690.
28) Yang, J. P.; Silks, L.; Wu, R. L.; Isern, N.; Unkefer, C.; Kennedy, M. A., Improvements for measuring H-1-H-1 coupling constants in DNA via new Stripe-COSY and superstripe-COSY pulse sequences combined with a novel strategy of selective deuteration. Journal of Magnetic Resonance 1997, 129, (2), 212-218.
29) Buchko, G. W.; Ni, S. S.; Thrall, B. D.; Kennedy, M. A., Human nucleotide excision repair protein XPA: Expression and NMR backbone assignments of the 14.7 kDa minimal damaged DNA binding domain (Met(98)-Phe(219)). Journal of Biomolecular NMR 1997, 10, (3), 313-314.
30) Buchko, G. W.; Ni, S. S.; Thrall, B. D.; Kennedy, M. A., Structural features of the minimal DNA binding domain (M98-F219) of human nucleotide excision repair protein XPA. Nucleic Acids Research 1998, 26, (11), 2779-2788.
31) Buchko, G. W.; Rozek, A.; Hoyt, D. W.; Cushley, R. J.; Kennedy, M. A., The use of sodium dodecyl sulfate to model the apolipoprotein environment. Evidence for peptide-SDS complexes using pulsed-field-gradient NMR spectroscopy. Biochimica Et Biophysica Acta-Lipids and Lipid Metabolism 1998, 1392, (1), 101-108.
32) Hess, N. J.; Buchko, G. W.; Conradson, S. D.; Espinosa, F. J.; Ni, S. S.; Thrall, B. D.; Kennedy, M. A., Human nucleotide excision repair protein XPA: Extended X-ray absorption fine-structure evidence for a metal-binding domain. Protein Science 1998, 7, (9), 1970-1975.
33) McAteer, K.; Jing, Y.; Kao, J.; Taylor, J. S.; Kennedy, M. A., Solution-state structure of a DNA dodecamer duplex containing a cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA. Journal of Molecular Biology 1998, 282, (5), 1013-1032.
34) Buchko, G. W.; Iakoucheva, L. M.; Kennedy, M. A.; Ackerman, E. J.; Hess, N. J., Extended X-ray absorption fine structure evidence for a single metal binding domain in Xenopus laevis nucleotide excision repair protein XPA. Biochemical and Biophysical Research Communications 1999, 254, (1), 109-113.
35) Cort, J. R.; Koonin, E. V.; Bash, P. A.; Kennedy, M. A., A phylogenetic approach to target selection for structural genomics: solution structure of YciH. Nucleic Acids Research 1999, 27, (20), 4018-4027.
36) Buchko, G. W.; Daughdrill, G. W.; de Lorimier, R.; Rao, S.; Isern, N. G.; Lingbeck, J. M.; Taylor, J. S.; Wold, M. S.; Gochin, M.; Spicer, L. D.; Lowry, D. F.; Kennedy, M. A., Interactions of human nucleotide excision repair protein XPA with DNA and RPA70 Delta C327: Chemical shift mapping and N-15 NMR relaxation studies. Biochemistry 1999, 38, (46), 15116-15128.
37) Buchko, G. W.; Hess, N. J.; Kennedy, M. A., Cadmium mutagenicity and human nucleotide excision repair protein XPA: CD, EXAFS and H-1/N-15-NMR spectroscopic studies on the zinc(II)- and cadmium(II)-associated minimal DNA-binding domain (M98-F219). Carcinogenesis 2000, 21, (5), 1051-1057.
38) Buchko, G. W.; Hess, N. J.; Kennedy, M. A., Human nucleotide excision repair protein XPA: Summary of exafs studies on the Zn (II), Co (II) and Cd (II) associated minimal DNA-binding domain. Protein and Peptide Letters 2000, 7, (1), 49-56.
39) Buchko, G. W.; Rozek, A.; Kanda, P.; Kennedy, M. A.; Cushley, R. J., Structural studies of a baboon (Papio sp.) plasma protein inhibitor of cholesteryl ester transferase. Protein Science 2000, 9, (8), 1548-1558.
40) McAteer, K.; Kennedy, M. A., NMR evidence for base dynamics at all TpA steps in DNA. Journal of Biomolecular Structure & Dynamics 2000, 17, (6), 1001-1009.
41) Yang, J. P.; McAteer, K.; Silks, L. A.; Wu, R. L.; Isern, N. G.; Unkefer, C. J.; Kennedy, M. A., A comprehensive approach for accurate measurement of proton-proton coupling constants in the sugar ring of DNA. Journal of Magnetic Resonance 2000, 146, (2), 260-276.
