Publications
PUBLICATIONS: (195 since 1989)
A complete citation history of these publications can be found at Google Scholars at: https://scholar.google.com/citations?user=7rWzfjkAAAAJ&hl=en
NCBI My Bibliography https://www.ncbi.nlm.nih.gov/myncbi/1L3_kwfzxCU/bibliography/public/
underlined names indicate undergraduate student co-authors
2023
195) Imani L. Ross, Julie A. Beardslee, Maria M. Steil, Tafadzwa Chihanga and Michael A. Kennedy Statistical Considerations and Database Limitations in NMR-Based Metabolic Profiling Studies. Metabolomics, 19:64, 2023. https://doi.org/10.1007/s11306-023-02027-5 DOI 10.1007/s11306-023-02027-5
194) Ethan H. Li, Laura Spaman, Roberto Tejero, Yuanpeng Janet Huang, Theresa A. Ramelot, Keith J. Fraga, James H. Prestegard, Michael A. Kennedy, and Gaetano T. Montelione Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data. Journal of Magnetic Resonance 352, 107481, 2023. https://doi.org/10.1016/j.jmr.2023.107481
193) Huan Zhang, Eric C. Johnson, Anne Carroll, Cecily Pryor, Ben Shurina, Nuwanthika Kumarage, Kundi Yang, Michael A. Kennedy, and Michael W. Crowder, 1H NMR spectroscopic analysis of bourbon whiskeys. , Journal of Food Composition and Analysis, 115, 105119, 2023.
2022
192) Ruojing Zhang, Michael C. Stahr, and Michael A. Kennedy, Introduction of a new scheme for classifying β turns in protein structures PROTEINS: Structure, Function, and Bioinformatics, 90(1), 110-122, 2022.
2021
191) Shenyuan Xu , Kristen Rose McGinnis , Yang Liu , Pengwei Huang , Ming Tan , Michael Robert Stuckert , Riley Erin Burnside , Elsa Grace Jacob , Shuisong Ni, Xi Jiang , Michael A Kennedy Structural basis of P[II] rotavirus evolution and host ranges under selection of histo-blood group antigens, Proceedings of the National Academy of Sciences USA, 118 (36) e2107963118, 2021. https://doi.org/10.1073/pnas.2107963118.
190) Xi Jiang, Ming Tan, Ming Xia, Pengwei Huang and Michael A. Kennedy Intra-species sialic acid polymorphism in humans: a common niche for influenza and coronavirus pandemics?, Emerging Microbes and Infections, 10(1):1191-1199, 2021.
189) Ruojing Zhang and Michael A. Kennedy Current Understanding of the Structure and Function of Pentapeptide Repeat Proteins, Biomolecules, 11,638, 2021.
188) Steven Standage, Shenyuan Xu, Lauren Brown, Qing Ma, Adeleine Koterba, Patrick Lahni, Prasad Devarajan, Michael A Kennedy NMR-Based Serum and Urine Metabolomic Profile Reveals Suppression of Mitochondrial Pathways in Experimental Sepsis-Associated Acute Kidney Injury American Journal of Physiology: Renal Physiology, 320(5), F984-F1000, 2021.
2020
187) Ilana Chertok, Zalalem Haile, Shuisong Ni, Michael A. Kennedy Differences in human milk lactose and citrate concentrations based on gestational diabetes status, Breastfeeding Medicine, 15(12), 798-802, 2020.
186) Shenyuan Xu, Michael A. Kennedy, Structural dynamics of pentapeptide repeat proteins, PROTEINS: Structure, Function, and Bioinformatics, 88 (11), 1493-1512, 2020
185) Ruojing Zhang, Shuisong Ni, Michael A. Kennedy, Crystal structure of Alr1298, a pentapeptide repeat protein from the cyanobacterium Nostoc sp. PCC 7120, determined at 2.1 Å resolution, PROTEINS: Structure, Function, and Bioinformatics, 2020. https://doi.org/10.1002/prot.25882
184) Shenyuan Xu, Luay U. Ahmed, Michael Robert Stuckert, Kristen Rose McGinnis, Yang Liu, Ming Tan, Pengwei Huang, Weiming Zhong, Dandan Zhao, Xi Jiang, Michael A. Kennedy Molecular basis of P[II] major human rotavirus VP8* domain recognition of histo-blood group antigens, PLoS Pathogens,16(3): e1008386,, 2020.
2019
183) Yao Nie, Jiang Zhu, Theresa A Ramelot, Michael A Kennedy, Maili Liu, Ting He, Yunhuang Yang Solution NMR structure and ligand identification of human Gas7 SH3 domain reveal a typical SH3 fold but a non-canonical ligand-binding mode Biochemical and biophysical research communications, 516(4) 1190-1195, 2019.
182) Shuangli Li, Guoliang Lu, Xiang Fang, Theresa A Ramelot, Michael A Kennedy, Xin Zhou, Peng Gong, Xu Zhang, Maili Liu, Jiang Zhu, Yunhuang Yang Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins Nucleic acids research, 48(1):432-444. doi: 10.1093/nar/gkz1045.
181) William C. Joesten, Audrey H. Short, Michael A Kennedy, Spatial variations in gut permeability are linked to type 1 diabetes development in non-obese diabetic mice. British Medical Journal (BMJ) Open Diabetes Research & Care, 7:e000793, 2019.
