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Biology Department 2009 Publications

Agarwal R., Schmidt J.J., Stafford R.G., and Swaminathan S.
Mode of VAMP substrate recognition and inhibition of Clostridium botulinum neurotoxin F.
Nature Structural and Molecular Biology, 16:789-794 (2009). PubMed
Anderson C.W., and Appella E.
Signaling to the p53 tumor suppressor through pathways activated by genotoxic and non-genotoxic stresses.
Handbook of Cell Signaling 2^nd Edition, R.A. Bradshaw and E.A. Dennis, Editors, Vol. 3, Chapter 264, pp. 2185-2204, Oxford: Academic Press (September 2009).
Appella E. and Anderson C.W.
Dynamic protein interactions in complex networks.
FEMS Journal 276(19): 5380 (October, 2009). PubMed
Badri D.V., Weir T.L., van der Lelie, D., and Vivanco J.M.
Rhizosphere chemical dialogues: plant-microbe interactions.
Current Opinion in Biotechnology (in press).
Barac T., Weyens N., Oeyen L., Taghavi S., van der Lelie D., Dubin D., Spliet M., and Vangronsveld J.
Field Note: Hydraulic containment of a BTEX plume using poplar trees.
International Journal of Phytoremediation, 11(5):416-424 (July, 2009).
Bera A.K., Atanasova V., Robinson H., Eisenstein E., Coleman J.P., Pesci E. C., and Parsons J.F.
Structure of PqsD, a Pseudomonas quinolone signal biosynthetic enzyme, in complex with anthranilate.
Biochemistry, 48(36):8644-8655 (September, 2009). PubMed
Bernhards R.C., Jing X., Vogelaar N.J., Robinson H., and Schubot F.D.
Structural evidence suggests that antiactivator EXsD from Pseudomonas aeruginosa is a DNA binding protein.
Protein Science, 18(3):503-513 (March, 2009). PubMed
Bewley M.C., Graziano V., Griffin K., and Flanagan J.M.
Turned on for degradation ATPase-independent degradation by ClpP.
Journal of Structural Biology, 165(2):118-125 (February, 2009). PubMed
Bhuiya M.W. and Liu C.-J.
A cost-effective colorimetric assay for phenolic O methyltransferases and characterization of caffeate 3-O-methyltransferases from Populus trichocarpa.
Analytical Biochemistry, 384(1): 151-158 (January, 2009). PubMed
Bhuiya M.W. and Liu C.-J.
Engineering monolignol 4-O-methyltransferases to modulate lignin biosynthesis.
Journal of Biological Chemistry (in press).
Brandao T. A. S., Robinson H., Johnson S.J., and Hengge A.C.
Impaired acid catalysis by mutation of a protein loop hinge residue in a YopH mutant revealed by crystal structures.
Journal of the American Chemical Society, 131(2):778-786 (January, 2009). PubMed
Buchko G.W., Robinson H., and Addlagatta A.
Structural characterization of the protein cce_0567 from Cyanothece 51142, a metalloprotein associated with nitrogen fixation in the DUF683 family.
Biochimica et Biophysica Acta ,1794(4):627-633 (April, 2009). PubMed
Daegelen P., Studier F.W., Lenski R. E., Cure S., and Kim J.F.
Tracing ancestors and relatives of Escherichia coli B, and the derivation of B strains REL606 and BL21(DE3).
Journal of Molecular Biology (in press).
Gallagher D.T., Smith N., Kim S.-K., Robinson H., and Reddy P.T.
Profound asymmetry in the structure of the cAMP-free cAMP receptor protein (CRP) from Mycobacterium tuberculosis.
Journal of Biological Chemistry, 284(13):8228-8232 (March, 2009). PubMed
Gallagher D.T., Smith N.N., Kim S.-K., Robinson H., and Reddy P.T.
Protein crystal engineering of YpAC-IV using a strategy of excess charge reduction.
Crystal Growth & Design, 9(8):3570-3574 (August, 2009).
