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Publication Archive

2011

Behrens, M. A., Botkjaer, K. A., Goswami, S., Oliveira, C. L., Jensen, J. K., Schar, C. R., Declerck, P. J., Peterson, C. B., Andreasen, P. A., and Pedersen, J. S. (2011) J Mol Biol 411, 417-429. “Activation of the zymogen to urokinase-type plasminogen activator is associated with increased interdomain flexibility”

B. Collignon, R. Schulz, J.C. Smith and J. Baudry (2011) Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. J. Comput. Chem., 32(6), 1202–1209

Grubbs, J.Rahmanian, S., DeLuca, A., Padmashali, C., Jackson, M., and Howell, E.E. (2011) “Thermodynamicsand Solvent Effects on Substrate andCofactor Binding in E. coli Chromosomal Dihydrofolate Reductase,”Biochemistry 50, 3673-3685.

W.I. Hembree and J. Baudry (2011) Three-dimensional mapping of micro-environmental control of methyl rotational barriers. J Phys Chem B. 2011 115(26), 8575-80

Kim H, Helmbrecht E, Stalans MBSchmitt CLPatel N, Wen C-K, Wang W, Binder BM (2011) Domain Requirements for Different Roles of the ETR1 Ethylene Receptor. Plant Physiology. 156, 417-429.

Lee G, Wang Z, Sehgal R, Chen C-H, Kikuno K, Hay B, Park JH (2011) Drosophila caspases involved in developmentally regulated programmed cell death of peptidergic neurons during early metamorphosis. Journal of Comparative Neurology, 519, 34-48.

Tian Li, Won-Gyu Choi, Ian S. WallaceJerome Baudry, and Daniel M. Roberts (2011) Arabidopsis thaliana NIP7;1: An Anther-Specific Boric Acid Transporter of the Aquaporin Superfamily Regulated by an Unusual Tyrosine in Helix 2 of the Transport Pore. Biochemistry 50(31), 6633–6641

E. ParkA. Nebenführ (2011) Cytoskeleton and Root Hair Growth. in: The Plant Cytoskeleton (Ed. B. Liu) Advances in Plant Biology 2:259-275.

V. Philip, J. Harris, R, Adams, D. Nguyen, J. Spiers, J. Baudry, E.E. Howell and R.J. Hinde. (2011) A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-pairs. Biochemistry, 50(14), 2939-2950 (Note: this paper was chosen to be highlighted on the journal home page)

Roy, B., Copenhaver, G.P., and von Arnim, A.G. (2011). Fluorescence-tagged transgenic lines reveal genetic defects in pollen growth – application to the eIF3 complex. Plos One 6:e17640.

Ruiqiang C, Binder BM, Garrett WM, Tucker ML, Cooper B, and Chang C (2011) Proteomic Responses in Arabidopsis thaliana Seedlings Treated with Ethylene.Molecular Biosystems. In press. DOI: 10.1039/c1mb05159h

Tsai, J. H., and McKee, B. D. (2011) Homologous pairing and the role of pairing centers in meiosis. J Cell Sci 124, 1955-1963.

Thompson, L. C., Goswami, S., Ginsberg, D. S., Day, D. E., Verhamme, I. M. and Peterson, C. B. (2011) Metals Affect the Structure and Activity of Human Plasminogen Activator Inhibitor-1: I. Modulation of stability and protease inhibition. Protein Sci. 20, 353-365.

Thompson, L. C.Goswami, S., and Peterson, C. B. (2011) Metals Affect the Structure and Activity of Human Plasminogen Activator Inhibitor-1: II. Binding Affinity and Conformational Effects. Protein Sci. 20, 366-378.

Wang, S.S., Shen, T., & Wolynes, P.G. (2011) The interplay of nonlinearity and architecture in equilibrium cytoskeletal mechanics, J. Chem. Phys. 134(1), 014510

Wieninger, S. A, Serpersu, E. H. and Ullmann, G. M. (2011) ATP Binding Enables Broad Antibiotic Selectivity of Aminoglycoside Phosphotransferase(3?)-IIIa– An Elastic Network Analysis. J. Mol. Biol. 409, 450-465.

Wright, E., Busby, S.A., Wisecarver, S.Vincent, J., Griffin, P.R., Fernandez, E. J. (2011) Helix 11 Dynamics Is Critical for Constitutive Androstane Receptor Activity. Structure (Cell Press) 19(1), 37-44.

Yao, J., Nellas, R., Glover, M.M., & Shen, T. (2011) Stability and sugar recognition ability of ricin-like carbohydrate binding domains. Biochemistry 50(19), 4097-4104.

Zmijewski, J. W., Bae, H. B., Deshane, J. S., Peterson, C. B., Chaplin, D. D., and Abraham, E. (2011) Am J Physiol Lung Cell Mol Physiol 301, L247-254. “Inhibition of neutrophil apoptosis by PAI-1”

 

2010

Alexandre, G. (2010) Coupling metabolism and chemotaxis-dependent behaviours by energy taxis receptors. Microbiology 156, 2283-2293

Banerjee, P., Schoenfeld, B.P., Bell, A.J., Choi, C.H., Bradley, M.P., Hinchey P., Kollaros, M., Park J.H., McBride, S.M.J., and Dockendorff, T.C. (2010) Short and long-term memory are modulated by multiple isoforms of the fragile X mental retardation protein. J. Neurosci. 30, 6782-6792.

Bellesia, G., Asztalos, A., Shen, T., Langan, P., Redondoe, A., & Gnanakaran, S. (2010) Computational studies of crystalline cellulose and its degradation by enzymes, Acta Cryst. D66 1184-1188

Berezniak T, Zahran M, Imhof P, Jaeschke A, and Smith J. (2010) Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme. Journal of the American Chemical Society, 132(36),12587–12596.

Binder BM, Rodriguez FI, Bleecker AB. (2010). The Copper Transporter RESPONSIVE-TO-ANTAGONIST1 (RAN1) is Essential for the Biogenesis of Ethylene Receptors in Arabidopsis. Journal of Biological Chemistry. 285, 37263-37270

Bondar AN, Smith J, and Elstner M. Mechanism of a Proton Pump Analyzed with Computer Simulations. Theoretical Chemistry Accounts, 125(3-6):353-363. (2010)

Brager AJ, Ruby CL, Prosser RA and Glass JD (2010) Chronic ethanol disrupts circadian photic entrainment and daily locomotor activity in the mouse. Alcohol.Clin.Expt.Res. 34: 1266-1273.

Buchan, A., Crombie, B. and G. M. Alexandre (2010) Temporal dynamics and genetic diversity of chemotactic-competent microbial populations in the rhizosphere. Environnmental Microbiology12 (12): 3171-3184.

Chen Y-F, Gao Z, Kerris RJ, Wang W, Binder BM, Schaller GE (2010) Ethylene Receptors Function as Components of High-Molecular-Mass Protein Complexes in Arabidopsis. PLoS ONE. 5:e8640. doi:10.1371/journal.pone.0008640.

Cho D, Zheng M, Min C, Ma L, Kurose H, Park JH, Kim K-M. 2010. Agonist-induced endocytosis and receptor phosphorylation mediate resensitization of dopamine receptors. Molecular Endocrinology 24: 574-586.

Chu, Y., Xu, Q and Hong Guo (2010) Understanding Energetic Origins of Product Specificity of SET8 from QM/MM Free Energy Simulations: What Causes the Stop of Methyl Addition during Histone Lysine Methylation? J. Chem. Theory Comput., 2010, 6, 1380-1389.

Chung, E., H. Kweon, S. Yiacoumi, I. Lee, D.C. Joy, A.V. Palumbo, and C. Tsouris, “Adhesion of Spores of Bacillusthuringiensis on a Planar Surface,” Environmental Science & Technology, 44, 290-296 (2010)

Daidone I, Neuweiler H, Doose S, Sauer M, and Smith J. Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains. PLoS Computational Biology, 6(1):e1000645. (2010)

Feng, J., Grubbs, J., Dave, A., Goswami, S.Horner, CG., and Howell, E.E. (2010) Radical Redesign of a Tandem Array of Four R67 Dihydrofolate Reductase Genes Yields a Functional, Folded Protein Possessing 45 Substitutions. Biochemistry 49, 7384–7392.

