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Biology Department 2011 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 (in press) (2011).
Alexieva-Botcheva K., and Anderson C. W.
p53.
Encyclopedia of Signaling Molecules S. Choi, Editor, Springer Science + Business Media, LLC, New York, NY (in press).
Anderson C.W. and Appella E.
Signaling to the p53 tumor suppressor through pathways activated by genotoxic and non-genotoxic stresses.
Regulation in Organelle and Cell Compartment Signaling, R. A. Bradshaw and E. A. Dennis, Editors, Chapter 264, pp. 235-254, Elsevier B.V., San Diego, CA (April, 2011).
Bagaria A., Kumaran D., Burley S.K., and Swaminathan S.
Structural basis for a ribofuranosyl binding protein: Insights into the furanose specific transport.
PROTEINS: Structure, Function, and Bioinformatics 79(4): 1352-1357 (April, 2011). PubMed
Batsford S., Dunn J., and Mihatsch M.
Induction of experimental arthritis by borrelial lipoprotein and CpG motifs: Are toll-like receptors 2, 4, 9 or CD-14 involved?
The Open Rheumatology Journal, 5:18-23 (June, 2011).

Baxa U., Keller P.W., Cheng N., Wall J.S., and Steven A.C.
In Sup35p filaments (the [PSI+] prion), the globular C-terminal domains are widely offset from the amyloid fibril backbone.
Molecular Microbiology, 79(2):523-532 (January, 2011). (Cover) PubMed
Berman L.E., Allaire M., Chance M.R., Hendrickson W.A., Heroux A., Jakoncic J., Liu Q., Orville A.M., Robinson H.H., Schneider D.K., Shi W., Soares A.S., Stojanoff V., Stoner-Ma D., and Sweet R.M.
Optics concept for a pair of undulator beamlines for MX.
Nuclear Instruments and Methods in Physics Research A: Accelerators, Spectrometers, Detectors and Associated Equipment 649(1):131-135 (September, 2011). PubMed
Botcheva K., McCorkle S., McCombie W.R., Dunn J., and Anderson C.W.
Distinct p53 genomic binding patterns in normal and cancer-derived human cells.
Cell Cycle, (in press) (2011).
Brown J.H., Kumar V.S., O’Neall-Hennessey E., Reshetnikova L., Robinson H., Nguyen-McCarty M., Szent-Gyorgyi A.G., and Cohen C.
Visualizing key hinges and a potential major source of compliance in the lever arm of myosin.
Proceedings of the National Academy of Sciences USA, 108(1):114-119 (January, 2011). PubMed
Casjens S.R., Fraser-Liggett C.M., Mongodin E.F., Qiu W.G., Dunn J.J., Luft B.J., and Schutzer S.E.
Whole genome sequence of an unusual Borrelia burgdorferi sensu lato isolate.
Journal of Bacteriology, 193(6):1489-1490 (March, 2011). PubMed
Chen W., Yu X.-H., Zhang K., Shi J., Schreiber L., Shanklin J., and Zhang D.
Male Sterile 2 encodes a plastid-localized fatty acyl-ACP reductase required for pollen exine development in Arabidopsis thaliana.
Plant Physiology, 157(2):842-853 (October, 2011). PubMed
Close D., Johnson S.J., Sdano M.A., McDonald S.M., Robinson H., Formosa T., and Hill C.P.
Crystal structure of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain.
Journal of Molecular Biology, 408(4):697-713 (May, 2011). PubMed
Das B., Bennett P.V., Cutter N.C., Sutherland J.C., and Sutherland B.M.
Melatonin protects human cells from clustered DNA damages, killing and acquisition of soft agar growth induced by X-rays or 970 MeV/n Fe ions.
International Journal of Radiation Biology, 87(6):545-555 (June, 2011). PubMed
Das P. and Sutherland B.M.