180) Irina Petrova, Shenyuan Xu, William Joesten, Shuisong Ni, Michael Kennedy, Influence of Drying Method on NMR-Based Metabolic Profiling of Human Cell Lines, Metabolites, 9(11), 256, 2019.
179) Ruojing Zhang, Shuisong Ni, Michael A. Kennedy, Type I Beta Turns Make A New Twist in Pentapeptide Repeat Proteins: Crystal Structure of Alr5209 from Nostoc sp. PCC 7120 Determined at 1.7 Angstro ̈m Resolution, Journal of Structural Biology, 3, 100010, 2019.
178) Cong Cai, Yao Nie, Yixuan Gong, Shuangli Li, Theresa A. Ramelot, Michael A. Kennedy, Xiali Yue, Jiang Zhu, Maili Liu, and Yunhuang Yang Solution NMR structure of CGL2373, a polyketide cyclase_like protein from Corynebacterium glutamicum, Proteins: Structure, Function and Bioinformatics, 88(1): 237-241, 2020.
177) Faizule Hassan, Shuisong Ni, Taylor L Becker, Christine M Kinstedt, Jana L Abdul-Samad, Michael A. Kennedy Evaluation of the Antibacterial Activity of 75 Mushrooms Collected in the Oxford, Ohio USA Vicinity, International Journal of Medicinal Mushrooms, 21(2), 131-141, 2019.
176) William C. Joesten and Michael A. Kennedy, RANCM - A new ranking scheme for assigning confidence levels to metabolite assignments in NMR-based metabolomics studies, Metabolomics, 15, 5, 2019.
175) Chunjie Liang, Jiang Zhu, Theresa A. Ramelot, Michael A. Kennedy, Maili Liu, Ting He, and Yunhuang Yang, Solution NMR structure of CHU_1110 from Cytophaga hutchinsonii, an AHSA1 protein potentially involved in metal ion stress response, Proteins: Structure, Function, and Bioinformatics, 87(1):91-95, 2019. doi: 10.1002/prot.25622. Epub 2018 Nov 11.
2018
174) Ting He, Shuangli Li, Rui Hu, Theresa A Ramelot, Michael A Kennedy, Yunhuang Yang, Jiang Zhu, Maili Liu Chemical shift assignments of Mb1858 (24-155), a FHA domain-containing protein from Mycobacterium bovis Biomolecular NMR assignments 12(1), 1-4, 2018.
173) Zi Wang, Yao Nie, Kunxiao Zhang, Henghao Xu, Theresa A. Ramelot, Michael A. Kennedy, Maili Liu, Jiang Zhu, Yunhuang Yang Solution structure of SHIP2 SH2 domain and its interaction with a phosphotyrosine peptide from c-MET, Archives of Biochemistry and Biophysics, Volume 656, Pages 31-37, 2018.
172) Michelle J Schmahl, Daniel P Regan, Adam C Rivers, William C Joesten, Michael A Kennedy. NMR-based metabolic profiling of urine, serum, fecal, and pancreatic tissue samples from the Ptf1a-Cre; LSL-KrasG12D transgenic mouse model of pancreatic cancer, PLoS-ONE, 13(7): e0200658. https://doi.org/10.1371/journal.pone.0200658
171) Tafadzwa Chihanga, Hannah N. Ruby, Qing Ma, Sabina Bashir, Prasad Devarajan, Michael A. Kennedy NMR-Based Urine Metabolic Profiling and Immunohistochemistry Analysis of Nephron Changes in a Mouse Model of Hypoxia-Induced Acute Kidney Injury American Journal of Physiology - Renal Physiology, 315(4):F1159-F1173, 2018.
170) Faizule Hassan, Sarah L Lossie, Ellen P Kasik, Audrey M Channon, Shuisong Ni, Michael A. Kennedy* A Mouse Model Study of Toxicity and Biodistribution of a Replication Defective Adenovirus Serotype 5 Virus with its Genome Engineered to Contain a Decoy Hyper Binding Site to Sequester and Suppress Oncogenic HMGA1 as a New Cancer Treatment Therapy PLoS-ONE, 13(2): e0192882 , 2018. https://doi.org/10.1371/journal.pone.0192882.
169) Faizule Hassan, Shuisong Ni, Tyler C. Arnett, Melanie C McKell, Michael A. Kennedy* Adenovirus mediated delivery of decoy hyper binding sites targeting oncogenic HMGA reduces pancreatic and liver cancer cell viability Molecular Therapy Oncolytics, 8: 52–61, 2018.
168) Jiang Zhu; Shuangli Li; Theresa Ramelot; Michael Kennedy; Maili Liu; Yunhuang Yang. Structural insights into the impact of two holoprosencephaly-related mutations on human TGIF1 homeodomain. Biochemical and Biophysical Research Communications (BBRC), 496(2):575-581, 2018.
167) Tafadzwa Chihanga, Sarah M. Hausmann, Shuisong Ni, and Michael A. Kennedy* Influence of media selection on NMR based metabolic profiling of human cell lines, Metabolomics, 14, 28, 2018.
