Archive of Kirill's Paper of the Week - 2005

by Kirill Degtyarenko

Last modified: Fri Jan 13 15:56:06 GMT 2006

30 December 2005.

Lauga, E., Diluzio, W.R., Whitesides, G.M. and Stone, H.A. (2006) Swimming in circles: Motion of bacteria near solid boundaries. Biophys. J. 90, 400-412.

Superimposed phase-contrast video microscopy images show E. coli cells swimming in circular trajectories near a glass surface

23 December 2005.

Ohtsuki, T., Manabe, T. and Sisido, M. (2006) Multiple incorporation of non-natural amino acids into a single protein using tRNAs with non-standard structures. FEBS Lett. 579, 6769-6774.

16 December 2005.

Mercogliano, C.P. and Derosier, D.J. (2006) Gold nanocluster formation using metallothionein: mass spectrometry and electron microscopy. J. Mol. Biol. 355, 211-223.

9 December 2005.

Shkrob, M.A., Yanushevich, Yu.G., Chudakov, D.M., Gurskaya, N.G., Labas, Yu.A., Poponov, S.Y., Mudrik, N.N., Lukyanov, S. and Lukyanov, K.A. (2005) Far-red fluorescent proteins evolved from a blue chromoprotein from Actinia equina. Biochem. J. 392, 649-654.

2 December 2005.

Dalhoff, C., Lukinavicius, G., Klimašauskas S. and Weinhold, E. (2005) Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases. Nature Chemical Biology 2, 31-32.

25 November 2005.

Ghosh, A., Wasbotten, I.H., Davis, W. and Swarts, J.C. (2005) Norcorrole and dihydronorcorrole: a predictive quantum chemical study. Eur. J. Inorg. Chem. (22), 4479-4485.

18 November 2005.

Shapiro, E., Lu, C. and Baneyx, F. (2005) A set of multicolored Photinus pyralis luciferase mutants for in vivo bioluminescence applications. PEDS 18, 581-587.

Escherichia coli cells expressing variants of the North American firefly luciferase luminesce in the orange and red regions of the visible spectrum while bacteria synthesizing the wild-type enzyme emit yellow-green light

11 November 2005.

Castellano, S., Lobanov, A.V., Chapple, C., Novoselov, S.V., Albrecht, M., Hua, D., Lescure, A., Lengauer, T., Krol, A., Gladyshev, V.N. and Guigó, R. (2005) Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family. Proc. Natl. Acad. Sci. USA 102, 16188-16193.

Expression pattern of the SelJ gene during development in zebrafish embryos

4 November 2005.

Croft, M.T., Lawrence, A.D., Raux-Deery, E., Warren, M.J. and Smith, A.G. (2005) Algae acquire vitamin B₁₂ through a symbiotic relationship with bacteria. Nature 438, 90-93.

21 October 2005.

Drzewiecka-Matuszek, A., Skalna, A., Karocki, A., Stochel, G. and Fiedor, L. (2005) Effects of heavy central metal on the ground and excited states of chlorophyll. J. Biol. Inorg. Chem. 10, 453-462. [Supplementary Material]

14 October 2005.

Bonanni, B., Kamruzzahan, A.S., Bizzarri, A.R., Rankl, C., Gruber, H.J., Hinterdorfer, P. and Cannistraro, S. (2005) Single molecule recognition between cytochrome C 551 and gold-immobilized azurin by force spectroscopy. Biophys. J. 89, 2783-2791.

MAC-Mode AFM image of AZ monolayer over Au(111) substrate

7 October 2005.

McLuskey, K., Cameron, S., Hammerschmidt, F. and Hunter, W.N. (2005) Structure and reactivity of hydroxypropylphosphonic acid epoxidase in fosfomycin biosynthesis by a cation- and flavin-dependent mechanism. Proc. Natl. Acad. Sci. USA 102, 14221-14226.

30 September 2005.

Yamashita, E., Aoyama, H., Yao, M., Muramoto, K., Shinzawa-Itoh, K., Yoshikawa, S. and Tsukihara, T. (2005) Absolute configuration of the hydroxyfarnesylethyl group of haem A, determined by X-ray structural analysis of bovine heart cytochrome c oxidase using methods applicable at 2.8 Å resolution. Acta Crystallogr. D61, 1373-1377.

A schematic structural diagram of haem A

23 September 2005.

Merroun, M.L., Raff, J., Rossberg, A., Hennig, C., Reich, T. and Selenska-Pobell, S. (2005) Complexation of uranium by cells and S-layer sheets of Bacillus sphaericus JG-A12. Appl. Environ. Microbiol. 71, 5532-5543.

Model used for the fit of cell and S-layer uranium spectra

16 September 2005.

Lautru, S., Deeth, R.J., Bailey, L.M. and Challis, G.L. (2005) Discovery of a new peptide natural product by Streptomyces coelicolor genome mining. Nature Chemical Biology 1, 265-269. [Supplementary Material]

9 September 2005.

Srinivas, O., Mitra, N., Surolia, A. and Jayaraman, N. (2005) Photoswitchable cluster glycosides as tools to probe carbohydrate-protein interactions: synthesis and lectin-binding studies of azobenzene containing multivalent sugar ligands. Glycobiology 15, 861-873.

