Publications
See Also: 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000
List of publications coauthored by BCMB graduate students, undergraduate students, postdocs and faculty.
In Press
A. N. BONDAR and J.C. SMITH. Water molecules in short- and long-distance proton transfer steps of bacteriorhodopsin proton pumping. Israel Journal of Chemistry. In Press.
A.N. BONDAR, J.C. SMITH & M. ELSTNER. Mechanism of a proton pump analyzed with computer simulations. Theoretical Chemistry Accounts. In Press.
Goodman R, Echternacht A, Hall J, Deng L and Welch J (submitted) Do patterns of cell size and body size in an ectothermic vertebrate reflect geography and climatic gradients? Global Ecology and Biogeography.
H. Guo et al., QM/MM Analysis of the Catalytic Active Sites in Cellulases, in Computational Modeling in Lignocelluosic Biofuel Production, M. Nimlos and M.F. Crowley (Eds), ACS Publishing, invited contribution (Book Chapter), in revision.
P. IMHOF, S. FISCHER & J.C. SMITH. Catalytic Mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: A quantum mechanical/molecular mechanical analysis" Biochemistry. In press.
Kim SH, Gadiparthi K, Kron SJ, and Kitazono AA (in press) A phosphorylation-independent role for the yeast cyclin-dependent kinase activating kinase Cak1. Gene
Kitazono AA (in press) A journal-club based class that promotes active and cooperative learning of biology. Journal of College Science Teaching.
Kitazono AA (in press) “Improved gap-repair cloning method that uses oligonucleotides to target cognate sequences.” Yeast
M. KRISHNAN & J.C. SMITH. Response of Small-Scale, Methyl Rotors to Protein-Ligand Association : A Simulation Analysis of Calmodulin-Peptide Binding. Journal of the American Chemical Society. In press.
Leland S, Prabakaran N, Polyzos A, Thomas S, Samaan G, Donnell R, Marchetti F, and Venkatachalam S (in press) Heterozygosity for a Bub1 mutation causes female-specific germ cell aneuploidy in mice. (July 17th, 2009), PNAS,PMID: 19617567.
T. NEUSIUS, I.M. SOKOLOV & J.C. SMITH. Subdiffusion in time-averaged, confined random walks. Physical Review E. In press.
Norris AL and Serpersu EH (in press) NMR Detected Hydrogen-Deuterium Exchange Reveals Differential Dynamics of Antibiotic and Nucleotide Bound Aminoglycoside Phosphotransferase 3′-IIIa . J. Am. Chem. Soc.
J. PARKS, H. GUO, C. MOMANY, L. LIANG, S. MILLER, A. SUMMERS and J.C. SMITH. Mechanism of Hg-C protonolysis in the organomercurial lyase MerB. Journal of the American Chemical Society. In press.
Petridis L and Smith JC. (in press) A molecular mechanics force field for lignin. Journal of Computational Chemistry.
L. PETRIDIS, J. XU, M. CROWLEY, J.C. SMITH and X. CHENG. Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes Biofuels: ACS. In press.
Qin Xu, Xia Ye, (Max) Zong-Ming Cheng, and Hong Guo, Structural Basis for the Action of Xyloglucan Endotransglycosylases/hydrolases: Insights from Homology Modeling, Interdisciplinary Sciences-- Computational Life Sciences, in revision.
Qin Xu, Yuzhuo Chu, Hao-Bo Guo, Jeremy C. Smith, and Hong Guo, Energy Triplets for Writing Epigenetic Marks: Insights from QM/MM Free Energy Simulations of Protein Lysine Methyltransferases, Chemistry, a European Journal, in press.
M. SAHARAY, H.-B. GUO, J.C. SMITH and H. GUO. QM/MM Analysis of Cellulase Active Sites and Actions of the Enzymes on Substrates. Biofuels: ACS. In press.
Schulz R, Krishnan M, Daidone I, Smith JC. (in press) Instantaneous Normal Modes and the Protein Glass Transition. Biophysical Journal.
R. SCHULZ, B. LINDNER, L. PETRIDIS & J.C. SMITH. Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer. Journal of Chemical Theory and Computation. In press.
Spies MA, Reese J, Dodd D, Pankow K, Blanke SR, Baudry J. (in press) Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase. Journal of the American Chemical Society.
Splettstoesser T, Noe F, Smith JC. (in press) Molecular dynamics study of G-actin shows instability of the open state and suggests the existence of a superclosed state. Proteins: Structure, Function and Dynamics.
Tobe BTD, Kitazono AA, Suen JK, RGerber RA, Bevis BJ, Choy J, Chasman D, Kron SJ(in press) “Morphogenesis signaling components influence cell cycle regulation by cyclin dependent kinase.” Cell Division
J.P. ULMSCHNEIDER, J.C. SMITH, A. KILLIAN and M.B. ULMSCHNEIDER. Folding of membrane-embedded peptides. Journal of Chemical Theory and Computation. In press.
Wu L. and Serpersu EH (in press) Deciphering interactions of the aminoglycoside phosphotransferase(3′)-IIIa with its ligands. Biopolymers.
Q. XU, Y. CHU, H.-B. GUO, J.C. SMITH & H. GUO. Energy Triplets for Writing Epigenetic Marks: Insights from QM/MM Free Energy Simulations of Protein Lysine Methyltransferases. Chemistry: A European Journal. In press.