Gelinas A.D., Paschini M., Reyes F.E., Heroux A., Batey R.T., Lundblad V., and Wuttke D.S.
Telomere capping proteins are structurally related to RPA with an additional telomere-specific domain. Proceedings of the National Academy of Sciences USA (in press).
Gnatenko D.V., Dunn J.J., Schwedes J., and Bahou W.F.
Transcript profiling of human platelets using microarray and serial analysis of gene expression (SAGE).
DNA and RNA Profiling in Human Blood, P. Bugert, Editor, Chapter 16, Vol. 496, pp. 245-272, Humana Press Inc., Totowa, NJ (January, 2009).
Gou J.-Y., Yu X.-H., and Liu C.-J.
A hydroxycinnamoyltransferase responsible for synthesizing suberin aromatics in Arabidopsis.
Proceedings of the National Academy of Sciences USA (in press).
Han Q., Robinson H., Cai T., Tagle D.A., and Li J.
Biochemical and structural properties of mouse kynurenine aminotransferase III.
Molecular and Cellular Biology, 29(3):784-793 (February, 2009). PubMed
Han Q., Robinson H., Cai T., Tagle D.A., and Li J.
Structural insight into the inhibition of human kynurenine aminotransferase I/glutamine transaminase K.
Journal of Medicinal Chemistry, 52(9):2786-2793 (May, 2009). PubMed
Harada Y., Li Hua, Li H., and Lennarz W.J.
Oligosaccharyltransferase directly binds to ribosome at a location near the translocon-binding site.
Proceedings of the National Academy of Sciences USA, 106(17):6945-6949 (April, 2009). PubMed
Hayashi M.K., Tang C., Verpelli C., Narayanan R., Stearns M.H., Xu R.-M., Li H., Sala C., and Hayashi Y.
The postsynaptic density proteins Homer and Shank form a polymeric network structure.
Cell, 137(1):159-171 (April, 2009). PubMed
Heroux A., Bozinovski D.M., Valley M.P., Fitzpatrick P.F., and Orville A.M.
Crystal structures of intermediates in the nitroalkane oxidase reaction.
Biochemistry, 48(15):3407-3416 (April, 2009). PubMed
Hodgkinson J.L., Horsley A., Stabat D., Simon M., Johnson S., da Fonseca P.C., Morris E.P., Wall J.S., Lea S.M., and Blocker A.J.
Three-dimensional reconstruction of the Shigella T3SS transmembrane regions reveals 12-fold symmetry and novel features throughout.
Nature Structural and Molecular Biology 16(5): 477-485 (May, 2009). (News & Views: Waksman, G. Going round in circles: The structural biology of type III secretion systems.
Nature Structural & Molecular Biology, 16(5):459-460 (May, 2009). PubMed
Honda M., Wang R., Kong W.-P., Kanekiyo M., Akahata W., Xu L., Matsuo K., Natarajan K., Robinson H., Asher T.E., Price D.A., Douek D.C., Margulies D.H., and Nabel G.J.
Different vaccine vectors delivering the same antigen elicit CD8+ T cell responses with distinct clonotype and epitope specificity.
Journal of Immunology, 183(4):2425-2434 (August, 2009). PubMed
Inada H., Wu L., Wall J., Su D., and Zhu Y.
Performance and image analysis of the aberration corrected Hitachi HD-2700C STEM.
J. Electron Microscopy, 58(3):111-122 (June, 2009). PubMed
Ivanova M.I., Sievers S.A., Sawaya M.R., Wall J.S., and Eisenberg D.
Molecular basis for insulin fibril assembly.
Proceedings of the National Academy of Sciences USA (accepted).
Jeong H., Barbe V., Lee C.H., Vallenet D., Yu D.-S., Choi S.-H., Couloux A., Lee S.-W., Yoon S.H., Cattolico L., Hur C.-G., Park H.-S., Segurens B., Kim S.C., Oh T.K., Lenski R.E., Studier F.W., Daegelen P., and Kim J.F.