42) Cort, J. R.; Yee, A.; Edwards, A. M.; Arrowsmith, C. H.; Kennedy, M. A., Structure-based functional classification of hypothetical protein MTH538 from Methanobacterium thermoautotrophicum. Journal of Molecular Biology 2000, 302, (1), 189-203.
43) Buchko, G. W.; Rozek, A.; Kanda, P.; Kennedy, M. A.; and Cushley, R. J., Structural Studies of a baboon (Papio sp) Plasma Protein Inhibitor of Cholesteryl Ester Transferase. Protein Science, 2000, 9, 1548-1558.
44) Christendat, D.; Yee, A.; Dharamsi, A.; Kluger, Y.; Savchenko, A.; Cort, J. R.; Booth, V.; Mackereth, C. D.; Saridakis, V.; Ekiel, I.; Kozlov, G.; Maxwell, K. L.; Wu, N.; McIntosh, L. P.; Gehring, K.; Kennedy, M. A.; Davidson, A. R.; Pai, E. F.; Gerstein, M.; Edwards, A. M.; Arrowsmith, C. H., Structural proteomics of an archaeon. Nature Structural Biology 2000, 7, (10), 903-909.
45) Lipton, A. S.; Buchko, G. W.; Sears, J. A.; Kennedy, M. A.; Ellis, P. D. , Zn-67 solid-state NMR spectroscopy of the minimal DNA binding domain of human nucleotide excision repair protein XPA. Journal of the American Chemical Society 2001, 123, (5), 992-993.
46) Cort, J. R.; Yee, A.; Edwards, A. M.; Arrowsmith, C. H.; and Kennedy, M. A., NMR Structure Determination and Structure-Based Functional Characterization of a Conserved, Hypothetical Protein MTH1175 from Methanobacterium thermoautotrophicum. Journal of Structural & Functional Genomics 2000, 1, 15-25.
47) Buchko, G. W.; Hess, N. J.; Bandaru, V.; Wallace, S. S.; and Kennedy, M. A., Spectroscopic Studies of Zinc(II) and Cobalt (II) Associated Escherichia coli Formamidopyrimidine-DNA Glycosylase: Extended X-ray Absorption Fine Structure Evidence for a Metal-Binding Domain. Biochemistry 2000, 39, 12441-12449.
48) Buchko, G. W.; Isern, N. G.; Spicer, L. D.; Kennedy, M. A., Human nucleotide excision repair protein XPA: NMR spectroscopic studies of an XPA fragment containing the ERCC1-binding region and the minimal DNA-binding domain (M59-F219). Mutation Research-DNA Repair 2001, 486, (1), 1-10.
49) Buchko, G. W.; Tung, C. S.; McAteer, K.; Isern, N. G.; Spicer, L. D.; Kennedy, M. A., DNA-XPA interactions: a P-31 NMR and molecular modeling study of dCCAATAACC association with the minimal DNA-binding domain (M98-F219) of the nucleotide excision repair protein XPA. Nucleic Acids Research 2001, 29, (12), 2635-2643.
50) Cort, J. R.; Mariappan, S. V. S.; Kim, C. Y.; Park, M. S.; Peat, T. S.; Waldo, G. S.; Terwilliger, T. C.; Kennedy, M. A., Solution structure of Pyrobaculum aerophilum DsrC, an archaeal homologue of the gamma subunit of dissimilatory sulfite reductase. European Journal of Biochemistry 2001, 268, (22), 5842-5850.
51) Buchko, G. W.; Kennedy, M. A., Hydroxyapatite elution behavior of human nucleotide excision repair protein XPA and fragments of XPA. Protein and Peptide Letters 2001, 8, (5), 357-365.
52) Buchko, G. W.; Wallace, S. S.; Kennedy, M. A., Letter to the Editor: Base excision repair: NMR backbone assignments of Escherichia coli formamidopyrimidine-DNA glycosylase. Journal of Biomolecular NMR 2002, 22, (3), 301-302.
53) Pineda-Lucena, A.; Liao, J.; Wu, B.; Yee, A.; Cort, J. R.; Kennedy, M. A.; Edwards, A. M.; Arrowsmith, C. H., NMR structure of the hypothetical protein encoded by the YjbJ gene from Escherichia coli. Proteins-Structure Function and Genetics 2002, 47, (4), 572-574.