166) Tafadzwa Chihanga, Qing Ma, Jenna Nicholson, Hannah Ruby, Richard Edelmann, Prasad Devarajan, Michael A. Kennedy. "NMR Spectroscopy and Electron Microscopy Identification of Metabolic and Ultrastructural Changes to the Kidney Following Ischemia Reperfusion Injury" American Journal of Physiology - Renal Physiology, 314 (2), F154-166, 2018. DOI: 10.1152/ajprenal.00363.2017
2017
165) He T, Li S, Hu R, Ramelot TA, Kennedy MA, Yang Y, Zhu J, Liu M. Chemical shift assignments of Mb1858 (24-155), a FHA domain-containing protein from Mycobacterium bovis. Biomol NMR Assign. 2017 Aug 30. doi: 10.1007/s12104-017-9769-0. [Epub ahead of print]
164) Shenyuan Xu, Brian Long, Gabriel Boris, Angel Chen, Shuisong Ni, Michael A. Kennedy Structural rearrangement of the Switch I Region in G12A K-Ras stabilizes the precatalytic state contributing to reduced intrinsic GTP hydrolysis, Acta Cryst D, 73(Pt 12):970-984, 2017.
163) Michelle J Veite-Schmahl, Adam C Rivers, Daniel P Regan, Michael A Kennedy. The Mouse Model of Pancreatic Cancer Atlas (MMPCA) for classification of pancreatic cancer lesions: A large histological investigation of the Ptf1a-Cre; LSL-KrasG12D transgenic mouse model of pancreatic cancer PLoS ONE, 13(2): e0192882, 2017. https://doi.org/10.1371/journal.pone.0192882
162) Yang Liu; Shenyuan Xu; Andrew Woodruff; Ming Xia; Ming Tan; Michael A. Kennedy; Xi Jiang Structural basis of glycan specificity of P[19] VP8*: implications for rotavirus zoonosis and evolution, PLOS Pathogens, 13(11): e1006707, 2017. https://doi.org/10.1371/journal.ppat.1006707.
161) Daniel Elnatan, Miguel Betegon, Yanxin Liu, Theresa Ramelot, Michael A Kennedy, David Agard. "Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1", eLife, pii: e25235., 2017. doi: 10.7554/eLife.25235
160) Kari Pederson, Gordon R. Chalmers, Qi Gao, Daniel Elnatan, Theresa A. Ramelot, Li-Chung Ma, Gaetano T. Montelione, Michael A. Kennedy, David A. Agard, and James H. Prestegard. "NMR Characterization of HtpG, the E. coli Hsp90, Using Sparse Labeling with 13C-Methyl Alanine" Journal of Biomolecular NMR, 68(3), 225-236 2017. doi: 10.1007/s10858-017-0123-8.
159) Michelle Veite-Schmahl, William Joesten, and Michael Kennedy. “HMGA1 Expression Levels are Elevated in Pancreatic Intraepithelial Neoplasia Cells in the Ptf1a-Cre; LSL-KrasG12D Transgenic Mouse Model of Pancreatic Cancer” The British Journal of Cancer, 117, 639-647, 2017.
158) Michelle J Veite-Schmahl, Daniel P. Regan, Adam C. Rivers, Joesph F. Nowatzke, Michael A. Kennedy. "Dissection of the Mouse Pancreas for Histological Analysis and Metabolic Profiling" Journal of Visualized Experiments, issue 126, 2017.DOI: 10.3791/55647 HTTPS://WWW.JOVE.COM/VIDEO/55647/DISSECTION-MOUSE-PANCREAS-FOR-HISTOLOGICAL-ANALYSIS-METABOL
157) Shenyuan Xu, Shuisong Ni, Michael A. Kennedy. "NMR Analysis of Amide Hydrogen Exchange Rates in a Pentapeptide-Repeat Protein from A. thaliana" Biophysical Journal 112, 2075-2088, 2017. doi: 10.1016/j.bpj.2017.04.016
156) Soraya Rumbo-Feal, Astrid Pérez, Theresa A. Ramelot, Laura Alvarez-Fraga, Juan A. Vallejo, Alejandro Beceiro, Emily J. Ohneck, Brock A. Arivett, María Merino, Steven E. Fiester, Michael A. Kennedy, Luis A. Actis, German Bou, Margarita Poza "Contribution of the A. baumannii A1S_0114 gene to the interaction with eukaryotic cells and virulence" Frontiers in Cellular and Infection Microbiology, 7: 108, 2017.doi: 10.3389/fcimb.2017.0010
155) Chunjie Liang, Jiang Zhu, Rui Hu, Theresa A Ramelot, Michael A Kennedy, Maili Liu, Yunhuang Yang. Solution NMR structure of RHE_CH02687 from Rhizobium etli: A novel flavonoid-binding protein. Proteins 2017 Feb 3. Epub 2017 Feb 3.
154) Jiang Zhu, Huapu Wang, Theresa A Ramelot, Michael A Kennedy, Rui Hu, Xiali Yue, Maili Liu, Yunhuang Yang. Solution NMR structure of zinc finger 4 and 5 from human INSM1, an essential regulator of neuroendocrine differentiation. Proteins 2017 Feb 3. Epub 2017 Feb 3.
2016
153) John K Everett, Roberto Tejero, Sarath B K Murthy, Thomas B Acton, James M Aramini, Michael C Baran, Jordi Benach, John R Cort, Alexander Eletsky, Farhad Forouhar, Rongjin Guan, Alexandre P Kuzin, Hsiau-Wei Lee, Gaohua Liu, Rajeswari Mani, Binchen Mao, Jeffrey L Mills, Alexander F Montelione, Kari Pederson, Robert Powers, Theresa Ramelot, Paolo Rossi, Jayaraman Seetharaman, David Snyder, G V T Swapna, Sergey M Vorobiev, Yibing Wu, Rong Xiao, Yunhuang Yang, Cheryl H Arrowsmith, John F Hunt, Michael A Kennedy, James H Prestegard, Thomas Szyperski, Liang Tong, Gaetano T Montelione. A community resource of experimental data for NMR / X-ray crystal structure pairs. Protein Sci 2016 Jan 22;25(1):30-45. Epub 2015 Sep 22.