Glass D, Krishnan M, Nutt D, and Smith J. Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models. Journal of Chemical Theory and Computation, 6(4):1390-1400. (2010)

Guo HB, Johs A, Parks J, Oliff L, Miller S, Summers A, Liang L, and Smith J. Structure and Conformational Dynamics of the Metalloregulator MerR upon Binding of Hg(II). Journal of Molecular Biology, 398(4), 555-568. (2010)

Hammer SB, Ruby CL, Brager AJ, Prosser RA and Glass JD (2010) Environmental modulation of alcohol intake in hamsters: effects of wheel-running and constant light exposure. Alcohol.Clin.Expt.Res 34, 1651-1658.

Hwang, J. H., Ellingson, S. R., and Roberts, D. M. (2010) FEBS Lett 584, 4339-4343. “Ammonia permeability of the soybean nodulin 26 channel”

Iwuchukwu, I., Vaughn, M., Myers, N., O’Neill, H., Frymier, P., & Bruce, B. D. (2010) Selfassembled Photosynthetic Nanoparticle for Cell-free Hydrogen Production. Nature Nanotechnology, 5, 73-79.

Kamath, G., Howell, E.E. and Agarwal, P.K. (2010) The Tail Wagging the Dog: Insights into Catalysis in R67 Dihydrofolate Reductase. Biochemistry 49, 9078–9088.

J.-F. Li, A. Nebenführ (2010) FAST Technique for Agrobacterium-Mediated Transient Gene Expression in Seedlings of Arabidopsis and Other Plant Species. Cold Spring Harbor Protocols doi:10.1101/pdb.prot5428

Lopez M, Kurkal-Siebert V, Dunn R, Tehei M, Finney J, Smith J, and Daniel R. Activity and Dynamics of an Enzyme, Pig Liver Esterase, in Near-Anhydrous Conditions. Biophysical Journal, 99(8):L62-L64. (2010)

Johnson, Q., Doshi, U., Shen, T., & Hamelberg, D. (2010) Water’s contribution to the energetic roughness from peptide dynamics. J. Chem. Theo. Comput. 6(9), 2591-2597.

Joy, D C, Michael J, Griffin B J, (2010), “Evaluating SEM Performance from the Contrast Transfer Function”, Proc. SPIE 7638, 3J1 – 8(429)

Joy, D C, “Protons, Ions, Electrons and the future of the SEM”, J.Phys:Conference Series 241, 012002 (2010)  (see http://iopscience.iop.org/1742-6596/241/1/01002)

Lynch, R.M., Rong, R., Li, B., Shen, T., Honnen, W., Mulenga, J., Allen, S., Pinter, A., Gnanakaran, S., Derdeyn, C. A. (2010) Subtype-specific conservation of isoleucine 309 in the envelope V3 domain is linked to immune evasion in subtype C HIV-1 infection, Virol. 404(1), 59-70.

Masalkar, P., Wallace, I. S., Hwang, J. H., and Roberts, D. M. (2010) “Interaction of cytosolic glutamine synthetase of soybean root nodules with the C-terminal domain of the symbiosome membrane nodulin 26 aquaglyceroporin. J Biol Chem 285, 23880-23888. (Note: this paper was selected for as a featured “paper of the week”)

R. Morra, S. Kuruganti, V. Lam, J. C. Lucchesi and R. Ganguly (2010) Functional analysis of the cis-acting elements responsible for the induction of the Cyp6a8 and Cyp6g1 genes of Drosophila melanogaster by DDT, phenobarbital and caffeine. Insect Molecular Biology 19, 121–130

Moritsugu K, Njunda B, and Smith J. Theory and Normal Mode Analysis of Change in Protein Vibrational Dynamics on Ligand Binding. Journal of Physical Chemistry B, 114(3):1479–1485. (2010)

Norris, A.L., Özen, C., and Serpersu, E.H. (2010) Thermodynamics and Kinetics of Antibiotic Association with the Aminoglycoside Acetyltransferase(3)-IIIb: A Resistance Causing Enzyme. Biochemistry. 49, 4027-4035.

Norris, A.L. and Serpersu, E.H. (2010) Coenzyme A Interactions with the Aminoglycoside Acetyltransferase(3)-IIIb and Thermodynamics of a Ternary System. Biochemistry. 49, 4036-4042.

John Notte IV, Raymond Hill, Sean McVey, Ranjan Ramachandra, Brendan Griffin, David Joy, (2010) Diffraction Imaging in a He+ Ion Beam Scanning Transmission Microscope. Microscopy and Microanalysis 16, 1 – 5

Pelletier D A, Suresh A K, Holton G A,  McKeown C K, Wang W, Gu B, Motensen N P, Allison DP, Joy D C, Allison M R, Brown S D, Phelps T J, and Doctycz M J, (2010), “Effect of Engineered Cerium Oxide Nanoparticles on Bacterial Growth and Viability”, Applied and Environmental Microbiology, 76, 7981-7989

Roberts DMHwang JH and Choi WG (2010) Strategies for adaptation to waterlogging and hypoxia in nitrogen fixing nodules of legumes. in Waterlogging Signalling and Tolerance in Plants. (S. Mancuso and S. Shabala, eds.). Springer-Verlag Berlin Heidelberg, pp. 37-59.

Roy, B., Vaughn, J.N., Kim, B.H.Zhou, F., Gilchrist, M.A., and von Arnim, A.G. (2010). The h subunit of eIF3 controlsreinitiation on mRNAs harboring upstream open reading frames. RNA 16, 748-761.

Saharay M, Guo H, and Smith J. Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS. PLos ONE, 5(10):e12947. (2010)

Seki, S. and P. Mazur. (2010) The temperature and type of intracellular ice formation in preimplantation mouse embryos as a function of the developmental stage. Biology of Reproduction 82, 1198-1205.

Serpersu, E.H., Özen, C., Norris, A.L., Steren, C., and Whittemore, N. (2010) Backbone Resonance Assignments of a Promiscuous Aminoglycoside Antibiotic Resistance Enzyme: the Aminoglycoside Phosphotransferase(3’)-IIIa.Biomol. NMR Assign. 4, 9-12.

Schoborg TALabrador M. (2010) The phylogenetic distribution of non-CTCF protein insulators is limited to insects and reveals that insulator protein BEAF-32 is Drosophila lineage specific. Journal of Molecular evolution. Jan;70(1):74-84. Epub 2009 Dec 19.

Smith DA, Joy DC, and Rack P D, (2010) Monte Carlo Simulation of Helium Ion Beam Induced Deposition, Nanotechnology,21, 175302 (8pp)

Stahle, M.I., Kuehlich, J., Staron, L.A.von Arnim, A.G., and Golz, J.F. (2010). Role of YABBYs and the transcriptional co-repressors LEUNIG and LEUNIG HOMOLOG in maintaining leaf polarity and meristem activity in Arabidopsis. Plant Cell 21: 3105-3118.

Anil  K. Suresh,  Dale  A. Pelletier,  Wei  Wang, J I  Wonmoon  Baohuagu,  Ninnell, P. Mortensen, David  P. Allison,David C Joy, Tommy J. Phelps, and Mitchel J  Doktycz (2010), “Silver Nanocrystallites: Biofabrication using Shewanella oneidensis, and an Evaluation ofTheir Comparative Toxicity on Gram-negative and Gram-positiveBacteria”, Environmental Science and Technology 44, 5210-5215

Tsai, J. H., Yan, R., and McKee, B. D. (2010) Homolog pairing and sister chromatid cohesion in heterochromatin in Drosophila male meiosis I. Chromosoma 120, 335-351.

Ulmschneider M, Doux JP, Killian J, Smith J, and Ulmschneider J. Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides. Journal of the American Chemical Society, 132(10):3452–3460. (2010)

Ulmschneider M, Smith J, and Ulmschneider J. Peptide Partitioning Properties from Direct Insertion Studies. Biophysical Journal, 98(12):L60-L62. (2010)

Wallace HA, Plata MP, Kang HJ, Ross M, Labrador M. (2010) Chromatin insulators specifically associate with different levels of higher order chromatin organization in Drosophila. Chromosoma. Apr;119(2):177-94. Epub 2009 Dec 23.