54) Yee, A.; Chang, X. Q.; Pineda-Lucena, A.; Wu, B.; Semesi, A.; Le, B.; Ramelot, T.; Lee, G. M.; Bhattacharyya, S.; Gutierrez, P.; Denisov, A.; Lee, C. H.; Cort, J. R.; Kozlov, G.; Liao, J.; Finak, G.; Chen, L.; Wishart, D.; Lee, W.; McIntosh, L. P.; Gehring, K.; Kennedy, M. A.; Edwards, A. M.; Arrowsmith, C. H., An NMR approach to structural proteomics. Proceedings of the National Academy of Sciences of the United States of America 2002, 99, (4), 1825-1830.
55) Cort, J. R.; Chiang, Y. W.; Zheng, D. Y.; Montelione, G. T.; Kennedy, M. A., NMR structure of conserved eukaryotic protein ZK652.3 from C-elegans: A ubiquitin-like fold. Proteins-Structure Function and Genetics 2002, 48, (4), 733-736.
56) Kennedy, M. A.; Montelione, G. T.; Arrowsmith, C. H.; and Markley, J. L., Role for NMR in Structural Genomics. Journal of Struct. Funct. Gen., 2002, 2, 155-169.
57) Pineda-Lucena, A.; Yi, G. S.; Chang, X. Q.; Cort, J. R.; Kennedy, M. A.; Edwards, A. M.; Arrowsmith, C. H., Letter to the Editor: Solution structure of the hypothetical protein MTH0637 from Methanobacterium thermoautotrophicum. Journal of Biomolecular NMR 2002, 22, (3), 291-294.
58) Ramelot, T. A.; Cort, J. R.; Yee, A. A.; Liu, F. R.; Goshe, M. B.; Edwards, A. M.; Smith, R. D.; Arrowsmith, C. H.; Dever, T. E.; Kennedy, M. A., Myxoma virus immunomodulatory protein M156R is a structural mimic of eukaryotic translation initiation factor eIF2 alpha. Journal of Molecular Biology 2002, 322, (5), 943-954.
59) Ramelot, T. A.; Cort, J. R.; Yee, A. A.; Semesi, A.; Edwards, A. M.; Arrowsmith, C. H.; Kennedy, M. A., NMR structure of the Escherichia coli protein YacG: a novel sequence motif in the zinc-finger family of proteins. Proteins-Structure Function and Genetics 2002, 49, (2), 289-293.
60) Kennedy, M. A.; McAteer, K., Force field dependence of NMR-based, restrained molecular dynamics DNA structure calculations including an analysis of the influence of residual dipolar coupling restraints. Abstracts of Papers of the American Chemical Society 2002, 224, U482-U483.
61) McAteer, K.; Kennedy, M. A., Force field dependence of NMR-based, restrained molecular dynamics DNA structure calculations including an analysis of the influence of residual dipolar coupling restraints. Journal of Biomolecular Structure & Dynamics 2003, 20, (4), 487-506.
62) Ramelot, T. A.; Cort, J. R.; Yee, A. A.; Semesi, A.; Edwards, A. M.; Arrowsmith, C. H.; and Kennedy, M. A., Solution Structure of the Yeast Ubiquitin-Like Modifier Protein Hub1. Journal of Struct. Funct. Gen. 2003, 4, 25-30.
63) LiWang, A. C.; McCready, D. E.; Drobny, G. P.; Reid, B. R.; Kennedy, M. A., Observation of a distinct transition in the mode of interconversion of ring pucker conformers in non-crystalline D-ribose-2 '-d from H-2 NMR spin-alignment. Journal of Biomolecular NMR 2003, 26, (3), 249-257.
64) Miller, J. H.; Fan-Chiang, C. C. P.; Straatsma, T. P.; Kennedy, M. A., 8-Oxoguanine enhances bending of DNA that favors binding to glycosylases. Journal of the American Chemical Society 2003, 125, (20), 6331-6336.
65) Buchko, G. W.; Ni, S. S.; Holbrook, S. R.; Kennedy, M. A., H-1, C-13, and N-15 NMR assignments of the hypothetical Nudix protein DR0079 from the extremely radiation-resistant bacterium Deinococcus radiodurans. Journal of Biomolecular NMR 2003, 25, (2), 169-170.
66) Holbrook, E. L.; Schulze-Gahmen, U.; Buchko, G. W.; Ni, S. S.; Kennedy, M. A.; Holbrook, S. R., Purification, crystallization and preliminary X-ray analysis of two nudix hydrolases from Deninococcus radiodurans. Acta Crystallographica Section D-Biological Crystallography 2003, 59, 737-740.
67) Pineda-Lucena, A.; Liao, J. C. C.; Cort, J. R.; Yee, A.; Kennedy, M. A.; Edwards, A. M.; Arrowsmith, C. H., A novel member of the split beta alpha beta fold: Solution structure of the hypothetical protein YML108W from Saccharomyces cerevisiae. Protein Science 2003, 12, (5), 1136-1140.