152) Yang Liu, Theresa Ramelot, Pengwei Huang, Yan Liu, Zhen Li, Ten Feizi, weiming Zhong, Fang-Tzy Wu, Ming Tan, Michael Kennedy, and Xi Jiang. Glycan specificity of P[19] rotavirus and comparison with those of other related P genotypes, Journal of Virology 90 (21), 9983-9986, 2016.
151) Shuangli Li, Theresa A. Ramelot, Michael A. Kennedy, Maili Liu, and Yunhuang Yang Chemical Shift Assignments of Homodimer Protein SP_0782 (7-79) from Streptococcus pneumonia. Journal of Biomolecular NMR, 1-4, 2016. doi:10.1007/s12104-016-9697-4
2015
150) Antonio Rosato, Wim Vranken, Rasmus H. Fogh, Timothy J. Ragan, Roberto Tejero James Prestegard, Adlinda Yee, Cheryl Arrowsmith, Michael Kennedy, Thomas B. Acton, Rong Xiao, Gaohua Liu, Gaetano T. Montelione and Geerten W. Vuister. The Second Round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013, Journal of Biomolecular NMR, 62(4), 413-424, 2015.
149) Bo Wang, Sulaiman Sheriff, Ambikaipakan Balasubramaniam, Michael A. Kennedy NMR based metabonomics study of Y2 Receptor activation by neuropeptide Y in the SK-N-BE2 human neuroblastoma cell line Metabolomics, 11 (5), 1243-1252, 2015.
2014
148) Yunhuang Yang, Theresa A. Ramelot, Hsiau-Wei Lee, Rong Xiao, John K. Everett, Gaetano T. Montelione, James H. Prestegard, Michael A. Kennedy NMR Structure Note: Solution structure of a fragment (175-257) of CV_0373 protein from Chromobacterium violaceum adopts a winged helix-turn-helix (wHTH) fold. Journal of Biomolecular NMR, 60: 197-202, 2014.
147) Yunhuang Yang, Theresa A. Ramelot, Hsiau-Wei Lee, Rong Xiao, John K. Everett, Gaetano T. Montelione, James H. Prestegard, Michael A. Kennedy, NMR Structure Note: Solution structure of the free Z domain of human DLM-1 (ZBP1/DAI), a Z-DNA binding domain Journal of Biomolecular NMR, 60(2-3), 189-195, 2014.
146) Sherif I. Elshahawi, Theresa A. Ramelot, Jayaraman Seetharaman, Jing Chen, Shanteri Singh, Yunhuang Yang, Kari Pederson, Madan K. Kharel, Rong Xiao, Thomas B. Acton, John K. Everett, Ragothaman M. Yennamalli, Fengbin Wang, James H. Prestegard, Scott Lew, Liang Tong, Gaetano T. Montelione, Michael A. Kennedy, Craig A. Bingman, Haining Zhu, George N. Phillips Jr, and Jon S. Thorson Structure-Guided Functional Characterization of Enediyne Self-Sacrifice Resistance Proteins, CalU16 and CalU19, ACS Chemical Biology, 9(10), 2347-2358, 2014.
145) Zhanquan Shi, Bo Wang, Tafadzwa Chihanga, Michael A. Kennedy, Georg F. Weber Energy Metabolism during Anchorage Independence. Induction by Osteopontin-c, PLOS ONE, 9(8), 2014.
144) Laura A. Lavery, James R. Partridge, Theresa A. Ramelot, Daniel Elnatan, Michael A. Kennedy, David A. Agard Structural asymmetry in the closed state of mitochondrial Hsp90 (TRAP1) supports a two-step ATP hydrolysis mechanism, Molecular Cell 53, 330-343, 2014.
143) Bo Wang, Michael A. Kennedy Principal component analysis of protein sequence clusters, Journal of Structural and Functional Genomics, 15, 1-11, 2014.
142) Patrick Videau, Shuisong Ni, Orion S. Rivers, Blake Ushijima, Erik Feldmann, Loralyn M. Cozy, Michael A. Kennedy and Sean M. Callahan Expanding the Direct HetR Regulon in Anabaena sp. strain PCC 7120 Journal of Bacteriology 196, 1113-1121, 2014.
141) Mana Mirza, Zhanquan Shi, Bo Wang, Michael A. Kennedy, Georg F. Weber Osteopontin-a Alters Glucose Homeostasis in Anchorage Independent Breast Cancer Cells, Cancer Letters 344, 47-53, 2014.
2013
140) Theresa A. Ramelot, Yunhuang Yang, Hsiau-Wei Lee, Rong Xiao, Thomas B. Acton, John K. Everett, James H. Prestegard, Gaetano T. Montelione, and Michael A. Kennedy NMR structure and membrane association of the intermembrane space domain from the human mitochondrial AAA protease, AFG3L2, FEBS Letters, 587, 3522-3528, 2013.
139) Bo Wang, Zhanquan Shi, Georg F. Weber, and Michael A. Kennedy Introduction of a New Critical P-Value Correction Method for Statistical Significance Analysis of Metabonomics Data, Analytical and Bioanalytical Chemistry, published online September 13, 2013.