Wang, W., Howe J Y, Li Y, Qiu X, Joy D C, Paranthaman MP, Doktycz M J, and Gu B,  (2010),”A surfactant and template-free route for synthesizing ceria nanocrystals with tunable morphologies”, J.of Materials Chemistry, 20, 7776-778

Xie, Z., Ulrich, L. E., Zhulin, I. B. and G. Alexandre (2010) PAS domain containing chemoreceptor couples dynamic changes in metabolism with chemotaxis. Proceedings of the National Academy of Sciences USA 107(5), 2235-2240

Xu J, and Smith J. Probing the Mechanism of Cellulosome Attachment to the Clostridium thermocellum Cell Surface: Computer Simulation of the Type II Cohesin-Dockerin Complex and Its Variants. Protein Engineering, Design and Selection, 23(10):759-768. (2010)

Xu, Q., Li, L. and Hong Guo (2010) Understanding the mechanism of deacylation reaction catalyzed by the serine carboxyl peptidase kumamolisin-As: insights from QM/MM free energy simulations, J. Phys. Chem. B., Publication Date (Web): July 26, 2010

Xu, Q., Ye, X., Li, L.-Y, Cheng, Z. M., and Hong Guo (2010) Structural Basis for the Action of Xyloglucan Endotransglycosylases/hydrolases: Insights from Homology Modeling. Interdiscip. Sci., 2010; 2: 133-139.

Yan, R., Thomas, S. E., Tsai, J. H., Yamada, Y., and McKee, B. D. (2010) SOLO: a meiotic protein required for centromere cohesion, coorientation, and SMC1 localization in Drosophila melanogaster. J Cell Biol 188, 335-349.

Yang S, Land M, Klingeman D, Pelletier D, Lu TY, Martin S, Guo HB, Smith J, and Brown S. (2010) A Paradigm for Strain Improvement Identifies Sodium Acetate Tolerance Loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences USA, 107(23):10395-10400.

Zahran M, Daidone I, Smith J, and Imhof P.Mechanism of DNA Recognition by the Restriction Enzyme EcoRV. Journal of Molecular Biology, 401(3):415-432. (2010)

Zhou, F., Roy, B., and von Arnim, A.G. (2010). The translation initiation factor eIF3h cooperates with the large ribosomal subunit in mediating translation reinitiation on mRNAs harboring upstream open reading frames. BMC Plant Biology 10:193.

 

2009

Bahn JH, Lee G, Park JH. 2009. Comparative analysis of Pdf-mediated circadian behaviors between D. melanogasterand D. virilisGenetics 131: 965-975.

Blouse GE, Dupont DM, Schar CR, Jensen JK, Minor KH, Anagli JY, Gårdsvoll H, Ploug M, Peterson CB, Andreasen PA (2009) “Molecular Interactions of Plasminogen Activator Inhibitor-1 with Plasma Vitronectin Involve an Extended Binding Surface and Mutual Conformational Rearrangements.” Biochemistry, 48, 1723-1735.

Cord B, Yang J, Duan H, Joy D C, Klingfus J, Berggren K K, (2009), “Limiting Factors in sub- 10nm scanning electron beam lithography”, J Vac Sci Techol. B 27(6), 2616-2621

Galindo KA, Lu WJ, Park JH, Abrams JM (2009) The Bax/Bak ortholog in Drosophila, Debcl, exerts limited control over programmed cell death, Development 136, 275-283.

Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase. A.Spies, J.G. Reese, D. Dodd, K.L. Pankow, S.R. Blanke, and J. Baudry J. Am. Chem. Soc. (2009) 131 (14): 5274–5284

H-B. Guo, A. Gorin, and H. Guo*, A Peptide-Linkage Deletion Procedure for Estimate of Energetic Contributions of Individual Peptide Groups in a Complex Environment: Application to Parallel ?-Sheets, Interdisciplinary Sciences– Computational Life Sciences, 2009, 1, 12-20.

Hildebrand, M., G. Holton, D. C. Joy, M. J. Doktycz, D. P. Allison (2009) “Diverse and conserved nano-and mesoscale structures of diatom silica revealed by atomic force microscopy” J. Microscopy 2009; 235(2): 172-187

Jain, N.U. (2009) “Use of residual dipolar couplings in structural anlaysis of protein-ligand complexes by solution NMR spectroscopy Micro and Nano technologies in Bioanalysis:Methods in Molecular Biology Vol 544 Humana Press, 231-252

Joy, D C (2009), “Scanning Electron Microscopy: Second Best no more”, Nature Materials 8, (10), 776-777

Kleinhans, F.W. and P. Mazur. 2009. The determination of the water permeability (Lp) of mouse oocytes at –25°C and its activation energy at subzero temperatures. Cryobiology 58: 215-224.

M. KRISHNAN, R. SCHULZ & SMITH JCProtein Dynamical Transition : Role of Methyl Dynamics and Local Diffusion  Theory and Applications of Computational Chemistry 2008. AIP Conference Proceedings    1102    122-131   (2009).

Li JPark Evon Arnim AGNebenführ A (2009) The FAST technique: a simplified Agrobacterium-based transformation method for transient gene expression analysis in seedlings of Arabidopsis and other plant species.Plant Methods 5:6.

McKee, B. D. (2009) Genome Dyn 5, 56-68.”Homolog pairing and segregation in Drosophila meiosis”
Matsumoto, K., Vaughn, V., Bruce, B.D., Koutsopoulos, S & Zhang, S. (2009) Designer Peptide Surfactants Stabilize Functional Photosystem-I Membrane Complex In Aqueous Solution For Extended Time. J. Phys. Chem B. 113:1, 75-83.

Mershin, A., Matsumoto, K., Kaiser, L., Yu, D., Vaughn, M., Nazeeruddin, M., Bruce, B.D., Graetzel, M., and Zhang, S. (2009) Self-Assembled Photosystem-I Photovoltaics On Nanostructured TiO2 And ZnO. Nature Nanotechnology,accepted

Miller, L. D., Russell, M. H. and G. Alexandre (2009) Diversity in bacterial chemotactic responses and niche adaptation. Adv. Appl. Microbiol. 66:53-75

K. MORITSUGU & J.C. SMITH. REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics. Biophysical Journal. 87, 1158-1167 (2009).

K. MORITSUGU and J. C. SMITH, REACH: A Program for Coarse-Grained Biomolecular Simulation, Computer Physics Communications 180, 1188-1195 (2009).

Mou, X., Peterson, C. B., and Prosser, R. A. (2009) “Tissue-type Plasminogen Activator-Plasmin-BDNF Modulate of Glutamate-Induced Phase-Sifts of the Mouse Suprachiasmatic Circadian Clock in Vitro.” Eur. J. Neurosciencein press.

Mulder, C.L., Theogarajan, L., Currie, M., Mapel, J.K., Vaughn M., Willard, P., Moss, M.W., C.E. McLain, C.E, Morseman, J.P., Bruce, B.D., M.A. Baldo (2009) Luminescent Solar Concentrators Employing Phycobilisomes. Adv. Mat., 21:31, 3181-3185.

Norris, A. D. and Serpersu, E. H. (2009) NMR Detected Hydrogen-Deuterium Exchange Reveals Differential Dynamics of Antibiotic and Nucleotide Bound Aminoglycoside Phosphotransferase 3?-IIIa. J. Am. Chem. Soc.131,8487-8594.

Jerry M. Parks, Hong Guo, Cory Momany, Liyuan Liang, Susan M. Miller, Peckys DB, Veith GM, Joy DC,and de Jonge N, (2009), “Nanoscale Imaging of Whole Cells using a Liquid Enclosure and a STEM”, PLoS ONE 4(12) 1-7

L. PETRIDIS & J.C. SMITH. A molecular mechanics force field for lignin. Journal of Computational Chemistry. 30(3):457-67 (2009)

P. PHATAK, J.S. FRAEMCKE, M. WANKO, M. HOFFMANN, P. STRODEL, J.C. SMITH, S. SUHAI, A.-N. BONDAR & M. ELSTNER. Long-Distance Proton Transfer with a Break in the Bacteriorhodopsin Active Site. Journal of the American Chemical Society. 131 (20),  7064–7078 (2009).