Processing of abasic DNA clusters in hApeI-silenced primary fibroblasts exposed to low doses of X-irradiation.
Journal of Biosciences, 36(1):105-116 (March, 2011). PubMed
Fan J., Andre C., and Xu C.
A chloroplast pathway for the de novo biosynthesis of triacylglycerol in Chlamydomonas reinhardtii.
FEBS Letters, 585(12):1985-1991 (June, 2011). PubMed
Fan J., and Xu C.
Genetic analysis of Arabidopsis mutants impaired in plastid lipid import reveals a role of membrane lipids in chloroplast division.
Plant Signaling & Behavior, 6(3):458 460 (March, 2011). PubMed
Fernandez M.M., Cho S., De Marzi M.C., Kerzic M.C., Robinson H., Mariuzza R.A., and Malchiodi E.L.
Crystal structure of staphylococcal enterotoxin G (SEG) in complex with a mouse T-cell receptor β chain.
Journal of Biological Chemistry, 286(2):1189-1195 (January, 2011). PubMed
Gallagher D.T., Kim S.K., Robinson H., and Reddy P.T.
Active-site structure of class IV adenylyl cyclase and transphyletic mechanism.
Journal of Molecular Biology, 405(3):787-803 (January, 2011). PubMed
Giagnoni L., Magherini F., Landi L., Taghavi S., Modesti A., Bini L., Nannipieri P., van der Lelie D., and Renella G.
Extraction of microbial proteome from soil: potential and limitations assessed through a model study.
European Journal of Soil Science, 62(1):74-81 (February, 2011).
Goble A.M., Zhang Z., Sauder J.M., Burley S.K., Swaminathan S., and Raushel F.M.
Pa0148 from Pseudomonas aeruginosa catalyzes the deamination of adenine.
Biochemistry 50(30): 6589-6597 (August, 2011). PubMed
Goldsbury C., Baxa U., Simon M.N., Steven A.C., Engel A., Wall J.S., Aebi U., and Muller S.A.
Amyloid structure and assembly: Insights from scanning transmission electron microscopy.
Journal of Structural Biology, 173(1):1-13 (January, 2011). PubMed
Gou J.-Y., Felippes F.F., Liu C.-J., Weigel D., and Wang J.-W.
Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor.
Plant Cell, 23(4):1512-1522 (April, 2011).
Guy J.E., Whittle E., Moche M., Lengqvist J., Lindqvist Y., and Shanklin J.
Remote control of regioselectivity in acyl-acyl carrier protein-desaturases.
Proceedings of the National Academy of Sciences USA, 108(40):16594-16599 (October, 2011). PubMed
Hale M., Oyler G., Swaminathan S., and Ahmed S.A.
Basic tetrapeptides as potent intracellular inhibitors of type A Botulinum neurotoxin protease activity.
Journal of Biological Chemistry, 286(3):1802-1811 (January, 2011). PubMed
Han Q., Robinson H., Cai T., Tagle D.A., and Li J.
Biochemical and structural characterization of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-IV.
Biosciences Report, 31(5):323-332 (October, 2011). PubMed
Harada Y., Li Hua, Wall J.S., Li H., and Lennarz W.J.
Structural studies and the assembly of the heptameric post-translational translocon complex.
Journal of Biological Chemistry, 286(4):2956-2965 (January, 2011). PubMed
Hay J. and Schwender J.
Computational analysis of storage synthesis in developing Brassica napus L. (oilseed rape) embryos: flux variability analysis in relation to ¹³C metabolic flux analysis.
The Plant Journal 67, 513–525 (August, 2011). PubMed
Hay J., and Schwender J.
Metabolic network reconstruction and flux variability analysis of storage synthesis in developing oilseed rape (Brassica napus L.) embryos.
The Plant Journal 67, 526–541 (August, 2011). PubMed
He J., Scott J.L., Heroux A., Roy S., Lenoir M., Overduin M., Stahelin R.V., and Kutateladze T.G.
