Biology Department Biology Department  


    Biology Department 2012 Publications

  • Agarwal R., Burley S.K., and Swaminathan S.
    Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase.
    PROTEINS: Structure, Function, and Bioinformatics, 80(1):261-268 (January, 2012).   PubMed  3QDK 
  • Alexieva-Botcheva K. and Anderson C.W.
    Encyclopedia of Signaling Molecules, 1st Edition, S. Choi, Editor, Springer Science + Business Media, LLC, New York, NY (in press).
  • Amrich C.G., Davis C.P., Rogal W.P., Shirra M.K., Heroux A., Gardner R.G., Arndt K.M., and VanDemark A.P.
    Cdc73 subunit of Paf1 complex contains C terminal Ras like domain that promotes association of Paf1 complex with chromatin.
    Journal of Biological Chemistry 287(14): 10863-10875 (March, 2012).  PubMed
  • Andre C., Haslam R.P., and Shanklin J.
    Feedback regulation of plastidic acetyl-CoA carboxylase by 18:1-acyl carrier protein in Brassica napus.
    Proceedings of the National Academy of Sciences USA (Epub June 4, 2012, in press).  PubMed
  • Batra J., Robinson J., Soares A.S., Fields A.P., Radisky D.C., and Radisky E.S.
    Matrix metalloproteinase-10 (MMP-10) interaction with tissue inhibitors of metalloproteinases TIMP-1 and TIMP-2: Binding studies and crystal structure.
    Journal of Biological Chemistry, 287(19):15935-15946 (May, 2012).  PubMed
  • Buchko G.W. and Robinson H.
    Crystal structure of cce_0566 from Cyanothece 51142, a protein associated with nitrogen fixation in the DUF269 family.
    FEBS Letters, 586(4):350-355 (February, 2012).  PubMed  3NJ2 
  • Casjens S.R., Mongodin E.F., Qiu W.-G., Luft B.J., Schutzer S.E., Gilcrease E.B., Huang W.M., Vujadinovic M., Aron J.K., Vargas L.C., Freeman S., Radune D., Weldman J.F., Dimitrov G.I., Khouri H.M., Sosa J.E., Halpin R.A., Dunn J.J., and Fraser C.M.
    Genome stability of Lyme disease spirochetes: Comparative genomics of Borrelia burgdorferi plasmids.
    PLoS ONE, 7(3):e33280 (March, 2012).  PubMed
  • Chimenti M.S., Khangulov V.S., Robinson A.C., Heroux A., Majumdar A., Schlessman J.L., and Garcia-Moreno B.
    Structural reorganization triggered by charging of Lys residues in the hydrophobic interior of a protein.
    Structure, 20(6):1071-1085 (June, 2012).  PubMed
  • Daughtry K.D., Xiao Y., Stoner-Ma D., Cho E., Orville A.M., Liu P., and Allen K.N.
    Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance raman and UV-visible spectroscopic analysis of a Rieske-type demethylase.
    Journal of the American Chemical Society, 134(5):2823-2834 (February, 2012).  PubMed
  • Eswaramoorthy S., Poulain S., Hienerwadel R., Bremond N., Sylvester M.D., Zhang Y.-B., Berthomieu C., van der Lelie D., and Matin A.
    Crystal structure of ChrR-A quinone reductase with the capacity to reduce chromate.
    PLoS ONE, 7(4):e36017 (April, 2012).  PubMed  3SVL
  • Fan J., Yan C., Andre C., Shanklin J., Schwender J., and Xu C.
    Oil accumulation is controlled by carbon precursor supply for fatty acid synthesis in Chlamydomonas reinhardtii.
    Plant and Cell Physiology (Epub May 28, 2012, in press).  PubMed
  • Giagnoni L., Magherini F., Landi L., Taghavi S., van der Lelie D., Puglia M., Bianchi L., Bini L., Nannipieri P., Renella G., and Modesti A.
    Soil solid phases effects on the proteomic analysis of Cupriavidus metallidurans CH34.
    Biology and Fertility of Soils 48(4): 425-433 (May, 2012).
  • Gou J.-Y., Miller L.M., Hou G., Yu X.-H., Chen X.-Y., and Liu C.-J.
    Acetylesterase-mediated deacetylation of pectin impairs cell elongation, pollen germination, and plant reproduction.
    The Plant Cell, 24(1):50-65 (January, 2012).  PubMed
  • Hoch E., Lin W., Chai J., Hershfinkel M., Fu D., and Sekler I.
    Histidine pairing at the metal transport site of mammalian ZnT transporters controls Zn2+ over Cd2+ selectivity.