Plata MP, Kang HJ, Zhang S, Kuruganti S, Hsu SJLabrador M. 2009. Changes in chromatin structure correlate with transcriptional activity of nucleolar rDNA in polytene chromosomes. Chromosoma. 118(3):303-22. Epub 2008 Dec 9

Prabakaran N, Onami T, Rajagopalan S, Donnell R, Venkatachalam S (2009).  Role of Chromodomain Helicase DNA binding protein 2 in DNA damage response signaling and tumorigenesis. Oncogene 28:1053-1062.

Prosser, R.A., and Glass, J.D. (2009) The mammalian circadian clock exhibits acute tolerance to ethanol. Alcohol.Clin.Expt.Res.

Prosser, R.A., McElroy, B., Zakaria, A., and Glass, J.D. (2009) Ethanol modulates mammalian circadian clock phase resetting through extrasynaptic GABA receptor activation. Neuroscience

Putcha, B.-D. K. and Elias Fernandez. Direct inter-domain interactions can mediate allosterism in the thyroid receptor. J. Biol. Chem. (2009) 21;284(34):22517-24.

Reddick LE and Bruce BD. Creation of Novel GTPase Assay Using 32P-GTP. MP Biomedical Bioconcepts February.

Ruby, C.L., Brager, A.J., DePaul, M.A. Prosser, R.A., and Glass, J.D. (2009) Chronic ethanol disrupts circadian behavior and photic phase-resetting in the hamster. Am.J.Physiol. 297: R729-R737

Ruby CL, Prosser RA, Glass JD (2009) Acute Ethanol Impairs Photic and Nonphotic Circadian Phase-Resetting in the Syrian Hamster. Am.J.Physiol 296: R411-R418.

R. SCHULZ, M. KRISHNAN, I. DAIDONE and J.C. SMITH Instantaneous Normal Modes and the Protein Glass Transition. Biophysical Journal.  96(2):476-84 (2009)

Seki, S., F.W. Kleinhans, and P. Mazur 2009. Intracellular ice formation in yeast cells vs. cooling rate: Predictions from modeling vs, experimental observations by differential scanning calorimetry. Cryobiology 58: 157-165.

Seki, S. and P. Mazur. 2009 The dominance of warming rate over cooling rate in the survival of mouse oocytes subjected to a vitrification procedure, Cryobiology 59: 75-82

A.J. Shakesby, I.S. Wallace, H.V. Issacs, J. Pritchard, D.M. Roberts, and A.E. Douglas (2009)  A Water-Specific Aquaporin Involved in Aphid Osmoregulation, Insect Biochemistry and Molecular Biology 39, 1-10

Shen, T., Langan, P., French, A., Johnson, G.P., & Gnanakaran, S. (2009) Conformational flexibility of soluble cellulose oligomers: Chain length and temperature dependence, J. Am. Chem. Soc. 131(41), 14786-14794.

T. SPLETTSTOESSER, F. NOE, T. ODA & J.C. SMITH. Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state. Proteins: Structure, Function and Dynamics. 180, 1188-1195 (2009).

Anne O. Summers, and Jeremy C. Smith (2009) Mechanism of Hg-C Protonolysis in the Organomercurial Lyase MerB, J. Am. Chem. Soc., 131, 13278-13285.

Thomas, S. E., and McKee, B. D. (2009) Methods Mol Biol 558, 217-234. “Analysis of chromosome dynamics and chromosomal proteins in Drosophila spermatocytes”

Wasim, M., Bible, A. N., Xie, Z. and G. Alexandre. (2009) Alkyl hydroperoxide reductase has a role in oxidative stress resistance and in modulating changes in cell-surface properties in Azospirillum brasilense Sp245.Microbiology155:1192-1202

Wu, Lingzhi and Serpersu, E. H. (2009) Deciphering Interactions of the Aminoglycoside Phosphotransferase(3?)-IIIa with its Ligands. Biopolymers 91,801-809.

Qin XuYu-Zhuo Chu, Hao-Bo Guo, Jeremy C. Smith, and Hong Guo (2009) Energy triplets for writing epigenetic marks: insights from QM/MM free-energy simulations of protein lysine methyltransferases. Chem-Eur. J., 15, 12596-12599.

J. XU., M. CROWLEY & J.C. SMITH Building a Foundation for Structure-Based Cellulosome Design for Cellulosic Ethanol: Insight into Cohesin-Dockerin Complexation from Computer Simulation. Protein Science. 18(5):949-959 (2009).

Yahashiri, A., Nimrod, G., Ben-Tal, N., Howell, E.E. and Kohen, A, (2009) “Effect of electrostatic shielding on H-tunneling in R67 dihydrofolate reductase,” ChemBioChem.10, 2620-2623.

 

2008

Albright S, Chen B, Holbrook KJain NU. (2008) Solution NMR studies provide structural basis for endotoxin pattern recognition by the innate immune receptor CD14Biochem Biophys Res Commun. 368:231-7.

Alexandre, G. (2008) A sense of self-worth: energy taxis provides insight into how Helicobacter pylori navigates through its environment, J Bacteriol 190, 3095-3097

Becker V, Sengupta D, Ketteler R, Ullmann GM, Smith JC, Klingmuller U. (2008) Packing density of the erythropoietin receptor transmembrane domain correlates with amplification of biological responses. Biochemistry,47(45), 11771-11782.

Bhaskara S, Chandrasekharan MBGanguly R. 2008. Caffeine induction of Cyp6a2 and Cyp6a8 genes of Drosophila melanogaster is modulated by cAMP and D-JUN protein levelsGene 415: 49-59.

Bible AN, Stephens BB, Ortega DR, Xie Z, Alexandre G. (2008) Function of a chemotaxis-like signal transduction pathway in modulating motility, cell clumping and cell length in the alpha-proteobacterium Azospirillum brasilenseJ Bacteriol. Jul 18.

Binder BM (2008) Invited review- The Ethylene Receptors: Complex perception for a simple gas. Plant Science. 175: 8-17.

Bondair AN, Baudry J, Suhai S, Fischer S, Smith JC. (2008) Key role of water molecules in bacteriorhodopsin proton transfer reactions.  Journal of Physical Chemistry B 112(47):14729-41

Chen Y.J., Johnson M.A., Lieberman, M.D., Goodchild, R.E., Schobel, S., Lewandowski, N. Rosoklija, G., Liu, R.C., Gingrich, J.A., Small, S., Moore, H., Dwork, A.J., Talmage, D.A., Role, L.W. Type III neuregulin-1 is required for normal sensorimotor gating, memory-related behaviors, and corticostriatal circuit components. J Neuroscience 2008 Jul 2;28(27):6872-83.

Choi SH, Lee G, Monahan P, and Park JH. (2008) Spatial regulation of Corazonin neuropeptide expression requires multiple cis-acting elements in Drosophila melanogaster, J Comp Neurol 507, 1184-1195.

Chopra S, Dooling RM, Horner CG, Howell EE. (2008) A balancing act between net uptake of water during dihydrofolate binding and net release of water upon NADPH binding in R67 dihydrofolate reductase. J Biol Chem283:4690-8.

Feng J, Goswami SHowell EE. 2008. R67, the other dihydrofolate reductase: rational design of an alternate active site configurationBiochemistry 47:555-65.

Frymier, P.D., Counce, R.M. and Bruce, B. D. (2008) Photosynthetic Biohydrogen: A Case Study Integrating Sustainability into the Student Design Experience. Proceedings of Annual AIChE Meeting Philadelphia, PA

Gaysinsky, S., Taylor T.M., Davidson, P.M., Bruce, B.D., and Weiss, J. (2008) Antimicrobial efficacy of eugenol microemulsions in milk against Listeria monocytogenes and Escherichia coli O157:H7 J. Food Prot. 71:6: 1256-1261.

Griffin B J, and Joy D C, (2008), ‘Variation of Rutherford Backscattered Ion and Ion-Induced SE yield with atomic number in the ORION Scanning Helium Ion Microscope’, Microscopy and Microanalysis 14, 1190-2

Iwuchukwu, I.J., Myers, M., Vaughn, M., O’Neill, H., Frymier, P.D., and Bruce, B. D. (2008) Thermotolerant Photodependent Hydrogen Production by Platinized Photosystem I Reaction Centers and Recombinant Cytochrome c553 from Thermosynechococcus elongatusProceedings of Annual AIChE Meeting, Philadelphia, PA.