69) Zheng D.; Cort J. R.; Chiang Y.; Acton T.; Kennedy M. A.; and Montelione G. T., ¹H, ¹³C and ¹⁵N resonance assignments for methionine sulfoxide reductase B from Bacillus subtilis. Journal of Biomolecular NMR, 2003, 27, (2), 183-184.
70) Ramelot, T. A.; Ni, S. S.; Goldsmith-Fischman, S.; Cort, J. R.; Honig, B.; Kennedy, M. A., Solution structure of Vibrio cholerae protein VC0424: A variation of the ferredoxin-like fold. Protein Science 2003, 12, (7), 1556-1561.
71) Daughdrill, G. W.; Buchko, G. W.; Botuyan, M. V.; Arrowsmith, C.; Wold, M. S.; Kennedy, M. A.; Lowry, D. F., Chemical shift changes provide evidence for overlapping single-stranded DNA- and XPA-binding sites on the 70 kDa subunit of human replication protein A. Nucleic Acids Research 2003, 31, (14), 4176-4183.
72) Wu, B.; Yee, A.; Pineda-Lucena, A.; Semesi, A.; Ramelot, T. A.; Cort, J. R.; Jung, J. W.; Edwards, A.; Lee, W.; Kennedy, M.; Arrowsmith, C. H., Solution structure of ribosomal protein S28E from Methanobacterium thermoautotrophicum. Protein Science 2003, 12, (12), 2831-2837.
73) Aramini, J. M.; Huang, Y. P. J.; Cort, J. R.; Goldsmith-Fischman, S.; Xiao, R.; Shih, L. Y.; Ho, C. K.; Liu, J. F.; Rost, B.; Honig, B.; Kennedy, M. A.; Acton, T. B.; Montelione, G. T., Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Science 2003, 12, (12), 2823-2830.
74) Buchko, G. W.; Ni, S. S.; Holbrook, S. R.; Kennedy, M. A., Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium. Proteins-Structure Function and Bioinformatics 2004, 56, (1), 28-39.
75) Zheng, D.; Cort, J. R.; Swapna, G.V.T.; Aramini, J.; Chiang, Y.; Shastry, R.; Acton, T.; Kennedy, M. A.; and Montelione, G. T., Evidence for Conformational Dynamics in the Active Site of Methionine Sulfoxide Reductase B from Bacillus subtilis, submitted to Biochemistry, 2003.
76) Zheng, D. Y.; Cort, J. R.; Chiang, Y. W.; Acton, T.; Kennedy, M. A.; Montelione, G. T., H-1, C-13 and N-15 resonance assignments for methionine sulfoxide reductase B from Bacillus subtilis. Journal of Biomolecular NMR 2003, 27, (2), 183-184.
77) Ni, S. ; McAteer, K.; Bussiere, D. E.; Kennedy, M. A., Crystallization and preliminary crystallographic analysis of an Enterococcus faecalis repressor protein, CylR2, involved in regulating cytolysin production through quorum-sensing. Acta Crystallographica Section D-Biological Crystallography 2004, 60, 1145-1148.
78) Ramelot, T. A.; Cort, J. R.; Goldsmith-Fischman, S.: Kornhaber, G. J.; Xiao, R.; Shastry, R.; Acton, T. B.; Honig, B.; Montelione, G. T.; Kennedy, M. A., Solution NMR Structure of the Iron-Sulfur Cluster Assembly Protein U (IscU) with Zinc Bound at the Active Site. Journal of Molecular Bioliology, 344, 567-83, 2004.
79) McAteer, K.; Aceves-Gaona, A.; Michalczyk, R.; Buchko, G. W.; Isern, N. G.; Silks, L. A.; Miller, J. H.; and Kennedy, M. A., Compensating Bends in a 16 base-pair DNA Oligomer Containing a T3A3 Segment: A NMR Study of Global DNA Curvature. Biopolymers, 75, 497-511, 2004.
80) Ni, S.; Robinson, H.; Marsing, C.G.; Bussiere, D. E.; and Kennedy, M. A., Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase from Shewanella oneidensis at 1.6Å: Identification of Farnesyl Diphosphate Trapped in a Hydrophobic Cavity. Acta Crystallographica Section D, 60,1949-57, 2004.
81) Robert Powers1 , Thomas B. Acton2, Yiwen Chiang2, P.K. Rajan2, John R. Cort3, Michael A. Kennedy3, Jinfeng Liu4, LiChung Ma2, Burkhard Rost4 and Gaetano T. Montelione2, 5 (1)H, (13)C and (15)N assignments for the Archaeglobus fulgidis protein AF2095.J Biomol NMR. 2004 Sep;30(1):107-8.