Genome sequences of Escherichia coli B strains REL606 and BL21(DE3).
Journal of Molecular Biology (in press).
Kumaran D., Eswaramoorthy S., Furey W., Navaza J., Sax M., and Swaminathan S.
Domain organization in Clostridium botulinum neurotoxin type E is unique: Its implication in faster translocation.
Journal of Molecular Biology, 386(1):233-245 (February, 2009). PubMed
Latimer R., Podzelinska K., Soares A., Bhattacharya A., Vining L.C., Jia Z., and Zechel D.L.
Expression, purification and preliminary diffraction studies of CmlS.
Acta Crystallographica Section F: Structural Biology and Crystallography Communications, F65 (Pt. 3):260-263 (March, 2009). PubMed
Lee S.-K., Maye M.M., Zhang Y.-B., Gang O., and van der Lelie D.
Controllable g5p-protein-directed aggregation of ssDNA-gold nanoparticles.
Langmuir, 25(2):657-660 (January, 2009). PubMed
Li H., and Thanassi D.G.
Use of a combined cryo-EM and X-ray crystallography approach to reveal molecular details of bacterial pilus assembly by the chaperone/usher pathway.
Current Opinion in Microbiology, 12(2):326-332 (June, 2009). PubMed
Li H., Wolfe M.S., and Selkoe D.J.
Toward structural elucidation of the γ-secretase complex.
Structure, 17(3):326-334 (March, 2009). PubMed
Li L.-L., McCorkle S.R., Monchy S., Taghavi S., and van der Lelie D.
Bioprospecting metagenomes: Glycosyl hydrolases for converting biomass. (Review).
Biotechnology for Biofuels, 2(1):10 (May, 2009). PubMed
Li Y., Cao C., Jia W., Yu L., Mo M., Wang Q., Huang Y., Lim J.-M., Ishihara M., Wells L., Azadi P., Robinson H., He Y.-W., Zhang L., and Mariuzza R.A.
Structure of the F-spondin domain of mindin, an integrin ligand and pattern recognition molecule.
EMBO Journal, 28(3):286-297 (January, 2009). PubMed
Lin G., Li D., Sorio de Carvalho L.P., Deng H., Tao H., Vogt G., Wu K., Schneider J., Chidawanyika T., Warren J.D., Li H., and Nathan C.
Inhibitors selective for mycobacterial versus human proteasomes.
Nature, 461(7264):621-626 (October, 2009). PubMed
Lonien J., and Schwender J.
Analysis of metabolic flux phenotypes for two Arabidopsis thaliana mutants with severe impairment in seed storage lipid synthesis.
Plant Physiology, 151(3):1617-1634 (2009). PubMed Plant Physiology
Lu M., Chai J., and Fu D.
Structural basis for autoregulation of the zinc transporter YiiP.
Nature Structural & Molecular Biology, 16(10):1063-1067 (October, 2009). PubMed
Major D.T., Heroux A., Orville A.M., Valley M.P., Fitzpatrick P.F., and Gao J.
Differential quantum tunnel contributions in the proton transfer reaction catalyzed by nitroalkane oxidase and the uncatalyzed reaction in aqueous solution.
Proceedings of the National Academy of Sciences USA (accepted).
Makhov A.M., Sen A., Yu X., Simon M.N., Griffith J.D., and Egelman E.H.
The bipolar filaments formed by herpes simplex virus type 1 SSB/recombination protein (ICP8) suggest a mechanism for DNA annealing.
Journal of Molecular Biology, 386(2):273-279 (February, 2009). PubMed
Marshall N.M., Garner D.K., Wilson T.D., Gao Y.-G., Robinson H., Nilges M.J., and Lu Y.
Rationally tuning the reduction potential of a single cupredoxin beyond the natural range.