Molecular basis of phosphatidylinositol 4-phosphate and ARF1 GTPase recognition by the FAPP1 pleckstrin homology (PH) domain.
Journal of Biological Chemistry, 286(21):18650-18657 (May, 2011). PubMed
Kamada R., Nomura T., Anderson C.W., and Sakaguchi K.
Cancer-associated p53 tetramerization domain mutants: Quantitative analysis reveals a low threshold for tumor suppressor inactivation.
Journal of Biological Chemistry, 286(1):252-258 (January, 2011). PubMed
Kamat S.S., Bagaria A., Kumaran D., Holmes-Hampton G.P., Fan H., Sali A., Sauder J.M., Burley S.K., Lindahl P.A., Swaminathan S., and Raushel F.M.
Catalytic mechanism and three-dimensional structure of adenine deaminase.
Biochemistry, 50(11):1917-1927 (March, 2011). PubMed
Kamat S.S., Holmes-Hampton G.P., Bagaria A., Kumaran D., Tichy S.E., Gheyi T., Zheng X., Bain K., Groshong C., Emtage S., Sauder J.M., Burley S.K., Swaminathan S., Lindahl P.A., and Raushel F.M.
The catalase activity of diiron adenine deaminase.
Protein Science, 20(12):2080-2094 (December, 2011). PubMed
Keister J.W., Smedley J., Muller E.M., Bohon J., and Heroux A.
Diamond X-ray photodiode for white and monochromatic SR beams.
Nuclear Instruments and Methods in Physics Research A: Accelerators, Spectrometers, Detectors and Associated Equipment, 649(1):91-93 (September, 2011). PubMed
Kumari S.S., Eswaramoorthy S., Mathias R.T., and Varadaraj K.
Unique and analogous functions of aquaporin O for fiber cell architecture and ocular lens transparency.
Biochimica et Biophysica Acta 1812(9):1089-1097 (September, 2011). PubMed
Lebel E.A., Rusek A., Sivertz M.B., Yip K., Thompson K.H., and Tafrov S.T.
Analyses of the secondary particle radiation and the DNA damage it causes to human keratinocytes.
Journal of Radiation Research, 52(6):685-693 (November, 2011). PubMed
Li L.-L., Taghavi S., McCorkle S.M., Zhang Y.-B., Blewitt M.G., Brunecky R., Adney W.S., Himmel M.E., Brumm P., Drinkwater C., Mead D.A., Tringe S.G., and van der Lelie D.
Bioprospecting metagenomics of decaying wood: Mining for new glycoside hydrolases.
Biotechnology for Biofuels, 4(1):23 (August 2011). PubMed
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., Miao Y.C., and Zhang K.W.
Sequestration and transport of lignin monomeric precursors.
Molecules, 16(1):710-727 (January, 2011). PubMed
Livey I., O’Rourke M., Traweger A., Savidis-Dacho H., Crowe B.A., Barrett P.N., Yang X, Dunn J.J., and Luft B.J.
A new approach to a lyme disease vaccine.
Clinical Infectious Diseases,52(3):s266-s270 (February, 2011). PubMed
Lu S., Zhao H., Parsons E.P.,Xu C., Kosma D.K., Xu X., Chao D., Lohrey G., Bangarusamy D.K., Wang G., Bressan R.A., and Jenks M.A.
The glossyhead1 allele of ACC1 reveals a principal role for multidomain acetyl-coenzyme A carboxylase in the biosynthesis of cuticular waxes by Arabidopsis.
Plant Physiology, 157(3):1079-1092 (November, 2011). 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, doi: 10.1002/cbic.201100585 (in press) (epub Nov. 23, 2011). PubMed
Mace P.D., Wallez Y., Dobaczewska M.K., Lee J.J., Robinson H., Pasquale E.B., and Riedl S.J.
NSP-Cas protein structures reveal a promiscuous interaction module in cell signaling.