Joy D C, (2008), ‘What do we know about fundamental parameters for microanalysis?’, Microscopy and Microanalysis 14, 1080-2

Kim, B.H., and von Arnim, A.G. (2008). FIERY1 regulates light-mediated repression of cell elongation and flowering time via its 3’(2’),5’-bisphosphate nucleotidase activity. Plant Journal 58:208-19.

Klein KL, Melechko A V, McKnight T E, Retterer ST, Rack R D, Fowlkes J D, Joy DC and Simpson ML, (2008), ‘Surface Characterization and functionalization of carbon nanofibers’, J.Appl.Phys., 103 (6), 061301

Kulkarni S, Nagarajan P, Wall J, Donovan D, Donnell R, Ligon A, Venkatachalam S**, Quade BJ** (2008) Disruption of chromodomain helicase DNA binding protein 2 (CHD2) causes scoliosis **Corresponding authors.  Am.J. Med.Genet.A. 146(9):1117-27.

Kurkal-Siebert V, Agarwal R, Smith JC. (2008) Hydration-dependent dynamical transition in protein:protein interactions at ~240K. Physical Review Letters. 100(13), 13810.

Krishnan M, Kurkal-Siebert V, Smith JC. (2008) Methyl Group Dynamics and the Onset of Anharmonicity in Myoglobin. Journal of Physical Chemistry B. 112(17):5522-33.

Labrador M, Sha K, Li A, Corces VG. (2008) Insulator and Ovo proteins determine the frequency and specificity of insertion of the gypsy retrotransposon in Drosophila melanogaster, Genetics 180, 1367-1378.

Lee G, Kim KM, Kikuno K, Wang Z, Choi YJPark JH. (2008) Developmental regulation and functions of the expression of the neuropeptide corazonin in Drosophila melanogaster, Cell Tissue Res 331, 659-673.

Li JF and Nebenführ, A. (2008) Interdependence of dimerization and organelle binding in myosin XI. Plant J. 55, 478-490.

Li JF and Nebenführ A. (2008) The tail that wags the dog: the globular tail domain defines the function of myosin V/XITraffic 9, 290-298.

Matsumoto, K., Koutsopoulos, S., Vaughn, M., Bruce, B.D., and Zhang, S. (2009) Designer lipid-like peptides stabilize functional Photosystem-I membrane complex in aqueous solution. Accepted J. Phys. Chem. B 113:1, 75-83

Mazur, P., S.P. Leibo, G.E. Seidel. 2008  Cryopreservation of the germplasm of animals used in biological and medical research: Importance, impact, status, and future directions. Biology of Reproduction 78: 2-12.

Mazur, P. and  F.W. Kleinhans 2008. Relationship between intracellular ice formation in oocytes of the mouse andXenopus and the physical state of the external medium–a revisit. Cryobiology 56: 22-27.

McKee BD (2008) Does cohesin regulate developmental gene expression in Drosophila?, Proc Natl Acad Sci U S A105, 12097-12098.

McLain SE, Soper AK, Daidone I, Smith JC, Watts A. (2008) Charge based interactions between peptides observed as the dominant force for association in aqueous solution. Angewandte Chemie Intl. Ed. 47, 9059-9062.

Meinhold L, Clement D, Tehei M, Daniel R, Finney JL, Smith JC. (2008) Protein dynamics and stability: The distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering. Biophysical Journal. 94(12), 4812-4818.

Moritsugu K and Smith JC. (2008) REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes. Biophysical Journal. 95(4), 1639-1648.

Neusius T, Daidone I, Sokolov IM, Smith JC. (2008) Subdiffusion in peptides originates from fractal-like structure of configuration space. Physical Review Letters. 100(18), 188103.

Noe F, Daidone I,Smith JC, Di Nola A, Amadei A. (2008) Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi Gaussian Entropy Theory and Molecular Dynamics Simulation. Journal of Physical Chemistry B.  112(35)   11155-11163.

Normand P and Mullin BC. (2008) Prospects for the study of the ubiquitous actinomycete, Frankia, and its host plants. In. Nitrogen Fixation Research: Origins and Progress. Volume VI. Actinorhizal Symbiosis. eds. Newton and Pawlowski.

Nutt DR and Smith JC. (2008) Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations. Journal of the American Chemical Society. 130(39), 13066-13073.

Ozen CNorris AL, Land ML, Tjioe ESerpersu EH. (2008) Detection of specific solvent rearrangement regions of an enzyme: NMR and ITC studies with aminoglycoside phosphotransferase(3′)-IIIaBiochemistry 47:40-9.

Park D, Veenstra JA, Park JH, Taghert PH. (2008) Mapping peptidergic cells in Drosophila: where DIMM fits in, PLoS ONE 3, e1896.

Petridis L and Smith JC. (2008) Cellulosic ethanol: progress towards a simulation model of lignocellulosic biomassJournal of Physics Conference Series 125 012055.

Plata MP, Kang HJ, Zhang S, Kuruganti S, Hsu SJLabrador M. (2008) Changes in chromatin structure correlate with transcriptional activity of nucleolar rDNA in polytene chromosomes, Chromosoma

Prosser RA, and Glass JD. (2008) Acute ethanol modulates glutamatergic and serotonergic phase shifts of the mouse circadian clock in vitro. Neuroscience 152, 837-48.

Reddick LE, Chotewutmontri P, Crenshaw W, Dave A, Vaughn M, Bruce BD. (2009) Nano-scale Characterization of the Dynamics of the Chloroplast Toc Translocon. Methods in Cell Biology 2008, 90(16), 361-393.

Rosenfeldt G, Viana RM, von Arnim AG, Mootz M, Batschauer, A. (2008). Chemically induced and light-independent cryptochrome photoreceptor activation. Mol. Plant 1, 4-14. (epub June 7 2007. doi:10.1093/mp/ssm002)

Schar CR, Blouse GE, Minor KHPeterson CB. (2008) A deletion mutant of vitronectin lacking the somatomedin B domain exhibits residual plasminogen activator inhibitor-1-binding activityJ Biol Chem 283, 10297-10309.

Schar CR, Jensen JK, Christensen A, Blouse GE, Andreasen PA, Peterson CB. (2008) Characterization of a site on PAI-1 that binds to vitronectin outside the somatomedin B domain. J Biol Chem. 283, 28487-28496.

Seki, S. and P. Mazur. 2008. Kinetics and activation energy of recrystallization of intracellular ice in mouse oocytes subjected to interrupted rapid cooling. Cryobiology 56: 171-180.

Seki, S. and P. Mazur. 2008. Effect of warming rate on the survival of vitrified mouse oocytes and on the recrystallization of intracellular ice. Biology of Reproduction. 79: 727-737.

Sengupta D, Smith JC, Ullmann M. (2008) Partitioning of Amino-acid Analogues in a Five-slab Membrane ModelBiochimica et Biophysica Acta – Biomembranes. 1778(10), 2234-2243.

Serpersu EHOzen CWright E. (2008) Studies of enzymes that cause resistance to aminoglycosides antibiotics,Methods Mol Med 142, 261-271.

Tanaka M, Wallace IS, Takano J, Roberts DM, Fujiwara T. (2008) NIP6;1 is a boric acid channel for preferential transport of boron to growing shoot tissues in Arabidopsis, Plant Cell 20, 2860-2875.

Tanaka M, Wallace IS, Takano J, Roberts DM, Fujiwara T. (2008) NIP6;1 is a boric acid channel for preferential transport of boron to growing shoot tissues in Arabidopsis, Plant Cell 20, 2860-2875.

Voltz K, Trylska J, TozziniV. Kurkal-Siebert V, Smith JC, Langowski J. (2008) Coarse-Grained Force field for the Nucleosome from Self-Consistent Multiscaling. Journal of Computational Chemistry.  29(9), 1429-39.

Woo JC and von Arnim AG. (2008). Mutational optimization of the coelenterazine-dependent luciferase from Renilla.Plant Methods 4, 23.

Woo JC, Howell MH, von Arnim AG. 2008. Structure-function studies on the active site of the coelenterazine-dependent luciferase from RenillaProtein Sci. 17, 725-35.