    Proceedings of the National Academy of Sciences USA, 109(19):7202-7207 (May, 2012).  PubMed
  • Kumar G., Agarwal R., and Swaminathan S.
    Discovery of a fluorene class of compounds as inhibitors of Botulinum neurotoxin serotype E by virtual screening.
    Chemical Communications, 48(18):2412-2414 (February, 2012).  PubMed
  • Kumar G., Kumaran D., Ahmed S.A., and Swaminathan S.
    Peptide inhibitors of botulinum neurotoxin serotype A: Design, inhibition, cocrystal structures, structure-activity relationship and pharmacophore modeling.
    Acta Crystallographica D: Biological Crystallography, D68(Pt5):511 520 (May, 2012).
    Cover: Botulinum neurotoxin serotype A with inhibitor RRGF, p. 511.  PubMed  3QW8
  • Lin G., Li H., and Nathan C.F.
    Bacterial proteasome.
    Handbook of Proteolytic Enzymes, 3rd Edition, N. D. Rawlings and G. Salvesen, Editors, Chapter 847, Elsevier, B.V., Oxford, UK (in press). 
  • Liu C.-J.
    Deciphering the enigma of lignification: Precursor transport, oxidation, and the topochemistry of lignin assembly (Review).
    Molecular Plant, 5(2):304-317 (March, 2012).  PubMed
  • Lohr M., Schwender J., and Polle J.E.W.
    Isoprenoid biosynthesis in eukaryotic phototrophs: A spotlight on algae (Review).
    Plant Science, 185-186:9-22 (April, 2012).  PubMed
  • Lu X., Zhou R., Sharma I., Li X., Kumar G., Swaminathan S. , Tonge P.J., and Tan D.S.
    Stable analogues of OSB-AMP: Potent inhibitors of MenE, the o-succinylbenzoate-CoA synthetase from bacterial menaquinone biosynthesis.
    ChemBioChem, 13(1):129-136 (January, 2012).  PubMed
  • Manjasetty B.A., Yu X.-H., Panjikar S., Taguchi G., Chance M.R., and Liu C.-J.
    Structural basis for modification of flavonol and naphthol glucoconjugates by Nicotiana tabacum malonyltransferase (NtMaT1).
    Planta (Epub May 19, 2012, in press).  PubMed
  • Marmont L.S., Whitney J.C., Robinson H., Colvin K.M., Parsek M.R., and Howell P.L.
    Expression, purification, crystallization and preliminary X-ray analysis of Pseudomonas aeruginosa PelD.
    Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 68(Pt2):181-184 (February, 2012).  PubMed
  • Miller D.P., Bell J.K., McDowell J.V., Conrad D.H., Burgner J.W., Heroux A., and Marconi R.T.
    Structure of factor H-binding protein B (FhbB) of the periopathogen, Treponema denticola: Insights into progression of periodontal disease.
    Journal of Biological Chemistry, 287(16):12715-12722 (April, 2012).  PubMed  3QZ0
  • Miloslavina Y., Lambrev P.H., Javorfi T., Varkonyi Z., Karlicky V., Wall J.S., Hind G., and Garab G.
    Anisotropic circular dichroism signatures of oriented thylakoid membranes and lamellar aggregates of LHCII.
    Photosynthesis Research, 111(1-2):29-39 (March, 2012).  PubMed
  • Miner K.D., Mukherjee A., Gao Y.-G., Null E.L., Petrik I.D., Zhao X., Yeung N., Robinson H., and Lu Y.
    A designed functional metalloenzyme that reduces O2 to H2O with over one thousand turnovers.
    Angewandte Chemie International Edition, 51(3):5589-5592 (June, 2012).  PubMed
  • Mohan S., Rizaldy R., Das D., Bauer R. J., Heroux A., Trakselis M.A., Hildebrand J.D., and Vandemark A.P.
    Structure of the Shroom domain 2 reveals a three-segmented coiled-coil required for dimerization, Rock binding, and apical constriction.
    Molecular Biology of the Cell, 23(11):2131-2142 (June, 2012).  PubMed  3THF
  • Muller E.M., Smedley J., Bohon J., Yang X., Gaowei M., Skinner J., De Geronimo G., Sullivan M., Allaire M., Keister J.W., Berman L., and Heroux A.
    Transmission-mode diamond white-beam position monitor at NSLS.
    Journal of Synchrotron Radiation, 19(Pt3):381-387 (May, 2012).  PubMed
  • O’Grady J., Schwender J., Shachar-Hill Y., and Morgan J.A.
    Metabolic cartography: Experimental quantification of metabolic fluxes from isotopic labeling studies.
    Journal of Experimental Botany, 63(6):2293-2308 (March, 2012).  PubMed
  • Rawat R., Yu X.-H., Sweet R.M., and Shanklin J.
