Archive of Kirill's Paper of the Week - 2008

by Kirill Degtyarenko

Last modified: Fri Nov 28 14:02:02 GMT 2008

21 November 2008.

• Pompidor, G., Maillard, A.P., Girard, E., Gambarelli, S., Kahn, R. and Covès, J. (2008) X-ray structure of the metal-sensor CnrX in both the apo- and copper-bound forms. FEBS Lett. 582, 3954-3958.

14 November 2008.

• Jover, J., Bosque, R. and Sales, J. (2008) A comparison of the binding affinity of the common amino acids with different metal cations. Dalton Trans., 2008, no. 45, 6441-6453.

7 November 2008.

• Tucker, N.P., Hicks, M.G., Clarke, T.A., Crack, J.C., Chandra, G., Le Brun, N.E., Dixon, R. and Hutchings, M.I. (2008) The transcriptional repressor protein NsrR senses nitric oxide directly via a [2Fe-2S] cluster. PLoS ONE 3, e3623.

17 October 2008.

• Kannappan, B. and Gready, J.E. (2008) Redefinition of Rubisco carboxylase reaction reveals origin of water for hydration and new roles for active-site residues. J. Am. Chem. Soc. 130, 15063-15080.

10 October 2008.

• Palm, G.J., Lederer, T., Orth, P., Saenger, W., Takahashi, M., Hillen, W. and Hinrichs, W. (2008) Specific binding of divalent metal ions to tetracycline and to the Tet repressor/tetracycline complex. J. Biol. Inorg. Chem. 13, 1097-1110.

3 October 2008.

• Gold, B., Deng, H., Bryk, R., Vargas, D., Eliezer, D., Roberts, J., Jiang, X. and Nathan, C. (2008) Identification of a copper-binding metallothionein in pathogenic mycobacteria. Nature Chem. Biol. 4, 609-616.

26 September 2008.

• Strycharz, S.M., Woodard, T.L., Johnson, J.P., Nevin, K.P., Sanford, R.A., Löffler, F.E. and Lovley, D.R. (2008) Graphite electrode as a sole electron donor for reductive dechlorination of tetrachlorethene by Geobacter lovleyi. Appl. Environ. Microbiol. 74, 5943-5947.

19 September 2008.

• Kong, J.S., Sarshar, N. and Roychowdhury, V.P. (2008) Experience versus talent shapes the structure of the Web. Proc. Natl. Acad. Sci. USA 105, 13724-13729.

12 September 2008.

• Ousaka, N., Inai, Y. and Kuroda, R. (2008) Chain-terminus triggered chiral memory in an optically inactive 3₁₀-helical peptide. J. Am. Chem. Soc. 130, 12266-12267.

5 September 2008.

• Stoyanov, E.S., Stoyanova, I.V., Tham, F.S. and Reed, C.A. (2008) The nature of the hydrated proton H_(aq)⁺ in organic solvents. J. Am. Chem. Soc. 130, 12128-12138.

29 August 2008.

• Levin, E.J., Elsen, N.L., Seder, K.D., McCoy, J.G., Fox, B.G. and Phillips, G.N., Jr. (2008) X-ray structure of a soluble Rieske-type ferredoxin from Mus musculus. Acta Crystallogr. D64, 933-940.

15 August 2008.

• Kulp, T.R., Hoeft, S.E., Asao, M., Madigan, M.T., Hollibaugh, J.T., Fisher, J.C., Stolz, J.F., Culbertson, C.W., Miller, L.G. and Oremland, R.S. (2008) Arsenic(III) fuels anoxygenic photosynthesis in hot spring biofilms from Mono Lake, California. Science 321, 967-970.

8 August 2008.

• Reda, T., Plugge, C.M., Abram, N.J. and Hirst, J. (2008) Reversible interconversion of carbon dioxide and formate by an electroactive enzyme. Proc. Natl. Acad. Sci. USA 105, 10654-10658.

1 August 2008.

• Teixeira, J.E. and Huston, C.D. (2008) Evidence of a continuous endoplasmic reticulum in the protozoan parasite Entamoeba histolytica. Eukaryotic Cell 7, 1222-1226.

25 July 2008.

• Langkilde, A., Kristensen, S.M., Lo Leggio, L., Mølgaard, A., Jensen, J.H., Houk, A.R., Navarro Poulsen, J.-C., Kauppinen, S. and Larsen, S. (2008) Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase. Acta Crystallogr. D64, 851-863.

18 July 2008.

• Meyer, J.C., Girit, C.O., Crommie, M.F. and Zettl, A. (2008) Imaging and dynamics of light atoms and molecules on graphene. Nature 454, 319-322.

11 July 2008.

• Jormakka, M., Yokoyama, K., Yano, T., Tamakoshi, M., Akimoto, S., Shimamura, T., Curmi, P. and Iwata, S. (2008) Molecular mechanism of energy conservation in polysulfide respiration. Nature Structural & Molecular Biology 15, 730-737.

4 July 2008.

• Janowski, R., Auerbach-Nevo, T. and Weiss, M.S. (2008) Bacterioferritin from Mycobacterium smegmatis contains zinc in its di-nuclear site. Protein Science 17, 1138-1150.