Yahalom A, Kim TH, Roy R, Zinger R, von Arnim AG, Chamovitz DA (2008). Arabidopsis eIF3e is regulated by the COP9 signalosome and impacts development and protein translation.  Plant Journal 53, 300-311.

Yahashiri A, Howell EE, Kohen A. (2008) Tuning of the H-Transfer Coordinate in  Primitive versus Well-Evolved Enzymes. ChemPhysChem 9, 980-982.

Zhang W, Pochapsky SS, Pochapsky TC, Jain NU. (2008) Solution NMR structure of putidaredoxin-cytochrome P450cam complex via a combined residual dipolar coupling-spin labeling approach suggests a role for Trp106 of putidaredoxin in complex formation. J Mol Biol. 384(2), 349-63.

 

2007

Banerjee P, Nayar S, Hebbar S, Fox CF, Jacobs MC, Park JH, Fernandes JJ, Dockendorff TC. 2007.  Substitution of critical isoleucines in the KH domains of Drosophila fragile X protein result in partial loss-of-function phenotypes.Genetics 175: 1241-1250.

Bondar AN, Suhai S, Fischer S, Smith JC, Elstner M. (2007) Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements. Journal of Structural Biology 157 (3), 454-69.

Bolorizadeh M and Joy D C, (2007), “Effect of fast secondary electrons on low voltage electron beam lithography’, J. Micro. Nanolith. 6, 1-7

Choi Y R, Rack P D, Frost B, and Joy D C, (2007), ‘Effect of electron-beam induced deposition and etching under bias’, SCANNING 29, 171-17

Choi WGRoberts DM. (2007) Arabidopsis NIP2;1: A major intrinsic protein transporter of lactic acid induced by anoxic stress. J Biol Chem epub Jun 21.

Cournia Z, Ullmann GM, Smith JC. (2007) Differential Effects of Cholesterol, Ergosterol and Lanosterol on a Dipalmitoyl Phosphatidylcholine (DPPC) membrane: A Molecular Dynamics Simulations Study. Journal of Physical Chemistry B 111(7), 1786-1801.

Daidone I, Ulmschneider M, Di Nola A, Amadei A, Smith JC. (2007) Dehydration-Driven Solvent Exposure of Hydrophobic Surfaces as a Driving Force in Peptide Folding. Proceedings of the National Academy of Sciences (U.S.A.) 104(39), 15230-15235.

De Hatten X, Cournia Z, Huc I, Smith JC, Metzler-Nolte N. (2007) Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics. Chemistry 13(29), 8139-8152.

Guo HB and H. Guo (2007) Mechanism of Histone Methylation Catalyzed by Protein Lysine Methyltransferase SET7/9 and Origin of Product Specificity, Proc Natl Acad Sci  USA, 104, 8797-8802.

Jackson MR, Beahm R, Duvvuru S, Narasimhan C, Wu J, Wang HN, Philip VM, Hinde RJ, Howell EE. (2007) A preference for edgewise interactions between aromatic rings and carboxylate anions: the biological relevance of anion-quadrupole interactions. J Phys Chem B 111, 8242-9.

Joy D C, Meyer H M, Bolorizadeh M, Lin Y, and Newbury D E, (2007), ‘On the production of X-rays by low energy ion beams’, Scanning 29, 1-5

Joy D C, (2007), joint chapter in “Scanning Electron Microscopy for Nanotechnology”, ed Z L Wang, (Springer:NY), ISBN 0387333258

Joy D C, Deo S, and Griffin B J, (2007), in ‘Length calibration standards for Nanomanufacturing, in Instrumentation, Metrology and Standards for Nanomanufacturing’, eds. M T Postek, and J Allgair, Proc. of SPIE 6648, 664807 1-7

Kim J, Joy D C, Lee S-Y, (2007), ‘Controlling Resist Thickness and Etch Depth for Fabrication of 3-D structures in electron beam grayscale lithography’, Microelectronic Engineering 84(12), 2859-2864

Kim BH, Cai XVaughn JNvon Arnim AG. (2007) On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation. Genome Biol 8, R60.

Koppole S, Smith JC, Fischer S. (2007) The structural coupling between ATPase activation and recovery stroke in the myosin II motor. Structure 15 (7), 825-837.

Kuruganti S, Lam V, Zhou X, Bennett G, Pittendrigh BR, Ganguly R. (2007) High expression of Cyp6g1, a cytochrome P450 gene, does not necessarily confer DDT resistance in Drosophila melanogaster. Gene 388, 43-53.

Li JF, Nebenführ A. (2007) Organelle targeting of myosin XI is mediated by two globular tail subdomains with separate cargo binding sites. J Biol Chem. 282, 20593-602.

Meinhold L, Merzel F, Smith JC. (2007) Lattice dynamics of a protein crystal. Physical Review Letters 99(13), 138101.

Meinhold L and Smith JC. (2007) Protein Dynamics from X-ray Crystallography: Anisotropic, Global motion in Diffuse Scattering Patterns. ProteinsStructure, Function and Bioinformatics 66 (4), 941-953.

Meinhold L, Smith JC., Kitao A, Zewail AH. (2007) Picosecond Fluctuating Protein Energy Landscape Mapped by Pressure-Temperature Molecular Dynamics Simulation. Proceedings of the National Academy of Sciences (U.S.A.)104(44),17261-17265.

Mesentean S, Koppole S, Smith JC, Fischer S. (2007) The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor. Journal of Molecular Biology 367 (2), 591-602.

Miller, L. D., C. K. Yost, F. Hynes and G. Alexandre (2007) The major chemotaxis gene cluster of Rhizobium leguminosarum bv. viciae is essential for competitive nodulation. Molecular Microbiology 63(2):348-362

Moritsugu K and Smith JC. (2007) Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian. Biophysical Journal 93(10), 3460-3469.

Nelson BKCai XNebenführ A. (2007) A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. Plant J epub Jul 30.

Ngo VV, Hernandez M, Roth W, and Joy DC, (2007), ‘STEM imaging of Lattice Fringes in a UHR in-lens field emission SEM’, Microscopy Today 15. 12-16

Noe F, Horenko , Schutte C, Smith JC. (2007) Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states The Journal of Chemical Physics 126 (15), 155102.

Noe F and Smith JC. (2007) Transition Networks: A Unifying Theme for Molecular Simulation and Computer Science. In: Mathematical Modeling of Biological Systems, Volume I. A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.P. Herzel (eds). Birkhäuser, Boston, 125-144.

Nutt DR and Smith JC. (2007) Choosing an Appropriate Water Model for Use in Biomolecular Simulations. In“Physics and Chemistry of Ice”, RSC Publishing, 451-458.

Nutt DR and Smith JC. (2007) Molecular dynamics simulations of proteins: can the explicit water model be varied?Journal of Chemical Theory and Computation 3(4), 1550-1560.

Reddick LE, Vaughn MD, Wright SJCampbell IMBruce BD. (2007) In vitro comparative kinetic analysis of the chloroplast toc GTPases. J Biol Chem 282, 11410-26.

Soltani-Bejnood M, Thomas SE, Villeneuve L, Schwarz KT, Hong CS, McKee BD. (2007) Role of the mod(mdg4)common region in homolog segregation in Drosophila male meiosis. Genetics 176, 161-180.

Sutton M A, Li N, Joy D C, Reynolds A P, Li X, (2007), “SEM for quantitative and large deformation measurements Part 1: SEM imaging at magnifications from 200 to 10,000”,Experimental Mechanics 47, 775-787

Thomas SEMcKee BD. (2007) Meiotic pairing and disjunction of mini-X chromosomes in Drosophila is mediated by 240bp rDNA repeats and the homolog conjunction proteins SNM and MNM. Genetics epub Jul 29.

Topham C and Smith JC. (2007) Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form. Biophysical Journal 92(3), 769-86.

Wright E, Vincent J, Fernandez EJ. (2007) Thermodynamic characterization of the interaction between CAR-RXR and SRC-1 peptide by isothermal titration calorimetry. Biochemistry 46, 862-70.

Xu QGuo HB, Wlodawer A, Nakayama Y, and Guo H. (2007) The QM/MM molecular dynamics and free energy simulations of the acylation process catalyzed by the serine carboxyl peptidase kumamolisin-As, Biochemistry, 46, 3784-3792.