82) Buchko, G. W.; McAteer, K.; Wallace, S. S.; and Kennedy, M. A., Solution-State NMR Investigation of DNA Binding Interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): A Dynamic Description of the DNA /Protein Interface. DNA Repair, 4, 327-339, 2005.
83) Robert Powers, Nebojsa Mirkovic, Sharon Goldsmith-Fischman, Thomas B. Acton, Yiwen Chiang, Yuanpeng J. Huang, LiChung Ma,P. K. Rajan, John R. Cort, Michael A. Kennedy, Jinfeng Liu, Burkhard Rost, Barry Honig, Diana Murray, Gaetano T. Montelione^" Solution Structure of Archaeglobus fulgidis Peptidyl-tRNA Hydrolase (Pth2) Provides Evidence for an Extensive Conserved Family of Pth2 Enzymes in Archea, Bacteria and Eukaryotes, Protein Science 14 2849-2861,2005.
84) Savchenko A, Krogan N, Cort JR, Evdokimova E, Lew JM, Yee AA, Sanchez-Pulido L, Andrade MA, Bochkarev A, Watson JD, Kennedy MA, Greenblatt J, Hughes T, Arrowsmith CH, Rommens JM, Edwards AM. The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism. J Biol Chem. 2005 May 13;280(19):19213-20.
85) Ni, S., Farouhar, F., Robinson, H., Bussiere, D., Kennedy, M.A. (2005) "Structure Determination of VC0702 at 2.0Å, a Conserved Hypothetical Protein from Vibrio Cholerae. Proteins: Structure, Function, Bioinformatics, 63, 733-741, 2006.
86) Paolo Rossi, S.S. Theresa Ramelot, Rong Xiao, Chi K. Ho, Li-Chung Ma, Thomas B. Acton, Michael A. Kennedy, Gaetano T. Montelione “1H, 13C, and 15N Resonance Assignments for the Protein Coded by Gene Locus BB0938 of Bordetella bronchiseptica” J. Biomol. NMR 33(3), 197, 2005.
87) James M. Aramini, G. V. T. Swapna, Yuanpeng J. Huang, P. K. Rajan, Rong Xiao, Ritu Shastry, Thomas B. Acton, John R. Cort, Michael A. Kennedy, Gaetano T. Montelione “1H, 13C, and 15N Resonance Assignments for Escherichia coli ytfP, a Member of the Broadly Conserved UPF0131 Protein Domain Family” J. Biomol. NMR 33(3), 197, 2005.
88) G.W. Buchko, S. Ni, H. Robinson, E. Welsh, H.Pakrasi, and M.A. Kennedy“Characterization of two potentially universal turn motifs that shape the repeated five residuesfold- Crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142” Protein Science, 15, 2579-2595, 2006.
89) J.R. Cort, C. Dahl, M.A. Kennedy “Solution Structure and Characterization of redox properties of Allochromatium vinosium DsrC” to be submitted, J. Bacteriology, 2006.
90) J.R. Cort, T.A. Ramelot, D. Murray, T.B. Acton, L.-C. Ma, R. Xiao, G.T. Montelione, M.A. Kennedy “Characterization of a Novel Family of GCN5-related N-acetyltransferase Suggests Involvement of an Acetyl-Enzyme Intermediate: Definition of a GNAT subfamily, C-GNAT.” Submitted, J. Biol. Chem., 2006.
91) G.W. Buchko, Chang Y. Kim, Thomas C. Terwilliger, Michael A. Kennedy “Solution Structure of the Conserved Hypothetical Protein Rv2302 from Mycobacterium tuberculosis” in press, J. Bacteriology, 2006.
92) T.A. Ramelot, A. Yee, J.R. Cort, A. Semesi, C.A. Arrowsmith, M.A. Kennedy “NMR Structure and Binding Studies Confirm that PA4608 from Pseudomonas aeruginosa is a PilZ Domain and a c-di-GMP Binding Protein” Proteins: Structure, Function, and Bioinformatics, 66, 266-271, 2006.
93) Garry W. Buchko, Shuisong Ni, Natacha M. Lourette, Raymond Reeves & Michael A. Kennedy “ NMR resonance assignments of the human non-chromatin architectural transcription factor HMGA1” J. Biomol. NMR, in press, 2007.9
94) G.W. Buchko, H. Robinson, S. Ni, H.B. Pakrasi, M.A. Kennedy “Cloning, expression, crystallization, and preliminary crystallographic analysis of a pentapeptide repeat protein (Rfr23) from the bacterium Cyanothece sp 51142”, 62, 1251-1254, Acta, Cryst. F, 2007.