Nature, 462(7269):113-116 (November, 2009). PubMed
Mastretta C., Taghavi S., van der Lelie D., Mengoni A., Galardi F., Gonnelli C., Barac T., Boulet J., Weyens N., and Vangronsveld J.
Endophytic bacteria from seeds of Nicotiana tabacum can reduce cadmium phytotoxicity.
International Journal of Phytoremediation, 11(3):251-267 (March, 2009).
Maye M.M., Nykypanchuk D., Cuisinier M., van der Lelie D., and Gang O.
Stepwise surface encoding for high-throughput assembly of nanoclusters.
Nature Materials 8: 388-391 (May, 2009). [News & Views: Prabhu, V. M. and Hudson, S. D. Nanoparticle assembly: DNA provides control. Nature Materials, 8:365-366 (May, 2009)] PubMed
Meek D.W. and Anderson C.W.
Posttranslational modification of p53: Cooperative integrators of function.
Cold Spring Harbor Perspectives in Biology, Volume on The p53 Family, A. J. Levine and D. Lane, Editors, Cold Spring Harbor Laboratory Press (in press).
Nguyen H.T. and Shanklin J.
Altering Arabidopsis oilseed composition by a combined antisense-hairpin RNAi gene suppression approach.
Journal of the American Oil Chemists Society, 86:41-49 (January, 2009).
Orville A.M., Lountos G.T., Finnegan S., Gadda G., and Prabhakar R.
Crystallographic, spectroscopic, and computational analysis of a flavin-C4a-oxygen adduct in choline oxidase.
Biochemistry, 48(4):720-728 (February, 2009). PubMed
Osenkowski P., Li Hua, Ye W., Li Dongyang, Aeschbach L., Fraering P.C., Wolfe M.S., Selkoe D.J., and Li H.
Cryoelectron microscopy structure of purified gamma-secretase at 12 Å resolution.
Journal Molecular Biology, 385(2):642-652 (January, 2009). PubMed
Perez-Berna A.J., Marabini R., Scheres S.H.W., Menendez-Conejero R., Dmitriev I.P., Curiel D.T., Mangel W.F., Flint S.J., and San Martin C.
Structure and uncoating of immature adenovirus.
Journal of Molecular Biology 392(2): 547-557 (September, 2009). PubMed
Pieper U., Chiang R., Seffernick J.J., Brown S.D., Glasner M.E., Kelly L., Eswar N., Sauder J.M., Bonanno J.B., Swaminathan S., Burley S.K., Zheng X., Chance M.R., Almo S.C., Gerlt J.A., Raushel F.M., Jacobson M.P., Babbitt C., and Sali A.
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
Journal of Structural Functional Genomics, 10(2):107-125 (April, 2009). PubMed
Puglin N. and Schneider D.
MX frontiers at the one micron scale: Making the case for micro-beams.
Synchrotron Radiation News 22(5): 41-43 (September/October, 2009).
Ragumani S., Sauder J.M., Burley S.K., and Swaminathan S.
Structural studies on cytosolic domain of magnesium transporter MgtE from Enterococcus faecalis.
PROTEINS: Structure, Function, Bioinformatics (in press).
Ryan R.P., Monchy S., Cardinale M., Taghavi S., Crossman L., Avison M.B., Berg G., van der Lelie D., and Dow J.M.
Versatility and adaptation of bacteria from the genus Stenotrophomonas.
Nature Reviews in Microbiology, 7(7):514-525 (July, 2009). PubMed
Schwender J., Editor.
Plant Metabolic Networks, 334 p., Springer Science + Business Media, LLC, New York (June, 2009).
Schwender J.
Introduction. Plant Metabolic Networks, J. Schwender, Editor, Chapter 1, pp. 1-7, Springer Science + Business Media, LLC, New York (June, 2009).
Schwender J.
Isotopic steady state flux analysis.
Plant Metabolic Networks, J. Schwender, Editor, Chapter 9, pp. 245-284, Springer Science + Business Media, LLC, New York (June, 2009).