Q. XuH-B Guo, A. Gorin, and H. Guo (2007) Stabilization of a Transition-State Analogue at the Active Site of Yeast Cytosine Deaminase: Importance of Proton Transfers, J. Phys. Chem. B, 111, 6501-6506.

 

2006

Babin S, Gaevski M, Joy D C, Machin M, and Martynov A, (2006), “Technique to automatically measure electron beam diameter and astigmatism”, J.Vac.Sci.Technol. B24, 2956-2959

Badger, J.H., T. R. Hoover, Y. V. Brun, R. M. Weiner, M. T. Laub, G. Alexandre, J. Mrázek, Q. Ren, I. T. Paulsen, K. E. Nelson, H. M. Khouri, D. Radune, J. Sosa, R. J. Dodson, S. A. Sullivan, M. J. Rosovitz, R. Madupu, L. M. Brinkac, A. S. Durkin, S. C. Daugherty, S. P. Kothari, M. G. Giglio, L. Zhou, D. H. Haft, J. D. Selengut, T. M. Davidsen, Q. Yang, N. Zafar, and N. L. Ward (2006) Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentusJournal of Bacteriology 188: 6841-6850

Bennett B, Langan P, Coates L, Mustyakimov M, Schoenborn B, Howell EEDealwis C (2006). Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate. Proc Natl Acad Sci USA 103, 18493-18498.

Bhaskara S, Dean ED, Lam V, Ganguly R. (2006) Induction of two cytochrome P450 genes, Cyp6a2 and Cyp6a8, of Drosophila melanogaster by caffeine in adult flies and in cell culture. Gene 377, 56-64.

Binder BM, O’Malley RC, Wang W, Zutz TC, Bleecker AB. (2006) Ethylene Stimulates Nutations that are Dependent on the ETR1 Receptor. Plant Physiology 142: 1690-1700. [Article]

Choi Y R, Rack P D, Randolph S J, Smith D A, and Joy D C, (2006), “Pressure effect of Growing with EBID with WF6 and TEOH precursors”, SCANNING 28 311-318

Choi YJLee GPark JH. 2006. Programmed cell death mechanisms of identifiable peptidergic neurons in Drosophila melanogaster. Development 133:2223-2232.

Chopra S, Lynch R, Kim SH, Jackson MHowell EE. 2006. Effects of temperature and viscosity on R67 dihydrofolate reductase catalysis. Biochemistry 45, 6596-6605.

J.F. GuentherS. Seki, F.W. Kleinhans, K. Edashige, D.M. Roberts and P. Mazur (2006) Extra- and intracellular ice formation in stage I and II Xenopus laevis oocytes. Cryobiology 52, 401-16.

Guo HB, Wlodawer A, Nakayama T, Xu Q, and Guo H 2006. On the Catalytic role of Proton Transfers in The Formation of Tetrahedral Adduct in a Serine Carboxyl Peptidase, Biochemistry, 45:9129-9137.

H. Guo and N. Rao, (2006) Chorismate Mutase Catalyzed Claisen Rearrangement, in The Claisen Rearrangement, Nubbemeyer and Hiersemann (Eds.), Wiley-VCH, 1-21.

H. Guo and H-B Guo (2006) Biological Basics for Protein Structures, in Computational Methods for Protein Structure Prediction and Modeling, Ying Xu, Dong Xu and Jie Liang, Eds), Springer, 229-239.

Joy DC and Joy C S, (2006), “Scanning electron microscope imaging in liquids”, J. of Microscopy, 221, 84-89

Joy DC, (2006), “Low voltage scanning electron microscopy – current status, present problems, and future solutions”, e- J.Surf.Sci.Nanotech. 4, 1-7

Joy D C, and Vladar A, (2005), “The future of the critical dimension scanning electron microscope”, ISMI Confidential Document, SEMATECH Technology Transfer ID #05124722A-ENG

Kim J, Jalhadi K, Deo S, Lee S-Y, and Joy DC, (2006), “Tools to measure CD-SEM performance”, in Metrology, Inspection and Process Control for MicroLithography XX, ed. Chas. N. Archie, Proc. of SPIE 6152, OT1 – OT9

Kim, BH and von Arnim AG 2006. The early dark-response in Arabidopsis thaliana revealed by cDNA microarray analysis. Plant Molecular Biology 60, 321-342.

F.W. Kleinhans, J.F. GuentherD.M. Roberts and P. Mazur (2006) Analysis of intracellular ice nucleation inXenopus oocytes by differential scanning calorimetry. Cryobiology 52, 128- 38.

Lee G, Bahn JH, Park JH. 2006. Sex- and clock-controlled expression of the neuropeptide F gene in Drosophila.Proc Natl Acad Sci USA 103, 12580-12585.

Li W, and Joy D C, (2006), “Study of temperature influence on electron beam induced deposition”, J.Vac.Sci.Tech.A24, 431-436

Ozen C, Malek JM, Serpersu EH. 2006. Dissection of aminoglycoside-enzyme interactions: a calorimetric and NMR study of neomycin B binding to the aminoglycoside phosphotransferase(3′)-IIIa. J Am Chem Soc. 128, 15248-15254.

Prosser RA, Lee HM, Wehner A 2006. Serotonergic pre-treatments block in vitro serotonergic phase shifts of the mouse suprachiasmatic nucleus circadian clock. Neuroscience 142, 547-555.

Serpersu, E., H., Özen, C., and Wright, E. (2006) Thermodynamic Studies of Aminoglycoside Antibiotic-Enzyme Interactions. Turkish J. Biochem. 31, 79-85.

Stephens BB, Loar SN, Alexandre G. 2006. Role of CheB and CheR in the complex chemotactic and aerotactic pathway of Azospirillum brasilense. J Bacteriol. 188, 4759-4768.

Su, S., B. B. Stephens, G. Alexandre and S. K. Farrand (2006) Lon protease of the alpha-proteobacteriumAgrobacterium tumefaciens is required for normal growth, cellular morphology and full virulence. Microbiology 152: 1197-1207

Subramanian C, Woo JC, Cai X, Xu X, Servick S, Johnson CH, Nebenführ A, and von Arnim AG 2006. A suite of tools and application notes for in vivo protein interaction assays using Bioluminescence Resonance Energy Transfer (BRET). Plant Journal 48, 138-152.

Vladar A E, Radi Z, Postek M T, and Joy D C, (2006), “Nanotip electron gun for the Scanning Electron Microscope”, SCANNING 28, 133-141

von Arnim AG, Schwechheimer C 2006. Meeting Report: Life is degrading–thanks to some zomes. Mol Cell 23, 621-629.

I.S. Wallace, W.G. Choi, and D.M. Roberts (2006) The Structure, Function and Regulation of the Nodulin 26-like Intrinsic Protein Family of Plant Aquaglyceroporins, Biochim. Biophy. Acta Biomembranes, 1758, 1165-75.

Wang W, Esch JE, Shiu S-H, Agula H., Binder BM, Chang C, Patterson SE, Bleecker AB. (2006) Identification of Important Regions for Ethylene Binding and Signaling in the Transmembrane Domain of the ETR1 Ethylene Receptor of Arabidopsis The Plant Cell 18: 3429-03442. [Article]

Wells O C, and Joy D C, (2006), “The early history and future of the SEM”, Surface and Interface Analysis 38:1738-1742

Wright, E. and Serpersu, E. H. (2006) Molecular Determinants of Affinity for Aminoglycoside Binding to the Aminoglycoside Nucleotidyltransferase(2?)-Ia. Biochemistry 45, 10243-10250.

Xu H, Faber C, Uchiki T, Fairman JW, Racca J, Dealwis C 2006. Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation. Proc Natl Acad Sci USA 103, 4022-4027.

Xu Q, Guo HB, Wlodawer A, and Guo H 2006. The Importance of Dynamics in Substrate-Assisted Catalysis and Specificity, J Am Chem Soc 128, 5994-5995.

2005

Balbo A, Minor KH, Velikovsky CA, Mariuzza RA, Peterson CB, Schuck P (2005)  Studying Multi-Protein Complexes by Multi-Signal Sedimentation Velocity Analytical Ultracentrifugation. Proc Natl Acad Sci USA 102, 81-86.