138) Bo Wang, Aaron M. Goodpaster, and Michael A. Kennedy Coefficient of Variation, Signal-to-Noise Ratio, and Effects of Normalization in Validation of Biomarkers from NMR-based Metabonomics Studies, Chemometrics and Intelligent Laboratory Design, 128, 9-16, 2013.
137) Surya VSRK Pulavarti, Yunfen He, Erik A. Feldmann,Alexander Eletsky,Thomas B. Acton • Rong Xiao • John K. Everett • Gaetano T. Montelione • Michael A. Kennedy • Thomas Szyperski Solution NMR Structures Provide First Structural Coverage of the Large Protein Domain Family PF08369 and Complement Structural Coverage of Dark Operative Protochlorophyllide Oxidoreductase Complexes, Journal of Structural and Functional Genomics, 14, 119-126, 2013.
136) Lindsey E. Romick-Rosendale, Neil B. Patel, and Michael A. Kennedy Antibiotic induced intestinal injury in mice is repaired after removing antibiotic pressure: Implications for Empiric Antibiotic Therapy, Metabolomics, published on-line, 2013.
135) Yunhuang Yang, Theresa A. Ramelot, Shuisong Ni, Robert M. McCarrick, Michael A. Kennedy Applications of NMR-based PRE and EPR-based DEER Spectroscopy to Homodimer Subunit Exchange Characterization and Structure Determination Methods in Molecular Biology, in press, 2013.
134) Ardythe L. Morrow, Anne J. Lagomarcino, Kurt R. Schibler, Diana H. Taft, Zhuoteng Yu, Bo Wang, Michael Wagner, Dirk Gevers, Doyle V. Ward, Michael A. Kennedy, Curtis Huttenhower, David S. Newburg Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants Microbiome, 1, 13, 2013.
133) Daniil V. Zaytsev, Jiufeng Fan, Xianchun Zhu, Madhumita Mukherjee, Shuisong Ni, Michael A. Kennedy, Borries Demeler, and Michael Y. Ogawa Metal-binding properties of a self-assembled coiled coil: formation of a polynuclear Cd-thiolate cluster J Inorganic Biochemistry, 119, 1-9, 2013.
132) Yunhuang Yang, Theresa A. Ramelot, Shuisong Ni, Robert M. McCarrick, Michael A. Kennedy Measurement of Rate Constants for Homodimer Subunit Exchange Using Double Electron-Electron Resonance and Paramagnetic Relaxation Enhancement. Journal Biomolecular NMR, 55(1), 47-58, 2013.
131) Miki Watanabe, Shuisong Ni, Amy L. Lindenberger, Junho Cho, Stuart L. Tinch, and Michael A. Kennedy Characterization of the Stoichiometry of HMGA1/DNA Complexes The Open Biochemistry Journal, 7, 73-81, 2013.
2012
130) Theresa A. Ramelot, Paolo Rossi, Farhad Forouhar, Hsiau-Wei Lee, Yunhuang Yang, Shuisong Ni, Sarah Unser, Scott Lew, Jayararaman Seetharaman, Rong Xiao, Thomas B. Acton, John K. Everett, James H. Prestegard, John F. Hunt, Gaetano T. Montelione and Michael A. Kennedy Structure of the specialized acyl carrier protein AcpXL, an essential protein for lipid A biosynthesis with very long chain fatty acids, in an open and closed conformation Biochemistry, 51, 7239-49, 2012.
129) Erik A. Feldmann, Jayaraman Seetharaman, Theresa A. Ramelot, Scott Lew, Li Zhao, Keith Hamilton, Colleen Ciccosanti, Rong Xiao, Thomas B. Acton, John K. Everett, Liang Tong, Gaetano T. Montelione, Michael A. Kennedy Solution NMR and X-ray crystal structure of Pspto_3016 from Pseudomonas syringae, a member of protein domain family PF04237 (DUF419) that adopts a “double wing” DNA binding motif Journal of Structural and Functional Genomics, 13,155-162, 2012.
128) Yunhuang Yang, Theresa A. Ramelot, John R. Cort, Maite Garcia, Adelinda Yee, Cheryl H. Arrowsmith, Gaetano T. Montelione and Michael A. Kennedy Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum International Journal of Molecular Sciences 13, 7354-7364, 2012.
127) Miki Watanabe, Sulaiman Sheriff, Kenneth B. Lewis, Junho Cho, Stuart L. Tinch, Ambikaipakan Balasubramaniam and Michael A. Kennedy Metabolic profiling comparison of human pancreatic ductal epithelial cells and three pancreatic cancer cell lines using NMR based metabonomics Journal of Molecular Biomarkers and Diagnosis, S3, 1-17, 2012.
126) Erik A. Feldmann, Shuisong Ni, Indra D. Sahu, Clay H. Mishler, Jeffrey D. Levengood, Yegor Kushnir, Robert M. McCarrick, Gary A. Lorigan, Blanton S. Tolbert, Sean M. Callahan and Michael A. Kennedy Differential Binding between PatS C-terminal Peptide Fragments and HetR from Anabaena sp. PCC 7120 Biochemistry, 51, 2436-2442, 2012.
125) David A. Snyder, James M. Aramini, Bomina Yu, Yuanpeng J. Huang, Rong Xiao, John R. Cort Ritu Shastry, Li-Chung Ma, Jinfeng Liu, Burkhard Rost, Thomas B. Acton, Michael A. Kennedy, and Gaetano T. Montelione Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus Proteins: Structure, Function and Bioinformatics, 80, 1901-1906, 2012.