Nature Structural & Molecular Biology (in press) doi: 10.1038/nsmb.2152 (epub Nov. 13, 2011). PubMed
Matilla M.A., Pizarro P., Roca A., Fernández M., Duque E., Molina L., van der Lelie D., Gómez M., Segura A., and Ramos J.-L.
Complete genome of the plant growth-promoting rhizobacterium Pseudomonas putida BIRD-1.
Journal of Bacteriology,193(5):1290 (March, 2011). PubMed
Miloslavina Y., Lambrev P.H., Javorfi T., Varkonyi Z., Wall J.S., Hind G., and Garab G.
Anisotropic circular dichroism signatures of oriented thylakoid membranes and lamellar aggregates of LHCII.
Photosynthesis Research, 1-11 (in press) (epub June 12, 2011). PubMed
Naidu M.D., Agarwal R., Pena L.A., Cunha L., Mezei M., Shen M., Wilson III D.M., Sanchez Z., and Waring M.J.
Lucanthone and its derivative Hycanthone inhibit Apurinic Endonuclease-1 (APE1) by direct protein binding.
PLoS ONE 6(9):e23679 (September, 2011). PubMed
Orville A.M., Buono R., Cowan M., Heroux A., Shea-McCarthy G., Schneider D.K., Skinner J.M., Skinner M.J., Stoner-Ma D., and Sweet R.M.
Correlated single-crystal electronic absorption spectroscopy and X-ray crystallography at NSLS beamline X26-C.
Journal of Synchrotron Radiation, 18(Pt 3):358-366 (May, 2011). PubMed
Phan G., Remaut H., Wang T., Allen W.J., Pirker K.F., Lebedev A., Henderson N.S., Geibel S., Volkan E., Yan J., Kunze M.B., Pinkner J.S., Ford B., Kay C.W., Li H., Hultgren S.J., Thanassi D.G., and Waksman G.
Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate.
Nature, 474(7349):49-53 (June, 2011). PubMed
Polewski K., Zinger D., Trunk J., and Sutherland J.C.
Ultraviolet absorption and luminescence of matrix-isolated adenine.
Radiation Physics and Chemistry 80(10): 1092-1098 (October, 2011).
Ravindran P.P., Heroux A., and Ye J.-D.
Improvement of the crystallizability and expression of an RNA crystallization chaperone.
Journal of Biochemistry 150(5): 535-543 (November, 2011). 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 (in press) (epub Sept. 8, 2011). PubMed
Salameh M.A., Soares A.S., Hockla A., Radisky D.C., and Radisky E.S.
The P2’ residue is a key determinant of mesotrypsin specificity: Engineering a high-affinity inhibitor with anticancer activity.
Biochemical Journal 440(1): 95-105 (November, 2011). PubMed
Schluter P.M., Xu S., Gagliardini V., Whittle E.J., Shanklin J., Grossniklaus U., and Schiestl F.P.
Stearoyl-ACP desaturases are associated with floral isolation in sexually deceptive orchids.
Proceedings of the National Academy of Sciences USA 108(14): 5696-5701 (April, 2011). PubMed
Schutzer S.E., Fraser-Liggett C.M., Casjens S.R., Qiu W.G., Dunn J.J., Mongodin E.F, and Luft B.J.
Whole-genome sequences of thirteen isolates of Borrelia burgdorferi.
Journal of Bacteriology, 193(4):1018-1020 (February, 2011). PubMed
Schwender J.
Experimental flux measurements on a network scale.
Frontiers in Plant Physiology 2(63): 1-7 (October, 2011).
Scotto-Lavino E., Bai M., Zhang Y.-B., and Freimuth P.
Export is the default pathway for soluble unfolded polypeptides that accumulate during expression in Escherichia coli.