Bishop M, and Joy D C, (2005), “Feasibility Study for High-Energy Based Reference Measurement System for Litho Metrology”, in Characterization and Metrology for ULSI Technology 2005, ed D G Seiler, A C Diebold, R McDonald, C R Ayre, R P Khosla, S Zollner and E M Secula, (American Institute of Physics:Mellville, NY), 407 – 410

Choi YJ, Lee G, Hall JC, Park JH. 2005. Comparative analysis of Corazonin-encoding genes (Crz‘s) in Drosophilaspecies and functional insight into Corazonin-expressing neurons. J. Comp. Neurol. 482: 372-385

Guo H, Rao N, Xu QGuo H (2005).  Origin of Tight Binding of a Near-perfect Transition State Analog by Cytidine Deaminase: Implications for Enzyme Catalysis.  J Am Chem Soc 127, 3191-.

H-B. Guo, A. Wlodawer and H. Guo (2005) A General Acid-Base Mechanism for the Stabilization of a Tetrahedral Adduct in a Serine-Carboxyl Peptidase: A Computational Study, J. Am. Chem. Soc., 127, 15662-15663.

Gentry A and Venkatachalam S. (2005) Complicating the role of p53 in aging. Aging Cell 4, 157-160.

Jackson M, Chopra S, Smiley RD, Maynord PO, Rosowsky A, London RE, Levy L, Kalman TI, Howell EE. (2005). Calorimetric studies of ligand binding in R67 dihydrofolate reductase. Biochemistry 44, 12420-33.

Johnson EC, Shafer OT, Trigg JS, Schooley DA, Dow JA, Park JH, Taghert PT. 2005. A novel diuretic hormone receptor in Drosophila: Evidence for conservation of CGRP signaling. J. Exp. Biol. 208: 1239-1246

Joy D C, (2005), “Electron time of transit spectroscopy for analysis and imaging”, Microsc. and Microanalysis 11(suppl 2), 190-1

Joy D C, (2005), “The Aberration Corrected SEM”, in Characterization and Metrology for ULSI Technology 2005, ed D G Seiler, A C Diebold, R McDonald, C R Ayre, R P Khosla, SZollner and E M Secula, (American Institute of Physics:Mellville, NY), 535 – 542

Lin Y and Joy D.C, (2005), “A new examination of secondary electron yield data”, Surface and Interface Analysis,37, 895-900

Minor KH, Schar CR, Blouse GE, Shore JD, Lawrence DA, Schuck P, Peterson CB (2005). A Mechanism for Assembly of Complexes of Vitronectin and Plasminogen Activator Inhibitor-1 from Sedimentation Velocity Analysis. J Biol Chem 280, 28711-28720.

Tang X and Joy DC, (2005), “An experimental model of Beam Broadening in the VPSEM”, Scanning 27, 293-298

Thomas SE, Soltani-Bejnood M, Roth P, Dorn R, Logsdon JM, McKee BD. (2005) Identification of two proteins required for conjunction and accurate segregation of achiasmate homologs in Drosophila male meiosis.  Cell 123, 555-568.

Tournier AL, Reat V, Dunn R, Daniel R, Smith JC, Finney J. (2005) Temperature and timescale dependence of protein dynamics in methanol:water mixtures. Physical Chemistry Chemical Physics 71388–1393.

Vincill ED, Szczyglowski K, Roberts DM. (2005) GmN70 and LjN70: Anion transporters of the symbiosome membrane of nodules with a transport preference for nitrate.  Plant Physiol 137, 1435-44.

Wallace ISRoberts DM. (2005) Distinct transport selectivity of two structural subclasses of the Nodulin-like Intrinsic Protein family of plant aquaglyceroporin channels. Biochemistry 44, 16826-34.

Yoo S, McKee BD (2005) Functional analysis of the Drosophila Rad51 gene (spn-A) in repair of DNA damage and meiotic chromosome segregation. DNA Repair 4: 231-242.

 

2004

Binder BM, O’Malley RC, Moore JM, Parks BM, Spalding EP, Bleecker AB. (2004) Seedling Growth Response and Recovery to Ethylene: A Kinetic Analysis. Plant Physiology 136: 2913-2920. [Abstract ] (Included cover image for ethylene special issue)

Binder BM, Mortimore LA, Stepanova AN, Ecker JR, Bleecker AB. (2004) Short Term Growth Responses to Ethylene in Arabidopsis Seedlings Are EIN3/EIL1 Independent. Plant Physiology 136: 2921-2927. [Abstract] (Included cover image for ethylene special issue)

Gupta, V., Peterson, C. B, Dice, L. T., Uchiki, T., Racca, J., Guo, J.-t, Xu, Y., Hettich, R., Zhao, X., Rothstein, R., and Dealwis, C. (2004) Biochemistry 43, 8568-8578.  “Sml1p is a Dimer in Solution: Characterization of Denaturation and Renaturation of Recombinant Sml1p”

Hicks SN, Smiley RD, Stinnett LG, Minor KH, Howell EE. (2004). Role of Lys-32 residues in R67 dihydrofolate reductase probed by asymmetric mutations. J Biol Chem 279, 46995-7002.

Horn, N. A., Hurst, G. B., Mayasundari, A., Whittemore, N. A., Serpersu, E. H., and Peterson, C. B. (2004) J. Biol. Chem. 279, 35867-35878. “Assignment of the Four Disulfides in the N-terminal Somatomedin B Domain of Native Vitronectin Isolated from Human Plasma.”

Kim TH, Kim BH, Yahalom A, Chamovitz DA, and von Arnim AG. (2004). Developmental regulation via 5′ mRNA leader sequences through the translation initiation factor subunit eIF3h in Arabidopsis. Plant Cell 16, 3341-3356.

Lee G and Park JH. (2004). Hemolymph sugar homeostasis and starvation-induced hyperactivity affected by genetic manipulations of the adipokinetic hormone-encoding gene in Drosophila melanogaster. Genetics 167, 311-23.

Mayasundari, A., Whittemore, N. A., Serpersu. E. H. and Peterson, C. B. (2004) J. Biol. Chem. 279, 29359-29366.  “The Solution Structure of the N-terminal Domain of Human Plasma Vitronectin:  Location of Binding Sites that Regulate Fibrinolysis and Cell Migration.”

Shan L, Vincent J, Brunzelle JS, Dussault I, Lin M, Ianculescu I, Sherman MA, Forman BM, Fernandez EJ. (2004). Structure of the murine constitutive androstane receptor complexed to androstenol: a molecular basis for inverse agonism. Mol Cell 16, 907-17.

Sharan S, Pyle A, Benedict J, Coppola V, Martin B, Tessarollo L, Flaws J, Handel MA (2004) Partial Complementation of Brca2 Mutation in Mice by the Human BRCA2 Gene Shows a Sexually Dimorphic Meiotic Phenotype. Development 131, 131-4.

Stinnett L.G., Smiley R.D., Hicks S.N., Howell E.E. (2004) “Catch 222,” the effects of symmetry on ligand binding and catalysis in R67 dihydrofolate reductase as determined by mutations at Tyr-69. J Biol Chem 279:, 47003-9.

Subramanian C, Kim BH, Lyssenko NN, Xu X, Johnson CH, von Arnim AG. (2004). The Arabidopsis repressor of light signaling, COP1, is regulated by nuclear exclusion: Mutational analysis by bioluminescence resonance energy transfer. Proc Natl Acad Sci 101, 6798-6802.

Wallace ISRoberts DM. (2004). Homology modeling of representative subfamilies of Arabidopsis major intrinsic proteins. Classification based on the aromatic/arginine selectivity filter. Plant Physiol 135, 1059-68.

Wright E and Serpersu EH (2004) Isolation of Aminoglycoside Nucleotidyltransferase (2?)-Ia from Inclusion Bodies as Active, Monomeric Enzyme. Protein Express. Purif. 35: 373-380.

Xu Q and Guo H (2004) Quantum Mechanical/Molecular Mechanical Molecular-Dynamics Simulations of Cytidine Deaminase: from Stabilization of Transition-State Analogs to Catalytic Mechanisms, J Phys Chem B, 108, 2477-2483.

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