124) Lindsey E. Romick-Rosendale, Kurt R. Schibler, and Michael A. Kennedy A potential biomarker for acute kidney injury in preterm infants from Metabolic Profiling, Journal of Molecular Biomarkers and Diagnosis, S3, 2012.
2011
123) Ni S, McGookey ME, Tinch SL, Jones AN, Jayaraman S, Tong L, Kennedy MA. The 1.7 Å resolution structure of At2g44920, a pentapeptide-repeat protein in the thylakoid lumen of Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Dec 1;67(Pt 12):1480-4.
122) Antonio Rosato, James M. Aramini, Cheryl Arrowsmith, Anurag Bagaria, David Baker, Andrea Cavalli, Jurgen F. Doreleijers, Alexander Eletsky, Andrea Giachetti, Paul Guerry, Aleksandras Gutmanas, Peter Güntert, Yunfen He, Torsten Herrmann, Yuanpeng J. Huang, Victor Jaravine, Hendrik R.A. Jonker, Michael A. Kennedy, Oliver F. Lange, Gaohua Liu, Thérèse E. Malliavin, Rajeswari Mani, Binchen Mao, Gaetano T. Montelione, Michael Nilges, Paolo Rossi, Gijs van der Schot, Harald Schwalbe, Thomas A. Szyperski, Michele Vendruscolo, Robert Vernon, Wim F. Vranken, Sjoerd de Vries, Geerten W. Vuister, Bin Wu, Yunhuang Yang, Alexandre M.J.J. Bonvin Blind testing of routine, fully automated determination of protein structures from NMR data Structure, 20, 227-236, 2011.
121) Lindsey E. Romick-Rosendale, Hermine I. Brunner, Michael R. Bennett, Rina Mina, Shannen Nelson, Michelle Petri, Adnan Kiani, Prasad Devarajan, and Michael A. Kennedy Identification of Urinary Metabolites That Distinguish Proliferative From Membranous Lupus Nephritis by NMR-Based Metabonomics, Arthritis Research and Therapy, 13, R199, 2011.
120) Miki Watanabe, Sulaiman Sheriff, Nijiati Kadeer, Junho Cho, Kenneth B. Lewis, Ambikaipakan Balasubramaniam and Michael A. Kennedy NMR based metabonomics study of NPY Y5 Receptor activation in BT-549, a human breast carcinoma cell line Metabolomics, 8, 854-868, 2012. DOI: 10.1007/s11306-011-0380-6
119) Miki Watanabe, Sulaiman Sheriff, Kenneth B. Lewis, Stuart L. Tinch, Junho Cho, Ambikaipakan Balasubramaniam and Michael A. Kennedy HMGA1-targeted phosphorothioate DNA aptamers increase sensitivity to gemcitabine chemotherapy in human pancreatic cancer cell lines Cancer Letters, 315, 18-27, 2012.
118) Andriy Kryshtafovych, John Moult, Sergio G. Bartual, J. Fernando Bazan, Helen Berman, Darren E. Casteel, Evangelos Christodoulou, John K. Everett, Jens Hausmann, Tatjana Heidebrecht, Tanya Hills, Raymond Hui, John F. Hunt, Seetharaman Jayaraman, Andrzej Joachimiak, Michael A. Kennedy, Choel Kim, Andreas Lingel, Karolina Michalska, Gaetano T. Montelione, José M. Otero, Anastassis Perrakis, Juan C. Pizarro, Mark J. van Raaij, Theresa A. Ramelot, Francois Rousseau, Liang Tong, Amy K. Wernimont, Jasmine Young, Torsten Schwede Target Highlights in CASP9: Experimental Target Structures for the Critical Assessment of Techniques for Protein Structure Prediction Proteins: Structure Function and Bioinformatics, 79, 6-20, 2011.
117) Erik A. Feldmann, Theresa A. Ramelot, Yunhuang Yang, Rong Xiao, Thomas B. Acton, John K. Everett, Gaetano T. Montelione, Michael A. Kennedy Solution NMR structure of Asl3597 from Nostoc sp. PCC7120 and member of protein domain family PF12095, adopts a unique structure Proteins: Structure, Function and Bioinformatics, 80, 671-675, 2012.
116) Theresa A. Ramelot, Yunhuang Yang, Rong Xiao, Thomas B. Acton, John K. Everett, Gaetano T. Montelione and Michael A. Kennedy Solution NMR structure of BT_0084 lipoprotein from Bacteroides thetaiotamicron, found in a conjugate transposon, Proteins: Structure, Function, and Bioinformatics, 80, 667-670, 2011.
115) Erik A. Feldmann, Shuisong Ni, Indra Dev Sahu, Douglas D. Risser, Jodi L. Murakami, Sasa K. Tom, Robert M. McCarrick, Gary A. Lorigan, Sean M. Callahan and Michael A. Kennedy Evidence for Direct Binding Between HetR from Anabaena sp. PCC 7120 and PatS-5 Biochemistry, 50, 9212-9224, 2011.
114) Aaron M. Goodpaster and Michael A. Kennedy Quantification and Statistical Significance Analysis of Group Separation in NMR-Based Metabonomics Studies Chemometrics and Intelligent Laboratory Systems” 9, 162-170, 2011.