Schwender J.
Kinetic properties of metabolic networks.
Plant Metabolic Networks, J. Schwender, Editor, Chapter 11, pp. 307-322, Springer Science + Business Media, LLC, New York (June, 2009).
Scott F.L., Stec B., Pop C., Dobaczewska M.K., Lee J.J., Monosov E., Robinson H., Salvesen G.S., Schwarzenbacher R., and Riedl S.J.
The Fas-FADD death domain complex structure unravels signaling by receptor clustering.
Nature, 457(7232):1019-1022 (February, 2009). PubMed

Shanklin J., Guy J.E., Mishra G., and Lindqvist Y.
Desaturases: Emerging models for understanding functional diversification of diiron-containing enzymes.
Journal of Biological Chemistry 284(28): 18559-18563 (July, 2009).
Cover: View down the four-helix bundle to the dirron active site of the castor desaturase mutant T199D, which displays decreased desaturation activity and increased oxidase functionality consistent with that of its hypothesized ancestor. The non-coordinating residue on the lower left is Asp199. For details see the article by Shanklin et al., pages 18559-18563. PubMed
Stadtmueller B.M., Ferrell K., Whitby F.G., Heroux A., Robinson H., Myszka D.G., and Hill C.P.
Structural models for interactions between the 20S proteasome and its PAN/19S activators.
Journal of Biological Chemistry (in press).
Studier F.W., Daegelen P., Lenski R.E., Maslov S., and Kim J.F.
Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3), and comparison of the E. coli B and K-12 genomes.
Journal of Molecular Biology (in press).
Sutherland J.C.
Measurement of circular dichroism and related spectroscopies with conventional and synchrotron light sources: Theory and instrumentation.
Advances in Biomedical Spectroscopy, Vol. 1: Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy, B. A. Wallace and R. W. Janes, Editors, pp. 19-72, IOS Press, Amsterdam, The Netherlands (June, 2009).
Swaminathan S.
Molecular structures and functional relationships of botulinum neurotoxins.
Botulinum Toxin: Therapeutic Clinical Practice and Science, J. Jankovic, A. Albanese, M. Z. Atassi, J. O. Dolly, M. Hallett, and N. H. Mayer, Editors, Chapter 2, pp. 15-29, Saunders Elsevier Inc., Philadelphia, PA (February, 2009).
Taghavi S., Garafola C., Monchy S., Newman L., Hoffman A., Weyens N., Barac T., Vangronsveld J., and van der Lelie D.
Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees.
Applied and Environmental Microbiology, 75(3):748-757 (February, 2009). PubMed
Taghavi S., Lesaulnier C., Monchy S., Wattiez R., Mergeay M., and van der Lelie D.
Lead(II) resistance in Cupriavidus metallidurans CH34: Interplay between plasmid and chromosomally-located functions.
Antonie van Leeuwenhoek ,96(2):171-182 (August, 2009). PubMed
van der Lelie D., Taghavi S., Monchy S., Schwender J., Miller L., Ferrieri R., Rogers A., Wu X., Zhu W., Weyens N., Vangronsveld J., and Newman L.
Poplar and its bacterial endophytes: Coexistence and harmony.
Critical Reviews in Plant Sciences, 28(5):346-358 (September, 2009).
Vangronsveld J., Herzig R., Weyens N., Boulet J., Adriaensen K., Ruttens A., Thewys T., Vassilev A., Meers E., Nehnevajova E., van der Lelie D., and Mench M.
Phytoremediation of contaminated soils and groundwater: Lessons from the field.
Environmental Science and Pollution Research International (in press).
Wall J.S., Simon M.N., and Hainfeld J.F.
History of the STEM at BNL. Advances in Imaging & Electron Physics, P. W. Hawkes, Editor, Vol. 158, Elsevier Academic Press, U.K. (accepted).
Wang T., Li Hua, Lin G., Tang C., Li D., Nathan C., Darwin K.H., and Li Huilin.