2 September 2005.

Sugahara, M., Asada, Y., Ayama, H., Ukawa, H., Taka, H. and Kunishima, N. (2005) Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions. Acta Crystallogr. D61, 1302-1305.

5 August 2005.

Bunkóczi, G., Vértesy, L. and Sheldrick, G.M. (2005) Structure of the lipopeptide antibiotic tsushimycin. Acta Crystallogr. D61, 1160-1164.

29 July 2005.

Liang, H. and Landweber, L.F. (2005) Molecular mimicry: Quantitative methods to study structural similarity between protein and RNA. RNA 11, 1167-1172.

The tertiary structures of tRNA-mimic translation factors and tRNA

22 July 2005.

Collet, J.-F., Peisach, D., Bardwell, J.C.A. and Xu, Z.(2005) The crystal structure of TrxA(CACA): Insights into the formation of a [2Fe-2S] iron-sulfur cluster in an Escherichia coli thioredoxin mutant. Protein Science 14, 1840-1849.

Model for the formation of a thioredoxin dimer bridged by a [2Fe-2S] iron-sulfur cluster

15 July 2005.

Schnell, R., Sandalova, T., Hellman, U., Lindqvist, Y. and Schneider, G. (2005) Siroheme and [Fe₄-S₄] dependent NirA from Mycobacterium tuberculosis is a sulfite reductase with a covalent Cys-Tyr bond in the active site. J. Biol. Chem. 280, 27319-27328.

8 July 2005.

Habuchi, S., Ando, R., Dedecker, P., Verheijen, W., Mizuno, H., Miyawaki, A. and Hofkens J. (2005) Reversible single-molecule photoswitching in the GFP-like fluorescent protein Dronpa. Proc. Natl. Acad. Sci. USA 102, 9511-9516.

Schematic diagram of the photoswitching of Dronpa

1 July 2005.

Bönisch, H., Schmidt, C.L., Bianco, P. and Ladenstein, R. (2005) Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 Å X-ray structure of mutant W4L/R5S. Acta Crystallogr. D61, 990-1004.

The structure of air-oxidized P. abyssi rubredoxin mutant W4L/R5S solved by direct methods and refined by partially restrained full-matrix least-squares refinement to 0.69 A resolution

17 June 2005.

Wang, Q., Suzuki, A., Mariconda, S., Porwollik, S. and Harshey, R.M. (2005) Sensing wetness: a new role for the bacterial flagellum. EMBO J. 24, 2034-2042. [Supplementary Material]

Flagellar staining following hydration and restoration of swarming motility...

10 June 2005.

Ogata, J., Kanno, Y., Itoh, Y., Tsugawa, H. and Suzuki, M. (2005) Plant biochemistry: Anthocyanin biosynthesis in roses. Nature 435, 757-758. [Supplementary Material]

A previously undiscovered rose anthocyanidin glucosyltransferase and its phylogeny

3 June 2005.

Endres, D., Miyahara, M., Moisant, P. and Zlotnick, A. (2005) A reaction landscape identifies the intermediates critical for self-assembly of virus capsids and other polyhedral structures. Protein Science 14, 1518-1525. [Supplementary Material]

27 May 2005.

Sauerwald, A., Sitaramaiah, D., McCloskey, J.A., Söll, D. and Crain, P.F. (2005) N⁶-Acetyladenosine: A new modified nucleoside from Methanopyrus kandleri tRNA. FEBS Lett. 579, 2807-2810.

20 May 2005.

Kinjo, A.R. and Nishikawa, K. (2005) Recoverable one-dimensional encoding of three-dimensional protein structures. Bioinformatics 21, 2167-2170.

13 May 2005.

Okabe, S., Ito, T., Sugita, K. and Satoh, H. (2005) Succession of internal sulfur cycles and sulfur-oxidizing bacterial communities in microaerophilic wastewater biofilms. Appl. Environ. Microbiol. 71, 2520-2529.

6 May 2005.

Goede, A., Dunkel, M., Mester, N., Frommel, C. and Preissner, R. (2005) SuperDrug: a conformational drug database. Bioinformatics, 21, 1751-1753.

Check http://bioinf.charite.de/superdrug!

29 April 2005.

Beller, H.R. (2005) Anaerobic, nitrate-dependent oxidation of U(IV) oxide minerals by the chemolithoautotrophic bacterium Thiobacillus denitrificans. Appl. Environ. Microbiol. 71, 2170-2174.

22 April 2005.

Rajagopal, S. and Vishveshwara, S. (2005) Short hydrogen bonds in proteins. FEBS J. 272, 1819-1832.