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INVITED TALKS:

41 Kennedy, M.A. “Combining NMR Spectroscopy and X-ray Crystallography to Improve NMR Protein
Structures”, Eastern Analytical Symposium, Somerset, New Jersey, November 13-16, 2006, Invited by
Gaetano Montelione, Rutgers University.

40 Kennedy, M.A. “NMR-Based Metabonomic Studies at Miami University: Ovarian Cancer and Yersinia
Pestis Exposure” Proctor and Gamble, Invited by Fuoad Ezra, September 11, 2006, Mason, Ohio.

39 Kennedy, M.A. “ Nuclear Magnetic Resonance Spectroscopy: An Evolving Tool for Human Health
Research” Miami University, Oxford, Ohio, April 21, 2006, Invited by Gil Pacey.

38 Kennedy, MA “Molecular Replacement by NMR” University of Florida, April 17, 2006, Invited by
Mavis Agbandje-McKenna.

37 Kennedy, MA “Molecular Replacement by NMR” University of Buffalo, April 14, 2006, Invited by
Thomas Szyperski

36  Kennedy, M.A. “Structural Genomics: Exploring the Universe of Protein Fold Space”, Miami
      University, Oxford, Ohio August 22, 2005. Department of Chemistry and Biochemistry, Invited by
     Chairman of the Department, Chris Makaroff.