Structural insights on the Mycobacterium tuberculosis proteasomal ATPase Mpa.
Structure, 17(10):1377-1385 (October, 2009). PubMed
Wang H., Liu S., Zhang P., Zhang S., Naidu M.D., Wang H., and Wang Y.
S-phase cells are more sensitive to high-linear energy transfer radiation.
International Journal of Radiation Oncology, Biology, Physics, 74(4):1236-1241 (July, 2009). PubMed
Weyens N., van der Lelie D., Taghavi S., Newman L., and Vangronsveld J.
Exploiting plant-microbe partnerships to improve biomass production and remediation.
Trends in Biotechnology, 27(10):591-598 (October, 2009). PubMed
Weyens N., Taghavi S., Barac T., van der Lelie D., Boulet J., Artois T., Carleer R., and Vangronsveld J.
Bacterial associated with oak and ash on a TCE-contaminated site: Characterization of isolates with potential to avoid evapotranspiration of TCE.
Environ Sci Pollut Res Int. 2009 Apr 25. [Epub ahead of print] PubMed
Weyens N., van der Lelie D., Taghavi S., and Vangronsveld J.
Phytoremediation: Plant-endophyte partnerships take the challenge.
Current Opinion in Biotechnology, 20(2):248-254 (April, 2009). PubMed
Woo J.-S., Lim J.-H., Shin H.-C., Suh M.-K., Ku B., Lee K.-H., Joo K., Robinson H., Lee J., Park S.-Y., Ha N.-C., and Oh B.-H.
Structural studies of a bacterial condensin complex reveal ATP-dependent disruption of intersubunit interactions.
Cell, 136(1):85-96 (January, 2009). PubMed
Xiang D.F., Xu C., Kumaran D., Brown A. C., Sauder J.M., Burley S. K., Swaminathan S., and Raushel F. M.
Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes.
Biochemistry, 48(21):4567-4576 (April, 2009). PubMed
Xiong H., van der Lelie D., and Gang O.
Phase behavior of nanoparticles assembled by DNA linkers.
Physical Review Letters, 102:015504-1 to -4 (January, 2009). PubMed
Yu X.-H., Gou J.-Y., and Liu C.-J.
BAHD superfamily of acyl-CoA dependent acyltransferases in Populus and Arabidopsis: Bioinformatics and gene expression.
Plant Mol Biol., 70(4):421-442 (July, 2009). PubMed
Zhang Y., Cao R., Yin F., Hudock M.P., Guo R.-T., Krysiak K., Mukherjee S., Gao Y.-G., Robinson H., Song Y., No J.H., Bergan K., Leon A., Cas L., Goddard A., Chang T.-K., Lin F.-Y., Van Beek E., Papapoulos S., Wang A.H.-J., Kubo T., Ochi M., Mukkamala D., and Oldfield E.
Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl disphosphate synthase inhibitors: An x-ray and NMR investigation.
Journal of the American Chemical Society, 131(14):5153-5162 (April, 2009). PubMed
Zhang Y.-B., Monchy S., Greenberg B., Mergeay M., Gang O., Taghavi S., and van der Lelie D.
ArsR arsenic-resistance regulatory protein from Cupriavidus metallidurans CH34.
Antonie van Leeuwenhoek 96(2): 161-170 (August, 2009). PubMed
Zhao H., Heroux A., Sequeira R.D., and Tang L.
Preliminary crystallographic studies of the regulatory domain of response regulator YycF from an essential two-component signal transduction system.
Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 65(Pt 7):719-722 (July, 2009). PubMed
Zhu Y., Inada H., Nakamura K., and Wall J.
Imaging single atoms using secondary electrons with an aberration-corrected electron microscope.
Nature Materials 8(10): 808-812 (October, 2009). [News & Views: Joy, D. C. Scanning electron microscopy: Second best no more. Nature Materials 8(10): 776-777 (October, 2009)]. PubMed

Last Modified: November 18, 2009
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