Archive of Kirill's Paper of the Week - 2002

By Kirill Degtyarenko

Last modified: Fri Jul 30 17:19:11 BST 2004

20 December 2002.

Reader, J.S. and Joyce, G.F. (2002) A ribozyme composed of only two different nucleotides. Nature 420, 841-844.

ligase ribozymes containing either three or two different nucleotide subunits

13 December 2002.

Proposed metabolic pathway for selenosugars

Kobayashi, Y., Ogra, Y., Ishiwata, K., Takayama, H., Aimi, N. and Suzuki, K.T. (2002) Selenosugars are key and urinary metabolites for selenium excretion within the required to low-toxic range. Proc. Natl. Acad. Sci. USA 99, 15932-15936.

6 December 2002.

Wernimont, A.K., Huffman, D.L., Finney, L.A., Demeler, B., O'Halloran, T.V. and Rosenzweig, A.C. (2003) Crystal structure and dimerization equilibria of PcoC, a methionine-rich copper resistance protein from Escherichia coli. J. Biol. Inorg. Chem. 8, 185-194.

29 November 2002.

Larsen, N.A., Heine, A., de Prada, P., Redwan, E.-R, Yeates, T.O., Landry, D.W. and Wilson, I.A. (2002) Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal. Acta Crystallogr. D58, 2055-2059.

22 November 2002.

Blokesch, M. and Böck, A. (2002) Maturation of [NiFe]-hydrogenases in Escherichia coli: the HypC cycle. J. Mol. Biol. 324, 287-296.

15 November 2002.

Lyubchenko, Y.L., Shlyakhtenko, L.S., Binus, M., Gaillard, C. and Strauss, F. (2002) Visualization of hemiknot DNA structure with an atomic force microscope. Nucleic Acids Res. 30, 4902-4909.

8 November 2002.

Itoh, T., Yano, K., Inada, Y. and Fukushima, Y. (2002) Photostabilized chlorophyll a in mesoporous silica: adsorption properties and photoreduction activity of chlorophyll a. J. Am. Chem. Soc. 124, 13437-13441.

1 November 2002.

Milne, J.L.S., Shi, D., Rosenthal, P.B., Sunshine, J.S., Domingo, G.J., Wu, X., Brooks, B.R., Perham, R.N., Henderson, R. and Subramaniam, S. (2002) Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine. EMBO J. 21, 5587-5598.

25 October 2002.

Huang, C.-Y., He, S., DeGrado, V.F., McCafferty, D.G. and Gai, F. (2002) Light-induced helix formation. J. Am. Chem. Soc. 124, 12674-12675. [Electronic Supplementary Material]

tris-bipyridyl complex and the dipole moment change between ground and excited states

18 October 2002.

Doukov, T.I., Iverson, T.M., Seravalli, J., Ragsdale, S.W. and Drennan, C.L. (2002) A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Science 298, 552-553.

mechanistic proposal for acetyl-CoA synthase activity

11 October 2002.

Schmitt, S., Kuhn, D. and Klebe, G. (2002) A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol. 323, 387-406.

4 October 2002.

Sun, J., Hoshino, H., Takaku, K., Nakajima, O., Muto, A., Suzuki, H., Tashiro, S., Takahashi, S., Shibahara, S., Alam, J., Taketo, M.M., Yamamoto, M. and Igarashi, K. (2002) Hemoprotein Bach1 regulates enhancer availability of heme oxygenase-1 gene. EMBO J. 21, 5216-5224.

27 September 2002.

Liao, M.-S. and Scheiner, S. (2002) Comparative study of metal-porphyrins, -porphyrazines, and -phthalocyanines. J. Comput. Chem. 23, 1391-1403.

20 September 2002.

Locci, E., Casu, M., Saba, G., Lai, A., Reisse, J. and Bartik, K. (2002) The potential of ¹²⁹Xe NMR relaxation measurements for the study of heme proteins. ChemPhysChem 3, 812-814.

13 September 2002.

Pant, K., Bilwes, A.M., Adak, S., Stuehr, D.J. and Crane, B.R. (2002) Structure of a nitric oxide synthase heme protein from Bacillus subtilis. Biochemistry 41, 11071-11079.

6 September 2002.

Forde, N.R., Izhaky, D., Woodcock, G.R., Wuite, G.J.L. and Bustamante, C. (2002) Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase. Proc. Natl. Acad. Sci. USA 99, 11682-11687.

30 August 2002.

Wilkins, A.L., Ye, Y., Yang, W., Lee, H.-W., Liu, Z.-r. and Yang, J.J. (2002) Metal-binding studies for a de novo designed calcium-binding protein. Protein Engineering 15, 571-574.

CD2-D1, with the designed calcium-binding site

23 August 2002.

Jakubowski, H. (2002) Homocysteine is a protein amino acid in humans: implications for homocysteine-linked disease. J. Biol. Chem. 277, 30425-30428.

16 August 2002.

Mertig, M., Ciacchi, L.C., Seidel, R., Pompe, W. and De Vita, A. (2002) DNA as a selective metallization template. Nano Lett. 2, 841-844.