2009
Bahn JH, Lee G, Park JH. 2009. Comparative analysis of Pdf-mediated circadian behaviors between D. melanogaster and D. virilis. Genetics 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.
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.
Jain, NU (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
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 JC. Protein Dynamical Transition : Role of Methyl Dynamics and Local Diffusion Theory and Applications of Computational Chemistry 2008. AIP Conference Proceedings 1102 122-131 (2009).
Li J, Park E, von Arnim AG, Nebenführ 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.
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. Neuroscience, in press.
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.
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).
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
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).
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.
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).
2008
Albright S, Chen B, Holbrook K, Jain NU. (2008) Solution NMR studies provide structural basis for endotoxin pattern recognition by the innate immune receptor CD14. Biochem 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 MB, Ganguly R. 2008. Caffeine induction of Cyp6a2 and Cyp6a8 genes of Drosophila melanogaster is modulated by cAMP and D-JUN protein levels. Gene 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 brasilense. J Bacteriol. Jul 18.
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 Chem 283:4690-8.
Feng J, Goswami S, Howell EE. 2008. R67, the other dihydrofolate reductase: rational design of an alternate active site configuration. Biochemistry 47:555-65.
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 YJ, Park 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/XI. Traffic 9, 290-298.
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 and Xenopus 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 A 105, 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 C, Norris AL, Land ML, Tjioe E, Serpersu EH. (2008) Detection of specific solvent rearrangement regions of an enzyme: NMR and ITC studies with aminoglycoside phosphotransferase(3')-IIIa. Biochemistry 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 biomass Journal of Physics Conference Series 125 012055.
Plata MP, Kang HJ, Zhang S, Kuruganti S, Hsu SJ, Labrador 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 KH, Peterson CB. (2008) A deletion mutant of vitronectin lacking the somatomedin B domain exhibits residual plasminogen activator inhibitor-1-binding activity. J 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 Model Biochimica et Biophysica Acta – Biomembranes. 1778(10), 2234-2243.
Serpersu EH, Ozen C, Wright 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 Renilla. Protein 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.
Choi WG, Roberts 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.
Jin Y, Rodriguez AM, Stanton JD, Kitazono AA, Wyrick JJ (2007) “Simultaneous mutation of methylated lysine residues in histone H3 causes enhanced gene silencing, cell cycle defects, and cell lethality in Saccharomyces cerevisiae.” Mol Cell Biol. 19, 6832-41.
Kim BH, Cai X, Vaughn JN, von 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.
McSherry TD, Kitazono AA, Javaheri A, Kron SJ, Mueller PR (2007) “Non-catalytic function for ATR in the checkpoint response.” Cell cycle 16, 2019-30.
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. Proteins: Structure, 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 BK, Cai X, Nebenführ A. (2007) A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. Plant J epub Jul 30.
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 SJ, Campbell IM, Bruce 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.
Thomas SE, McKee 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 Q, Guo 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.
2006
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 crescentus. Journal of Bacteriology 188: 6841-6850
Bennett B, Langan P, Coates L, Mustyakimov M, Schoenborn B, Howell EE, Dealwis 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.
Choi YJ, Lee G, Park JH. 2006. Programmed cell death mechanisms of identifiable peptidergic neurons in Drosophila melanogaster. Development 133:2223-2232.
Chopra S, Lynch R, Kim SH, Jackson M, Howell EE. 2006. Effects of temperature and viscosity on R67 dihydrofolate reductase catalysis. Biochemistry 45, 6596-6605.
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.
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.
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.
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.
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-proteobacterium Agrobacterium 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.
von Arnim AG, Schwechheimer C 2006. Meeting Report: Life is degrading--thanks to some zomes. Mol Cell 23, 621-629.
Xu H, Faber C, Uchiki T, Racca J, Dealwis C 2006. Structures of eukaryotic ribonucleotide reductase I define gemcitabine diphosphate binding and subunit assembly. Proc Natl Acad Sci USA 103, 4028-4033.
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
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 7, 1388–1393.
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.
Guo H, Rao N, Xu Q, Guo 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-.
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.
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.
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.
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 IS, Roberts DM. (2005) Distinct transport selectivity of two structural subclasses of the Nodulin-like Intrinsic Protein family of plant aquaglyceroporin channels. Biochemistry 44, 16826-34.
2004
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.
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.
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 IS, Roberts 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.
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.
2003
Pyle AD, Handel MA (2003) Genetic and Phenotypic Complexity in PL/J Males with Multiple Meiotic Abnormalities Leading to Sperm Aneuploidy. Molecular Reproduction and Development 64, 471-481.
2002
Eaker S, Cobb J, Pyle A, Handel MA (2002) Meiotic Prophase Abnormalities in MLH1-Deficient Mouse Spermatocytes and Metaphase Cell Death: Insights into Regulation of Spermatogenic Progress. Developmental Biology 249, 85-95.
2001
Eaker S, Pyle AD, Cobb J, Handel MA (2001) Evidence for Meiotic Spindle Checkpoint from Analysis of Spermatocytes from Robertsonian Chromosome Heterozygous Mice. Journal of Cell Science 114, 2953-2965.
2000
Cobb JA and Roberts DM. (2000) Structural requirements for N-trimethylation of lysine-115 of calmodulin. Journal of Biological Chemistry, 275, 18969-18975.