35 Kennedy, M.A. "NMR-Based Structural Genomics at Pacific Northwest National Laboratory" International Conference on Magnetic Resonance in Biological Systems, Hyderabad, India, January 17-21, 2005, Invited by Professor Chary.

34. Kennedy, M. A., “Structural Genomics at Pacific Northwest National Laboratory” University of Washington, Chemistry Department Seminar Series, Invited by David Ginger, Spring 2004.

33. Kennedy, M. A., “NMR-Based Structural Genomics” Association of Biomolecular Resource Facilities Annual Meeting, Portland, Oregon, February 28 – March 2, 2004.

32. Kennedy, M. A., “Structural Genomics at the Pacific Northwest National Laboratory”, Australian and New Zealand Magnetic Resonance Meeting, Adelaide, Australia, February 14-19, 2003.

31. Kennedy, M. A., “Understanding Biofilms and Quorum Sensing in Pathogenic Bacteria” Battelle Memorial Institute, Columbus, Ohio, June 23, 2003.

30. Kennedy, M. A., “Characterization Network: Structural” Argonne National Laboratory, Argonne, Illinois, May 29-30, 2003.

29. Kennedy, M. A., “Automation of Protein Structure Determination by NMR” Workshop on Automated Protein Structure Determination, Lawrence Berkeley National Laboratory, Berkeley, California, December 6, 2002

28. Kennedy, M.A.; “Structural Genomics at the Pacific Northwest National Laboratory”, International Structural Genomics Organization, Berlin, Germany, October 10-13, 2002.

27. Kennedy, M. A., “NMR-Based Structural Genomics” International Conference on Magnetic Resonance in Biological Sciences, Toronto, CA, August 25-28, 2002.

26. Kennedy, M. A., “Force Field Dependence of NMR-Based, Restrained Molecular Dynamics DNA Structure Calculations Including an Analysis of the Influence of Residual Dipolar coupling Restraints” National ACS Meeting, Boston, MA August 20, 2002

25. Kennedy, M. A., “NMR Studies of DNA Repair and NMR Based Structural Genomics”, Washington State University Seminar Series, Invited by Dr. Jeremy Evans, October 4, 2001.

24. Kennedy, M. A., “New NMR Approaches for DNA Structure Determination” The Albany Conversation, Albany, NY, Invited by Dr. Sarma, June 23-25, 2001.

23. Kennedy, M. A., “Advances in NMR Spectroscopy for Biochemical Studies” Advances in Analytical Instrumentation Conference, Invited by Dr. Futrell, Seattle, Washington, June 15, 2001.

22. Kennedy, M. A., “New NMR Approaches for DNA Structure Determination” Vanderbilt Seminar Program, Invited by Dr. Stone, Vanderbilt University, Nashville, Tennessee, April 6, 2001.

21. Kennedy, M. A., “New NMR Approaches for DNA Structure Determination” Vanderbilt Seminar Program, Invited by Dr. Xu, Oak Ridge National Laboratory , Nashville, Tennessee, April 4, 2001.

20. Kennedy, M. A., “New NMR Approaches for DNA Structure Determination” , Biochemistry Department Seminar Program, Invited by Dr. Mann, ” University of Vermont , February 9, 2001.

19. Kennedy, M. A., “Structure-Based Functional Classification of Hypothetical Proteins for Structural Genomics” International Conference on Structural Genomics 2000, Invited by Dr. Yokoyama , Pacifico Yokohama, Yokohama, Japan, November 2-5, 2000.

18. Kennedy, M. A., “Structure-Based Functional Classification of Hypothetical Proteins” 2^nd EMSL Workshop on Structural Genomics, Richland, WA, July 28-29, 2000.

17. Kennedy, M. A., “Structure-Based Classification of Putative DNA Repair Proteins from Deinococcus radiodurans” Environmental Molecular Sciences Symposia and first Users Meeting, Invited by Dr. Koppenaal, Richland, WA, June 21-23, 2000.

16. Kennedy, M. A.; Mcateer, K.; Michalcsik, R.; Schmidt, J.; Isern, N.; Silks, L. A.; and Unkefer, C., “Measurement of Residual Dipolar Couplings in 15N-labeled and 13C-labeled DNA Aligned in Liquid Crystalline Bicelles using NMR Spectroscopy” 41^st ENC, Asilomar Center, Pacific Grove, CA April 9-14, 2000.

