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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.
p53.
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

Last Modified: July 17, 2012
Please forward all questions about this site to: Denise Monteleone