27 June 2008.

• Bröring, M., Köhler, S. and Kleeberg, C. (2008) Norcorrole: observation of the smallest porphyrin variant with a N₄ core. Angewandte Chemie International Edition 47, 5658-5660.

20 June 2008.

• Darcy, I.K., Scharein, R.G. and Stasiak, A. (2008) 3D visualization software to analyze topological outcomes of topoisomerase reactions. Nucleic Acids Res. 36, 3515-3521.

13 June 2008.

• Pfoh, R., Laatsch, H. and Sheldrick, G.M. (2008) Crystal structure of trioxacarcin A covalently bound to DNA. Nucleic Acids Res. 36, 3508-3514.

6 June 2008.

• Aragão, D., Mitchell, E.P., Frazão, C.F., Carrondo, M.A. and Lindley, P.F. (2008) Structural and functional relationships in the hybrid cluster protein family: structure of the anaerobically purified hybrid cluster protein from Desulfovibrio vulgaris at 1.35 Å resolution. Acta Crystallogr. D64, 665-674.

30 May 2008.

• Long, J.A., Trinajstic, K., Young, G.C. and Senden, T. (2008) Live birth in the Devonian period. Nature 453, 650-652.

23 May 2008.

• Regulski, E.E., Moy, R.H., Weinberg, Z., Barrick, J.E., Yao, Z., Ruzzo, W.L. and Breaker, R.R. (2008) A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol. Microbiol. 68, 918-932.

16 May 2008.

• Maeda, K., Henbest, K.B., Cintolesi, F., Kuprov, I., Rodgers, C.T., Liddell, P.A., Gust, D., Timmel, C.R. and Hore, P.J. (2008) Chemical compass model of avian magnetoreception. Nature 453, 387-390.

2 May 2008.

• Muñoz, E. and Deem, M.W. (2008) Amino acid alphabet size in protein evolution experiments: better to search a small library thoroughly or a large library sparsely? PEDS 21, 311-317.

25 April 2008.

• Taglieber, A., Schulz, F., Hollmann, F., Rusek, M. and Reetz, M.T. (2008) Light-driven biocatalytic oxidation and reduction reactions: scope and limitations. ChemBioChem 9, 565-572.

18 April 2008.

• Haranczyk, M. and Gutowski, M. (2008) Visualization of molecular orbitals and the related electron densities. J. Chem. Theory Comput. 4, 689-693.

11 April 2008.

• Zou, P., Groves, M.R., Viale-Bouroncle, S.D. and Orué Lucana, D.O. (2008) Crystallization and preliminary characterization of a novel haem-binding protein of Streptomyces reticuli. Acta Crystallogr. F64.

28 March 2008.

• Hoff, B., Pöggeler, S. and Kück, U. (2008) Eighty years after its discovery, Fleming's Penicillium strain discloses the secret of its sex. Eukaryotic Cell 7, 465-470.

21 March 2008.

• Hiraki, T., Shibayama, N., Akashi, S. and Park, S.Y. (2008) Crystal structures of the clock protein EA4 from the silkworm Bombyx mori. J. Mol. Biol. 377, 630-635.

14 March 2008.

• Lima-Mendez, G., Van Helden, J., Toussaint, A. and Leplae, R. (2008) Reticulate representation of evolutionary and functional relationships between phage genomes. Mol. Biol. Evol. 25, 762-777.

7 March 2008.

• Xu, Y., Feng, L., Jeffrey, P.D., Shi, Y. and Morel, F.M.M. (2008) Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms. Nature 452, 56-61.

29 February 2008.

• Dokmanić, I., Šikić, M. and Tomić, S. (2008) Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination. Acta Crystallogr. D64, 257-263.

22 February 2008.

• Neumann, H., Peak-Chew, S.Y. and Chin, J.W. (2008) Genetically encoding N^ε-acetyllysine in recombinant proteins. Nature Chemical Biology 4, 232-234.

8 February 2008.

• von Canstein, H., Ogawa, J., Shimizu, S. and Lloyd, J.R. (2008) Secretion of flavins by Shewanella species and their role in extracellular electron transfer. Appl. Environ. Microbiol. 74, 615-623.

1 February 2008.

• Birzele, F., Csaba, G. and Zimmer, R. (2008) Alternative splicing and protein structure evolution. Nucleic Acids Res. 36, 550-558.

25 January 2008.

• Frith, M.C., Valen, E., Krogh, A., Hayashizaki, Y., Carninci, P. and Sandelin, A. (2008) A code for transcription initiation in mammalian genomes. Genome Res. 18, 1-12.

18 January 2008.

• Errami, M., Hicks, J.M., Fisher, W., Trusty, D., Wren, J.D., Long, T.C. and Garner, H.R. (2008) Déjà vu - a study of duplicate citations in Medline. Bioinformatics 24, 243-249.

11 January 2008.

• Kim, J.D., Ohta, T. and Tsujii, J. (2008) Corpus annotation for mining biomedical events from literature. BMC Bioinformatics 9, 10.

4 January 2008.

• Lemaster, D.M., Anderson, J.S., Wang, L., Guo, Y., Li, H. and Hernandez, G. (2008) NMR and X-ray analysis of structural additivity in metal binding site-swapped hybrids of rubredoxin. BMC Struct. Biol. 7, 81.

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