15. Kennedy, M. A., “NMR Based Structural Genomics” Special Invitation, Dr. Struman, Wadsworth Center, SUNY Albany, March 15, 2000.

14. Kennedy, M. A., “Magnetic Resonance Strategies for Structural Genomics” Invited by Dr. Monetlione, Rutgers University, Piscataway, New Jersey, November 3^rd, 1999.

13. Kennedy, M. A., “Magnetic Resonance and Structural Genomics” Environmental Molecular Sciences Symposia and first Users Meeting, Invited by Dr. Koppenaal, Richland, WA, July 21-24, 1999.

12. Kennedy, M. A., “Magnetic Resonance and Structural Genomics” 1^st Environmental Molecular Sciences Laboratory Workshop on Structural Genomics, Richland, WA, June 25-26, 1999.

11. Kennedy, M. A., “NMR Studies of DNA Structure and Protein Recognition of DNA Damage” Northwest Regional Meeting of the American Chemical Society, Pasco, WA, June 17-20, 1998.

10. Kennedy, M. A.; Kubinec, M. G.; Lingbeck, J. M.; McAteer, K.; Thrall, B. D.; and Ellis, P. D., “750 MHz NMR Studies of Chemically Modified DNA Structure/Dynamics: Sequence Context Effects and Protein Recognition” Invited by Dr. Wallace, University of Vermont, Burlington, Vermont, March 16, 1996.

9. Kennedy, M. A.; Kubinec, M. G.; Lingbeck, J. M.; McAteer, K.; Thrall, B. D.; and Ellis, P. D., “750 MHz NMR Studies of Chemically Modified DNA Structure/Dynamics: Sequence Context Effects and Protein Recognition”, Invited by Dr. Taylor, Washington University in St. Louis, St. Louis, MO, March 16, 1996.

8. Kennedy, M. A.; Kubinec, M. G.; Lingbeck, J. M.; McAteer, K.; Thrall, B. D.; and Ellis, P. D., “750 MHz NMR Studies of Chemically Modified DNA Structure/Dynamics: Sequence Context Effects and Protein Recognition” 12^th Conference of the International Society of Magnetic Resonance, Sidney, Australia, July 16-21, 1995.

7. Kennedy, M. A.; Kubinec, M. G.; Lingbeck, J. M.; McAteer, K.; Thrall, B. D.; and Ellis, P. D., “750 MHz NMR Studies of DNA Structure/Dynamics: Correlation with Observed Molecular Interactions” 19^th Annual Meeting of the Australian Society for Biophysics held in conjunction with the British Biophysical Society, The University of Sydney, Sidney, Australia, July 16-21, 1995.

6. Kennedy, M. A., “NMR and Enzymology of Modified DNA/Protein Interactions” Annual Meeting of the Society of Plant Physiologists, Oregon Convention Center, Portland, Oregon, July 30 – August 3, 1994.

5. Kennedy, M. A., “NMR and Enzymology of Modified DNA/Protein Interactions” New York Academy of Science Conference entitled “DNA Damage: Effects on DNA Structure and Protein Recognition” Burlington Vermont, August, 1993.

4. Kennedy, M. A., “NMR and Enzymological Studies of Modified-DNA/ Protein Interactions” The Cell Kinetics Society, Richland, WA, April 15-18, 1993.

3. Kennedy, M. A., “DNA Structure and its Dynamics Using NMR” 25^th DOE Radiological and Chemical Physics Contractor’s Meeting, Wakulla Springs, Florida, June 8-10, 1992.

2. Kennedy, M. A., “Microscopic Structure and Macroscopic Properties: A Solid-State NMR Approach” Proctor and Gamble, Cincinatti, Ohio, 1992, November, 1991.

1. Kennedy, M. A., Vold R. R.; and Vold, R. L., “Stepped frequency NMR Spectroscopy of Quadrupolar Nuclei” 31^st ENC, Pacific Grove, California, April 1-5, 1990.

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