Molecular and Structural Biochemistry - 2009

Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. (2009). The Plant Cell. https://doi.org/10.1105/tpc.108.063958

Zhang, L., Bharadwaj, A. G., Casper, A., Barkley, J., Barycki, J. J., & Simpson, M. A. (2009). Hyaluronidase Activity of Human Hyal1 Requires Active Site Acidic and Tyrosine Residues. Journal of Biological Chemistry, 284(14), 9433–9442. https://doi.org/10.1074/jbc.M900210200

Biterova, E. I., & Barycki, J. J. (2009). Mechanistic Details of Glutathione Biosynthesis Revealed by Crystal Structures of Saccharomyces cerevisiae Glutamate Cysteine Ligase. Journal of Biological Chemistry, 284(47), 32700–32708. https://doi.org/10.1074/jbc.M109.025114

Williams, K., Cullati, S., Sand, A., Biterova, E. I., & Barycki, J. J. (2009). Crystal Structure of Acivicin-Inhibited γ-Glutamyltranspeptidase Reveals Critical Roles for Its C-Terminus in Autoprocessing and Catalysis†‡. Biochemistry, 48(11), 2459–2467. https://doi.org/10.1021/bi8014955

Yang, H., Gurgel, P. V., Williams, D. K., Jr, Bobay, B. G., Cavanagh, J., Muddiman, D. C., & Carbonell, R. G. (2009). Binding site on human immunoglobulin G for the affinity ligand HWRGWV. Journal of Molecular Recognition, n/a-n/a. https://doi.org/10.1002/jmr.967

Lopez-Ochoa, L., Nash, T. E., Ramirez-Prado, J., & Hanley-Bowdoin, L. (2009). Isolation of Peptide Aptamers to Target Protein Function. In Methods in Molecular Biology (pp. 333–360). https://doi.org/10.1007/978-1-59745-557-2_19

Meilleur, F., Weiss, K. L., & Myles, D. A. A. (2009). Deuterium Labeling for Neutron Structure-Function-Dynamics Analysis. Micro and Nano Technologies in Bioanalysis, pp. 281–292. https://doi.org/10.1007/978-1-59745-483-4_18

Jacquet, B. V., Salinas-Mondragon, R., Liang, H., Therit, B., Buie, J. D., Dykstra, M., … Ghashghaei, H. T. (2009). FoxJ1-dependent gene expression is required for differentiation of radial glia into ependymal cells and a subset of astrocytes in the postnatal brain. DEVELOPMENT, 136(23), 4021–4031. https://doi.org/10.1242/dev.041129

Vendeix, F. A. P., Munoz, A. M., & Agris, P. F. (2009). Free energy calculation of modified base-pair formation in explicit solvent: A predictive model. RNA, 15(12), 2278–2287. https://doi.org/10.1261/rna.1734309

Milam, S. L., & Clark, A. C. (2009). Folding and assembly kinetics of procaspase-3. PROTEIN SCIENCE, 18(12), 2500–2517. https://doi.org/10.1002/pro.259

Laws, S. C., Hotchkiss, M., Ferrell, J., Jayaraman, S., Mills, L., Modic, W., … Cooper, R. (2009). Chlorotriazine Herbicides and Metabolites Activate an ACTH-dependent Release of Corticosterone in Male Wistar Rats. TOXICOLOGICAL SCIENCES, 112(1), 78–87. https://doi.org/10.1093/toxsci/kfp190

Miller, W. L. (2009). Increasing gamete production with a gene switch.

Bilbille, Y., Vendeix, F. A. P., Guenther, R., Malkiewicz, A., Ariza, X., Vilarrasa, J., & Agris, P. F. (2009). The structure of the human tRNA(Lys3) anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs. NUCLEIC ACIDS RESEARCH, 37(10), 3342–3353. https://doi.org/10.1093/nar/gkp187

Melander, C., Moeller, P. D. R., Ballard, T. E., Richards, J. J., Huigens, R. W., III, & Cavanagh, J. (2009). Evaluation of dihydrooroidin as an antifouling additive in marine paint. INTERNATIONAL BIODETERIORATION & BIODEGRADATION, 63(4), 529–532. https://doi.org/10.1016/j.ibiod.2008.08.009

Walters, J., Pop, C., Scott, F. L., Drag, M., Swartz, P., Mattos, C., … Clark, A. C. (2009). A constitutively active and uninhibitable caspase-3 zymogen efficiently induces apoptosis. BIOCHEMICAL JOURNAL, 424, 335–345. https://doi.org/10.1042/bj20090825

Shultz, R. W., Lee, T.-J., Allen, G. C., Thompson, W. F., & Hanley-Bowdoin, L. (2009). Dynamic Localization of the DNA Replication Proteins MCM5 and MCM7 in Plants. PLANT PHYSIOLOGY, 150(2), 658–669. https://doi.org/10.1104/pp.109.136614