Protein Expression and Purification, 79(1):137-141 (September, 2011). PubMed
Senthil Kumar V.S., O’Neall-Hennessey E., Reshetnikova L., Brown J.H., Robinson H., Szent-Gyorgyi A.G., and Cohen C.
Crystal structure of a phosphorylated light chain domain of scallop smooth-muscle Myosin.
Biophysical Journal, 101(9):2185-2189 (November, 2011). PubMed
Sethi D.K., Schubert D.A., Anders A.K., Heroux A., Bonsor D.A., Thomas C.P., Sundberg E.J., Pyrdol J., and Wucherpfennig K.W.
A highly tilted binding mode by a self-reactive T cell receptor, results in altered engagement of peptide and MHC.
Journal of Experimental Medicine, 208(1):91-102 (January, 2011). PubMed
Sheng J., Hassan A.E., Zhang W., Zhou J., Xu B., Soares A.S., and Huang Z.
Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization.
Nucleic Acids Research, 39(9):3962-3971 (May, 2011). PubMed
Shi J., Tan H., Yu X.-H., Liu Y., Liang W., Ranathunge K., Franke R.B., Schreiber L., Wang Y., Kai G., Shanklin J., Ma H., and Zhang D.
Defective Pollen Wall is required for anther and microspore development in rice and encodes a fatty acyl carrier protein reductase.
Plant Cell, 23(6):2225-2246 (June, 2011). PubMed
Soares A.S., Engel M.A., Stearns R., Datwani S., Olechno J., Ellson R., Skinner J.M., Allaire M., and Orville A.M.
Acoustically mounted microcrystals yield high resolution x-ray structures.
Biochemistry, 50(21):4399-4401 (May, 2011). PubMed
Stadler A.L., Sun D., Maye M.M., van der Lelie D., and Gang O.
Site-selective binding of nanoparticles of double-stranded DNA via PNA ‘invasion’.
ACS NANO, 5(4):2467-2474 (April, 2011). PubMed
Stisova V., Abele W.H., Thompson K.H., Bennett P.V., and Sutherland B.M.
Response of primary human fibroblasts exposed to solar particle event protons.
Radiation Research 176(2): 217-225 (August, 2011). PubMed
Stoner-Ma D., Skinner J.M., Schneider D.K., Cowan M., Sweet R.M., and Orville A.M.
Single-crystal Raman spectroscopy and x-ray crystallography at beamline X26-C of the NSLS.
Journal of Synchrotron Radiation, 18(1):37-40 (January, 2011). PubMed
Suttisansanee U., Lau K., Lagishetty S., Rao K.N., Swaminathan S., Sauder J.M., Burley S.K., and Honek J.F.
Structural variation in bacterial glyoxalase I enzymes: Investigation of the metalloenzyme glyoxalase I from Clostridium acetobutylicum.
Journal of Biological Chemistry, 286(44):38367-38374 (November, 2011). PubMed
Sutherland J.C.
Measurement of the circular dichroism of electronic transitions.
Advances in Chiroptical Methods, N. Berova, P. Poiavarapu, K. Nakanishi, and R. W. Woody, Editors, John Wiley & Sons, Inc., Hoboken, NJ (in press).
Swaminathan S.
Molecular structures and functional relationships in clostridial neurotoxins.
FEBS Journal 278(23): 4467-4485 (December, 2011). PubMed
Taghavi S., Weyens N., Vangronsveld J., and van der Lelie D.
Improved phytoremediation of organic contaminants through engineering of bacterial endophytes of trees.
Endophytes of Forest Trees: Biology and Applications, Forestry Sciences Series, 1st Edition, A. M. Pirttila and A. C. Frank, Editors, Vol. 80, Chapter 13, Springer Science + Business Media, LLC, New York, NY (August, 2011).
Thomas M.F., Li L.L., Handley-Pendleton J.M., van der Lelie D., Dunn J.J., and Wishart J.F.
Enzyme activity in dialkyl phosphate ionic liquids.