113) Yunhuang Yang, Theresa A. Ramelot, John R. Cort, Huang Wang, Colleen Ciccosanti, Mei Jiang, Haleema Janjua, Thomas B. Acton, Rong Xiao, John K. Everett, Gaetano T. Montelione, Michael A. Kennedy Solution NMR Structure of the Dsy0195 Homodimer from Desulfitobacterium hafniense Journal of Structural and Functional Genomics, 17, 281-299, 2011.
112) Miki Watanabe, Sulaiman Sheriff, Theresa A. Ramelot, Nijiati Kadeer, Junho Cho, Kenneth B. Lewis, Ambikaipakan Balasubramaniam and Michael A. Kennedy NMR based metabonomics study of DAG treatment in a burn-injury mouse C2C12 cell model International Journal of Peptide Research and Therapeutics, 17, 281-299, 2011.
111) Theresa A. Ramelot, Matthew J. Smola, Hsiau-Wei Lee, Colleen Ciccosanti, Keith Hamilton, Thomas B. Acton, Rong Xiao, John K. Everett, James H. Prestegard, Gaetano T. Montelione, and Michael A. Kennedy NMR Structure of 4’-Phosphopantetheine - GmACP3 from Geobacter metallireducens: An Acyl Carrier Protein Associated with Lipopolysaccharide Biosynthesis Biochemistry, 50(9): 1442-53, 2011.
110) Aaron M. Goodpaster, Eshwar H. Ramadas, and Michael A. Kennedy Potential Effect of Diaper and Cotton Ball Contamination on NMR and LC/MS Based Metabonomic Studies of Urine from Newborn Babies Analytical Chemistry, 83(3): 896-902, 2011.
2010
109) Yunhuang Yang,Theresa A. Ramelot,Robert M. McCarrick, Shuisong Ni, Erik A. Feldmann, John R. Cort, Huang Wang, Erica L. Foote, Colleen Ciccosanti, Mei Jiang, Haleema Janjua, Thomas B. Acton, Rong Xiao, John K. Everett, Gaetano T. Montelione, Michael A. Kennedy Combining NMR, PRE, and EPR Methods For Homo-dimer Protein Structure Determination Journal of the American Chemical Society, 132 (34), 11910-11913, 2010.
108) Yunhuang Yang, Theresa A. Ramelot, John R. Cort, Dongyan Wang, Colleen Ciccosanti, Keith Hamilton,Rajesh Nair, Burkhard Rost, Thomas B. Acton, Rong Xiao, John K. Everett, Gaetano T. Montelione, Michael A. Kennedy Solution NMR structure of photosystem II reaction center protein Psb28 from Synechocystis sp. strain PCC 6803, Proteins: Structure, Function, and Bioinformatics, 79, 340344, 2011.
107) Srivatsan Raman, Oliver F. Lange, Paolo Rossi, Michael Tyka, Xu Wang, James Aramini, GaohuaLiu, Theresa Ramelot, Alexander Eletsky, Thomas Szyperski, Michael Kennedy, James Prestegard, Gaetano T. Montelione, David Baker NMR Structure Determination for Larger Proteins Using Backbone-Only Data, Science, 327 (5968), 1014-1018, 2010.
106) Aaron M. Goodpaster, Lindsey E. Romick-Rosendale, Michael A. Kennedy Statistical Significance of NMR-Based Metabonomics Data, Analytical Biochemistry, 401, 134-143, 2010.
2009
105) Denghui Xing, Shuisong Ni, Michael A. Kennedy, Qingshun Li Identification of a Plant-specific Zn2+-sensitive ribonuclease activity Planta, 230(4), 819-825, 2009. PMID: 19636588
104) Lindsey E. Romick-Rosendale, Aaron M. Goodpaster, Philip J. Hanwright, Neil B. Patel, Esther T. Wheeler, Deepika L. Chona, Michael A. Kennedy NMR-Based Metabonomics Analysis of Mouse Urine and Fecal Extracts Following Oral Treatment with the Broad-Spectrum Antibiotic Baytril, Magnetic Resonance in Chemistry, 47(S1), S36-S46, 2009. PMID: 19768747
103) Gaetano T. Montelione, Cheryl Arrowsmith, Mark E. Girvin, Michael A. Kennedy, John L. Markley, Robert Powers, James H. Prestegard, and Thomas Szyperski Unique Opportunities for NMR Methods in Structural Genomics J. Struct. Funct. Genomics, 10, 101-106, 2009. PMID: 19288278
102) Mercier KA, Cort JR, Kennedy MA, Lockert EE, Ni S, Shortridge MD, Powers R. Structure and function of Pseudomonas aeruginosa protein PA1324 (21-170). Protein Sci. 18(3): 606-18, 2009. PMID: 19241370
101) Shuisong Ni, Matthew M. Benning, Matthew J Smola, Erik A. Feldmann, and Michael A. Kennedy, Crystal structure of Npun_R1517, a putative negative regulator of heterocyst differentiation from Nostoc punctiforme PCC 73102, Proteins, 74(3), 794-798, 2009. PMID: 19089958
100) Shuisong Ni, George M. Sheldrick, Matthew M. Benning and Michael A. Kennedy, The 2 Å Resolution Crystal Structure of HetL, a Pentapeptide Repeat Protein Involved in Regulation of Heterocyst Differentiation in the Cyanobacterium Nostoc. Sp. Strain PCC 7120, Journal of Structural Biology, 165(1), 45-52, 2009. PMID: 18952182
2008
99) Claudia Bertonati, Marco Punta, Markus Fischer, Guy Yachdav, Farhad Forouhar, Weihong Zhou, A. Belachew, Alexander P. Kuzin, Jayaraman Seetharaman, Mariam Abashidze, Theresa A. Ramelot, John R. Cort, Michael A. Kennedy, John F. Hunt, Liang Tong, Gaetano T. Montelione and Burkhard Rost Structural genomics reveals EVE as a new ASCH/PUA-related domain. Proteins: Structure, Function & Bioinformatics, 75(3), 760-767, 2008. PMID: 19191354
98) John R Cort, Ute M Selan, Andrea Schulte, Frauke Grimm, Michael A Kennedy, Christiane Dahl, Allochromatium vinosum DsrC: Solution-State NMR Structure, Redox Properties and Interaction with DsrEFH, a Protein Essential for Purple Sulfur Bacterial Sulfur Oxidation, J. Mol. Biol., 382(3), 692-707 2008. PMID: 18656485
97) T.A. Ramelot, S. Raman, A. P. Kuzin, R. Xiao, L.-C. Ma, T. B. Acton, J. F. Hunt, G. T. Montelione, D. Baker, M. A. Kennedy, Improving NMR Protein Structure Quality by Rosetta Refinement: A Molecular Replacement Study, Proteins: Structure, Function & Bioinformatics, 75(1),147-167 2009. PMID: 18816799
96) Wu B, Yee A, Huang YJ, Ramelot TA, Cort JR, Semesi A, Jung JW, Lee W, Montelione GT, Kennedy MA, Arrowsmith CH. The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: a structural homolog of the FF domain. Protein Science,17(3). 583-8, 2008. PMID: 18218711
95) Garry W. Buchko, Olga Litvinova, Howard Robinson, Alexander F. Yakunin, and Michael A. Kennedy Functional and structural characterization of DR_0079 from Deinococcus radiodurans, a novelNudix hydrolase specific for cytosine (deoxy)ribonucleoside 5’-di- and triphosphates, Biochemistry,47(25), 6571-6582, 2008. PMID: 18512963
94) 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. Journal of Structural and Functional Genomics, 9(1-4), 7-20, 2008.
2007