An example of acceptor furcated multiple hydrogen bond in chlorella virus DNA ligase-adenylate

15 April 2005.

Colin, C., Leblanc, C., Michel, G., Wagner, E., Leize-Wagner, E., Dorsselaer, A.V. and Potin, P. (2005) Vanadium-dependent iodoperoxidases in Laminaria digitata, a novel biochemical function diverging from brown algal bromoperoxidases. J. Biol. Inorg. Chem. 10, 156-166.

8 April 2005.

Nie, B., Stutzman, J. and Xie, A. (2005) A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues. Biophys. J. 88, 2833-2847. [Supplementary Material]

Hydrogen-bond dissociation energy of a protonated carboxylic group interacting with a methanol molecule

1 April 2005.

Cashell, C., Corcoran, D. and Hodnett, B.K. (2005) Effect of amino acid additives on the crystallization of L-glutamic acid. Crystal Growth & Design 5, 593-597.

25 March 2005.

Huang, L.-s., Borders, T.M., Shen, J.T., Wang, C.-J. and Berry, E.A. (2005) Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 Å. Acta Crystallogr. D61, 380-387. [Supplementary Material]

Crystal packing in the orthorhombic complex II crystals

18 March 2005.

Shen, Y., Zhukovskaya, N.L., Guo, Q., Florian, J. and Tang, W.-J. (2005) Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor. EMBO J. 24, 929-941. [Supplementary Material]

Conformations of calcium-binding sites 1 and 2 of N-CaM

11 March 2005.

Gautier-Luneau, I., Merle, C., Phanon, D., Lebrun, C., Biaso, F., Serratrice, G. and Pierre, J.-L. (2005) New trends in the chemistry of iron(III) citrate complexes: Correlations between X-ray structures and solution species probed by electrospray mass spectrometry and kinetics of iron uptake from citrate by iron chelators. Chem. Eur. J. 11, 2207-2219. [Supplementary Material]

4 March 2005.

Janner, A. (2005a) Strongly correlated structure of axial-symmetric proteins. I. Orthorhombic, tetragonal, trigonal and hexagonal symmetries. Acta Crystallogr. D60, 247-255.
Janner, A. (2005b) Strongly correlated structure of axial-symmetric proteins. II. Pentagonal, heptagonal, octagonal, nonagonal and ondecagonal symmetries. Acta Crystallogr. D60, 256-268.
Janner, A. (2005c) Strongly correlated structure of axial-symmetric proteins. III. Complexes with DNA/RNA. Acta Crystallogr. D60, 269-277.

The double heptameric rings of the PA-Sm1 core protein in complex with RNA

25 February 2005.

Sharp, P.M., Bailes, E., Grocock, R.J., Peden, J.F. and Sockett, R.E. (2005) Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33, 1141-1153.

Phylogenetic relationships of the 80 bacterial genomes analysed

18 February 2005.

Snir, Y. and Kamien, R.D. (2005) Entropically driven helix formation. Science 307, 1067. [Supplementary Material]

11 February 2005.

Tanaka, T., Tateno, Y. and Gojobori, T. (2005) Evolution of vitamin B₆ (pyridoxine) metabolism by gain and loss of genes. Mol. Biol. Evol. 22, 243-250.

Distribution of the 10 genes related to the PLP biosynthetic pathways

4 February 2005.

Fenske, D., Gnida, M., Schneider, K., Meyer-Klaucke, W., Schemberg, J., Henschel, V., Meyer, A.-K., Knöchel, A. and Müller, A. (2005) A new type of metalloprotein: the Mo storage protein from Azotobacter vinelandii contains a polynuclear molybdenum-oxide cluster. ChemBioChem 6, 405-413.

"The molybdenum storage protein (MoSto), characterized in this work, represents a completely new type of molybdoprotein... MoSto can take up at least 90 Mo atoms per protein molecule."

28 January 2005.

Mahadevan, R. and Palsson, B.O. (2005) Properties of metabolic networks: Structure versus function. Biophys. J. 88, L7-L9.

21 January 2005.

Rai, P., Wemmer, D.E. and Linn, S. (2005) Preferential binding and structural distortion by Fe²⁺ at RGGG-containing DNA sequences correlates with enhanced oxidative cleavage at such sequences. Nucleic Acids Res. 33, 497-510. Supplementary Material]

Model of Fe2+ association with the AGGG duplex

14 January 2005.

Hiley, S.L., Jackman, J., Babak, T., Trochesset, M., Morris, Q.D., Phizicky, E. and Hughes, T.R. (2005) Detection and discovery of RNA modifications using microarrays. Nucleic Acids Res. 33, e2.

7 January 2005.

de Roos, A.D.G. (2005) Origins of introns based on the definition of exon modules and their conserved interfaces. Bioinformatics 21, 2-9.

Fundamental events in the evolution of multifunction, multi-exonic proteins

Back to Kirill's Paper of the Week

Archive of Kirill's Paper of the Week:
2004 2003 2002 2001 2000 1999 1998 1997 1996

Also visit:

Back to the Directory of P450-containing Systems home page:

Trieste site

Gödöllõ site