Shen, W., Reyes, M. I., & Hanley-Bowdoin, L. (2009). Arabidopsis Protein Kinases GRIK1 and GRIK2 Specifically Activate SnRK1 by Phosphorylating Its Activation Loop. PLANT PHYSIOLOGY, 150(2), 996–1005. https://doi.org/10.1104/pp.108.132787

Richards, J. J., Reyes, S., Stowe, S. D., Tucker, A. T., Ballard, T. E., Mathies, L. D., … Melander, C. (2009). Amide Isosteres of Oroidin: Assessment of Antibiofilm Activity and C. elegans Toxicity. JOURNAL OF MEDICINAL CHEMISTRY, 52(15), 4582–4585. https://doi.org/10.1021/jm900378s

Han, S.-O., & Miller, W. L. (2009). Activin A induces ovine follicle stimulating hormone beta using-169/-58 bp of its promoter and a simple TATA box. REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY, 7. https://doi.org/10.1186/1477-7827-7-66

Hobbs, C. A., Deterding, L. J., Perera, L., Bobay, B. G., Thompson, R. J., Darden, T. A., … Tomer, K. B. (2009). Structural Characterization of the Conformational Change in Calbindin-D-28k upon Calcium Binding Using Differential Surface Modification Analyzed by Mass Spectrometry. BIOCHEMISTRY, 48(36), 8603–8614. https://doi.org/10.1021/bi900350q

Hernandez, R., & Paredes, A. (2009). [Review of Sindbis virus as a model for studies of conformational changes in a metastable virus and the role of conformational changes in in vitro antibody neutralisation]. REVIEWS IN MEDICAL VIROLOGY, 19(5), 257–272. https://doi.org/10.1002/rmv.619

Oh, M.-H., Huber, J. L., Shen, W., Athwal, G. S., Wu, X., & Huber, S. C. (2009, July). Overexpression of a directed mutant of 14-3-3 omega in Arabidopsis leaves affects phosphorylation and protein content of nitrate reductase. BOTANY, Vol. 87, pp. 691–701. https://doi.org/10.1139/b09-003

Huggins, W., Ghosh, S. K., & Wollenzien, P. (2009). Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome. BMC Structural Biology, 9.

Bischoff, S. R., Tsai, S., Hardison, N., Motsinger-Reif, A. A., Freking, B. A., Nonneman, D., … Piedrahita, J. A. (2009). Characterization of Conserved and Nonconserved Imprinted Genes in Swine. BIOLOGY OF REPRODUCTION, 81(5), 906–920. https://doi.org/10.1095/biolreprod.109.078139

Bamunusinghe, D., Hemenway, C. L., Nelson, R. S., Sanderfoot, A. A., Ye, C. M., Silva, M. A. T., … Verchot-Lubicz, J. (2009). Analysis of potato virus X replicase and TGBp3 subcellular locations. VIROLOGY, 393(2), 272–285. https://doi.org/10.1016/j.virol.2009.08.002

Gagnon, K. T., Ju, S.-Y., Goshe, M. B., Maxwell, E. S., & Franzen, S. (2009). A role for hydrophobicity in a DielsAlder reaction catalyzed by pyridyl-modified RNA. NUCLEIC ACIDS RESEARCH, 37(9), 3074–3082. https://doi.org/10.1093/nar/gkp177

Nanda, K., Vancini, R., Ribeiro, M., Brown, D. T., & Hernandez, R. (2009). A high capacity Alphavirus heterologous gene delivery system. VIROLOGY, 390(2), 368–373. https://doi.org/10.1016/j.virol.2009.05.026

Dechene, M., Wink, G., Smith, M., Swartz, P., & Mattos, C. (2009). Multiple solvent crystal structures of ribonuclease A: An assessment of the method. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 76(4), 861–881. https://doi.org/10.1002/prot.22393

Hafer, A., Whittlesey, R., Brown, D. T., & Hernandez, R. (2009). Differential Incorporation of Cholesterol by Sindbis Virus Grown in Mammalian or Insect Cells. JOURNAL OF VIROLOGY, 83(18), 9113–9121. https://doi.org/10.1128/JVI.00755-09

Bleichert, F., Gagnon, K. T., Brown, B. A., II, Maxwell, E. S., Leschziner, A. E., Unger, V. M., & Baserga, S. J. (2009). A Dimeric Structure for Archaeal Box C/D Small Ribonucleoproteins. SCIENCE, 325(5946), 1384–1387. https://doi.org/10.1126/science.1176099

Kojetin, D. J., McLaughlin, P. D., Thompson, R. J., Dubnau, D., Prepiak, P., Rance, M., & Cavanagh, J. (2009). Structural and Motional Contributions of the Bacillus subtilis ClpC N-Domain to Adaptor Protein Interactions. JOURNAL OF MOLECULAR BIOLOGY, 387(3), 639–652. https://doi.org/10.1016/j.jmb.2009.01.046