93) Garry W. Buchko, Howard Robinson, Himadri B. Pakrasi, and Michael A. Kennedy Insights into the Structural Variation Between Pentapeptide Repeat Proteins - Crystal Structure of Rfr23 from Cyanothece 51142 J. Struct. Biol., 162(1), 184-192, 2007.
92) J. M. Aramini, G. V. T. Swapna, Y. J. Huang, P. K. Rajan, R. Xiao, R. Shastry, T. B. Acton, J. R. Cort, M. A. Kennedy, G. T. Montelione The solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family Proteins: Structure, Function and Bioinformatics, 68(3), 789-795 2007.
91) 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
90) G. 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, 38(2), 185, 2007.
2006
89) 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.
88) G.W. Buchko, Chang Y. Kim, Thomas C. Terwilliger, Michael A. Kennedy Solution Structure of the Conserved Hypothetical Protein Rv2302 from Mycobacterium tuberculosis 188, 5993-6001, J. Bacteriology, 2006.
87) 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 residues fold- Crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142 Protein Science, 15, 2579-2595, 2006.
86) 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.
85) 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.
84) 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.
2005
83) 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\
82) 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.
81) 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.
2004
80) Robert Powers, Thomas B. Acton, Yiwen Chiang, P.K. Rajan, John R. Cort, Michael A. Kennedy, Jinfeng Liu, LiChung Ma, Burkhard Rost and Gaetano T. Montelione, (1)H, (13)C and (15)N assignments for the Archaeglobus fulgidis protein AF2095. J Biomol NMR. 2004 Sep;30(1):107-8.
79) 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.
78) 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.
77) 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.
76) 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.
2003
75) 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.
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.
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.
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.
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.
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.
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.
68) 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.
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.
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.
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.
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.
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.
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.
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.
2002
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.
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.
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.
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.
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.
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.
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.
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.
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.
2001
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.
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.
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.
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.
2000
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
1999
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.
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.
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.
1998
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.
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.
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.
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.
29) 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.
1997
28) 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.
27) 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.
26) 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.
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.
1996
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.
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.
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.
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.
1995
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.
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.
1994
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.
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.
1993
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.
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.
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.
1992
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.
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.
1991
11) Kennedy, M. A.; Vold, R. L. and Vold, R. R., Stepped Frequency NMR Spectroscopy. Journal of Magnetic Resonance, 1991, 92, 320-331.
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.
1990
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.
8) Rivera, E.; Kennedy, M. A.; Adams, R. D.; and Ellis, P. D., Cadmium-113 Shielding Tensors of Cadmium Compounds. 7. Structure and 113Cd 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.
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.
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.
1989
5) Rivera, E.; Kennedy, M. A.; Ellis, P. D., 113Cd NMR of Cd2+-Substituted Carboxypeptidase. A perspective from 113Cd Shielding Tensors. Advances in Magnetic Resonance 1989, 13, 257-273.
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.
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.
2) Kennedy, M. A.; and Ellis, P. D., 113Cd Nuclear Magnetic Resonance Spectroscopy of Cd2+-Substituted Heme and Myoglobin. Journal of American Chemical Society, 1989, 111, 3195-3203.
1) Marchetti, P. S.; Bank, S.; Bell, T. W.; Kennedy, M. A.; and Ellis, P. D., Cadmium-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.