Bioresource Technology, 102(24):11200-11203 (December, 2011). PubMed
Truschel S.T., Sengupta D., Foote A., Heroux A., Macbeth M.R., Linstedt A.D.
Structure of the membrane-tethering GRASP domain reveals a unique PDZ ligand interaction that mediates Golgi biogenesis.
Journal of Biological Chemistry, 286(23):20125-20129 (June, 2011). PubMed
Wallace B.A., Gekko K., Hoffmann S.V., Lin Y.-H., Sutherland J.C., Tao Y., Wien F., and Janes R.W.
Synchrotron radiation circular dichroism (SRCD) spectroscopy: An emerging method in structural biology for examining protein conformations and protein interactions.
[Conference Paper: 16th Pan-American Synchrotron Radiation Instrumentation Conference, Argonne National Laboratory, September 21-24, 2010.] Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 649(1):177-178 (September, 2011).
Wei H., Wang Z., Zhang J., House S., Gao Y. G., Yang L., Robinson H., Tan L. H., Xing H., Hou C., Robertson I.M., Zuo J.M., and Lu Y.
Time-dependent, protein-directed growth of gold nanoparticles within a single crystal of lysozyme.
Nature Nanotechnology, 6(2):93-97 (February, 2011). PubMed
Weyens N., Boulet J., Adriaensen D., Timmermans J.-P., Prinsen E., Van Oevelen S., D’Haen J., Smeets K., van der Lelie D., Taghavi S., and Vangronsveld J.
Colonization and plant growth promoting capacity of the endophyte Pseudomonas putida W619 in hybrid poplar.
Plant Biology (in press).
Weyens N., Truyens S., Saenen E., Boulet J., Dupae J., Taghavi S., van der Lelie D., Carleer R., and Vangronsveld J.
Endophytes and their potential to deal with co-contamination of organic contaminants (toluene) and toxic metals (nickel) during phytoremediation.
Intl. J. Phytoremed., 13(3):244-255 (March, 2011). PubMed
Whitney J.C., Hay I.D., Li C., Eckford P.D.W., Robinson H., Amaya M.F., Wood L.F., Ohman D.E., Bear C.E., Rehm B.H., and Howell P.L.
Structural basis for alginate secretion across the bacterial outer membrane.
Proceedings of the National Academy of Sciences USA, 108(32):13083-13088 (August, 2011).
Wu X., Monchy S., Taghavi S., Zhu W., Ramos J., and van der Lelie D.
Comparative genomics and functional analysis of niche-specific adaptation of Pseudomonas putida.
FEMS Microbiology Reviews, 35(2):299-323 (March, 2011). PubMed
Yu X.-H., Rawat R., and Shanklin J.
Characterization and analysis of the cotton cyclopropane fatty acid synthase family and their contribution to cyclopropane fatty acid synthesis.
BMC Plant Biology, 11:97 (May, 2011). PubMed
Zhai Q., Landesman M.B., Robinson H., Sundquist W.I., and Hill C.P.
Identification and structural characterization of the ALIX-binding late domains of simian immunodeficiency virus SIV_mac239 and _SIVagmTan-1.
Journal of Virology 85(1): 632-637 (January, 2011). PubMed
Zhang Y., Buchko G.W., Qin L., Robinson H., and Varnum, S.M.
Crystal structure of the receptor binding domain of the botulinum C-D mosaic neurotoxin reveals potential roles of lysines 1118 and 1136 in member interactions.
Biochemical and Biophysical Research Communications, 404(1):407-412 (January, 2011). PubMed
Zhang Z., Zhou R., Sauder J.M., Tonge P.J., Burley S.K., and Swaminathan S.
Sructural and functional studies of fatty acyl-adenylate ligases from E. coli and L. pneumophila.
Journal of Molecular Biology, 406(2):313-324 (February, 2011). PubMed

Last Modified: December 1, 2011
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