Barakat, A., DiLoreto, D. S., Zhang, Y., Smith, C., Baier, K., Powell, W. A., … Carlson, J. E. (2009). Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC PLANT BIOLOGY, 9. https://doi.org/10.1186/1471-2229-9-51

Mitra, S. K., Walters, B. T., Clouse, S. D., & Goshe, M. B. (2009). An Efficient Organic Solvent Based Extraction Method for the Proteomic Analysis of Arabidopsis Plasma Membranes. JOURNAL OF PROTEOME RESEARCH, 8(6), 2752–2767. https://doi.org/10.1021/pr801044y

Walters, J., Milam, S. L., & Clark, A. C. (2009). [Review of Practical approaches to protein folding and assembly: Spectroscopic strategies in thermodynamics and kinetics]. Methods in enzymology: biothermodynamics,vol 455,  part a, 455, 1–39.

Blackburn, K., & Goshe, M. B. (2009). Mass Spectrometry Bioinformatics: Tools for Navigating the Proteomics Landscape. CURRENT ANALYTICAL CHEMISTRY, 5(2), 131–143. https://doi.org/10.2174/157341109787846135

Grattapaglia, D., Plomion, C., Kirst, M., & Sederoff, R. R. (2009). [Review of Genomics of growth traits in forest trees]. CURRENT OPINION IN PLANT BIOLOGY, 12(2), 148–156. https://doi.org/10.1016/j.pbi.2008.12.008

Chien, K.-yi, & Goshe, M. B. (2009). [Review of Advances in Quantitative Mass Spectrometry Analysis: Weighing in on Isotope Coding and Label-Free Approaches for Expression and Functional Proteomics]. CURRENT ANALYTICAL CHEMISTRY, 5(2), 166–185. https://doi.org/10.2174/157341109787846126

Brenke, R., Kozakov, D., Chuang, G.-Y., Beglov, D., Hall, D., Landon, M. R., … Vajda, S. (2009). Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. BIOINFORMATICS, 25(5), 621–627. https://doi.org/10.1093/bioinformatics/btp036

Kirchoff, B. K., Lagomarsino, L. P., Newman, W. H., Bartlett, M. E., & Specht, C. D. (2009). EARLY FLORAL DEVELOPMENT OF HELICONIA LATISPATHA (HELICONIACEAE), A KEY TAXON FOR UNDERSTANDING THE EVOLUTION OF FLOWER DEVELOPMENT IN THE ZINGIBERALES. AMERICAN JOURNAL OF BOTANY, 96(3), 580–593. https://doi.org/10.3732/ajb.0800305

Mbeunkui, F., & Johann, D. J. (2009). [Review of Cancer and the tumor microenvironment: A review of an essential relationship]. Cancer Chemotherapy and Pharmacology, 63(4), 571–582.

Oh, M.-H., Wang, X., Kota, U., Goshe, M. B., Clouse, S. D., & Huber, S. C. (2009). Tyrosine phosphorylation of the BRI1 receptor kinase emerges as a component of brassinosteroid signaling in Arabidopsis. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106(2), 658–663. https://doi.org/10.1073/pnas.0810249106

Kononchik, J. R., Jr., Nelson, S., Hernandez, R., & Brown, D. I. (2009). Helical virus particles formed from morphological subunits of a membrane containing icosahedral virus. VIROLOGY, 385(2), 285–293. https://doi.org/10.1016/j.virol.2008.12.015

Davis, M. F., Gracz, H., Vendeix, F. A. P., Serrano, V., Somasundaram, A., Decatur, S. M., & Franzen, S. (2009). Different Modes of Binding of Mono-, Di-, and Trihalogenated Phenols to the Hemoglobin Dehaloperoxidase from Amphitrite ornata. BIOCHEMISTRY, 48(10), 2164–2172. https://doi.org/10.1021/bi801568s

Cheng, F.-yi, Blackburn, K., Lin, Y.-min, Goshe, M. B., & Williamson, J. D. (2009). Absolute Protein Quantification by LC/MSE for Global Analysis of Salicylic Acid-induced Plant Protein Secretion Responses. JOURNAL OF PROTEOME RESEARCH, 8(1), 82–93. https://doi.org/10.1021/pr800649s

Sisler, E. C., Goren, R., Apelbaum, A., & Serek, M. (2009). The effect of dialkylamine compounds and related derivatives of 1-methylcyclopropene in counteracting ethylene responses in banana fruit. POSTHARVEST BIOLOGY AND TECHNOLOGY, 51(1), 43–48. https://doi.org/10.1016/j.postharvbio.2008.06.009

Chen, Z., Serrano, V., Betts, L., & Franzen, S. (2009). Distal histidine conformational flexibility in dehaloperoxidase from Amphitrite ornata. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 65, 34–40. https://doi.org/10.1107/S0907444908036548

Wheeler, N., & Sederoff, R. (2009). Role of genomics in the potential restoration of the American chestnut. TREE GENETICS & GENOMES, 5(1), 181–187. https://doi.org/10.1007/s11295-008-0180-y