    Conjugated fatty acid synthesis: Residues 111 and 115 influence product partitioning of the Momordica charantia conjugase.
    Journal of Biological Chemistry, 287(20):16230-16237 (May, 2012).  PubMed
  • Rimando A.M., Pan Z., Polashock J.J., Dayan F.E., Mizuno C.S., Snook M.E., Liu C.-J., and Baerson S.R.
    In planta production of the highly potent resveratrol analogue pterostilbene via stilbene synthase and O-methyltransferase co-expression.
    Plant Biotechnology Journal, 10(3):269-283 (April, 2012).  PubMed
  • Salameh M.A., Soares A.S., Alloy A., and Radisky E.S.
    Presence versus absence of hydrogen bond donor Tyr-39 influences interactions of cationic trypsin and mesotrypsin with protein protease inhibitors.
    Protein Science, (Epub May 18, 2012, in press).  PubMed
  • Schutzer S.E., Fraser-Liggett C.M., Qiu W.-G., Kraiczy P., Mongodin E.F., Dunn J.J., and Luft B.J.
    Whole-genome sequences of Borrelia bissettii, Borrelia valaisiana, and Borrelia spielmanii.
    Journal of Bacteriology, 194(2):545-546 (January, 2012).  PubMed
  • Sheng J., Zhang W., Hassan A.E., Gan J., Soares A.S., Geng S., Ren Y., and Huang Z.
    Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone. Nucleic Acids Research (Epub May 28, 2012, in press).  PubMed
  • Sun J., Kawakami H., Zech J., Speck C., Stillman B., and Li H.
    Cdc6-induced conformational changes in ORC bound to origin DNA revealed by cryo-electron microscopy. Structure, 20(3):534-544 (March, 2012).  PubMed
  • Sutherland J.C.
    Measurement of the circular dichroism of electronic transitions.
    Advances in Chiroptical Methods, N. Berova, R. W. Woody, P. L. Polavarapu, and K. Nakanishi, Editors, John Wiley & Sons, Ltd., Hoboken, NJ (in press). 
  • Sutherland J.C.
    Dichrometer errors resulting from large signals or improper modulator phasing.
    Chirality (Epub May 25, 2012, in press).  PubMed
  • van der Lelie D., Taghavi S., McCorkle S.M., Li L.-L., Malfatti S.A., Monteleone D., Donohoe B.S., Ding S.-Y., Adney W.S., Himmel M.E., and Tringe S.G.
    The metagenome of an anaerobic microbial community decomposing poplar wood chips.
    PLoS ONE, 7(5):e36740 (May, 2012).  PubMed
  • Vitali J., Singh A.K., Soares A.S., and Colaneri M.J.
    Structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase in a hexagonal crystal form: Insights into the path of carbamoyl phosphate to the active site of the enzyme.
    Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 68(Pt.5):527-534 (May, 2012).  PubMed
  • Wang H., Kunz S., Chen G., Seebeck T., Wan Y., Robinson H., Martinelli S., and Ke H.
    Biological and structural characterization of Trypanosoma cruzi phosphodiesterase C and implications for design of parasite selective inhibitors.
    Journal of Biological Chemistry, 287(15):11788-11797 (April, 2012).  PubMed
  • Wang Z., Xu C., and Benning C.
    TGD4 involved in endoplasmic reticulum-to-chloroplast lipid trafficking is a phosphatidic acid binding protein.
    Plant Journal, 70(4):614-623 (May, 2012).  PubMed
  • Whitney J.C., Colvin K.M., Marmont L.S., Robinson H., Parsek M.R., and Howell P.L.
    Structure of the cytoplasmic region of PelD, a degenerate diguanylate cyclase receptor that regulates exopolysaccharide production in Pseudomonas aeruginosa.
    Journal of Biological Chemistry, (Epub May 17, 2012, in press).  PubMed  4DN0  4DMZ  Jmol viewer
  • Yang S., Wang T., Bohon J., Gagne M.E., Bolduc M., Leclerc D., and Li H.
    Crystal structure of the coat protein of the flexible filamentous Papaya Mosaic Virus.
    Journal of Molecular Biology, (Epub May 29, 2012, in press).  PubMed
  • Yao Q., Song C.X., He C., Kumaran D., and Dunn J.J.
    Heterologous expression and purification of Arabidopsis thaliana VIM1 protein: In vitro evidence for its inability to recognize hydroxymethylcytosine, a rare base in Arabidopsis DNA.
    Protein Expression and Purification, 83(1):104-111 (May, 2012).   PubMed

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Last Modified: July 17, 2012
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