9 August 2002.

Schuffenhauer, A., Zimmermann, J., Stoop, R., van der Vyver, J.-J., Lecchini, S. and Jacoby, E. (2002) An ontology for pharmaceutical ligands and its application for in silico screening and library design. J. Chem. Inf. Comput. Sci. 42, 947-955. [Supplementary Material]

2 August 2002.

Guignard, L., Ozawa, K., Pursglove, S.E., Otting, G. and Dixon, N.E. (2002) NMR analysis of in vitro-synthesized proteins without purification: a high-throughput approach. FEBS Lett. 524, 159-162.

26 July 2002.

Cianci, M., Rizkallah, P.J., Olczak, A., Raftery, J., Chayen, N.E., Zagalsky, P.F. and Helliwell, J.R. (2002) The molecular basis of the coloration mechanism in lobster shell: -crustacyanin at 3.2-Å resolution. Proc. Natl. Acad. Sci. USA 99, 9795-9800.

19 July 2002.

Novoselov, S.V., Rao, M., Onoshko, N.V., Zhi, H., Kryukov, G.V., Xiang, Y., Weeks, D.P., Hatfield, D.L. and Gladyshev, V.N. (2002) Selenoproteins and selenocysteine insertion system in the model plant cell system, Chlamydomonas reinhardtii. EMBO J. 21, 3681-3693.

12 July 2002.

Shi, Z., Olson C.A., Rose, G.D., Baldwin, R.L. and Kallenbach, N.R. (2002) Polyproline II structure in a sequence of seven alanine residues. Proc. Natl. Acad. Sci. USA 99, 9190-9195.

5 July 2002.

Kerfeld, C.A., Sawaya, M.R., Krogmann, D.W. and Yeates, T.O. (2002) Structure of cytochrome c₆ from Arthrospira maxima: an assembly of 24 subunits in a nearly symmetric shell. Acta Crystallogr. D58, 1104-1110. [Supplementary Material]

21 June 2002.

Diaspro, A., Silvano, D., Krol, S., Cavalleri, O. and Gliozzi, A. (2002) Single living cell encapsulation in nano-organized polyelectrolyte shells. Langmuir 18, 5051-5054.

14 June 2002.

Roschitzki, B. and Vasák, M. (2002) A distinct Cu₄-thiolate cluster of human metallothionein-3 is located in the N-terminal domain. J. Biol. Inorg. Chem. 7, 611-616. [Supplementary Material]

31 May 2002.

Oshima, T., Goto, M. and Furusaki, S. (2002) Complex formation of cytochrome c with a calixarene carboxylic acid derivative: a novel solubilization method for biomolecules in organic media. Biomacromolecules 3, 438-444.

24 May 2002.

Tanda, S., Tsuneta, T., Okajima, Y., Inagaki, K., Yamaya, K. and Hatakenaka, N. (2002) Crystal topology: A Möbius strip of single crystals. Nature 417, 397-398.

Scanning electron microscopic images of NbSe3 crystal topology

17 May 2002.

Hovmöller, S., Zhou, T. and Ohlson, T. (2002) Conformations of amino acids in proteins. Acta Crystallogr. D58, 768-776.

Individual Ramachandran plots for each amino acid

10 May 2002.

Barbieri, R., Bertini, I., Cavallaro, G., Lee, Y.-M., Luchinat, C. and Rosato, A. (2002) Paramagnetically induced residual dipolar couplings for solution structure determination of lanthanide binding proteins. J. Am. Chem. Soc. 124, 5581-5587. [Supplementary Material]

3 May 2002.

Yamaoka, Y., Orito, E., Mizokami, M., Gutierrez, O., Saitou, N., Kodama, T., Osato, M.S., Kim, J.G., Ramirez, F.G., Mahachai, V. and Graham, D.Y. (2002) Helicobacter pylori in North and South America before Columbus. FEBS Lett. 517, 180-184.

26 April 2002.

Schoevaart, R. and Kieboom, T. (2002) Combined catalytic conversion involving an enzyme, a homogeneous and a heterogeneous catalyst: one-pot preparation of 4-deoxy-D-glucose derivatives from D-galactose. Tetrahedron Lett. 43, 3399-3400.

19 April 2002.

Hernández, G., Teng, C.-L., Bryant, R.G. and LeMaster, D.M. (2002) O₂ penetration and proton burial depth in proteins: applicability to fold family recognition. J. Am. Chem. Soc. 124, 4463-4472.

12 April 2002.

Kolisnychenko, V., Plunkett, G., III, Herring, C.D., Fehér, T., Pósfai, J., Blattner, F.R. and Pósfai, G. (2002) Engineering a reduced Escherichia coli genome. Genome Res. 12, 640-647.

Deletions MD1-MD12 on the circular map of the MG1655 genome

Supplementary Material

5 April 2002.

Mukhopadhyay, R., Lim, H.W.G. and Wortis, M. (2002) Echinocyte shapes: bending, stretching, and shear determine spicule shape and spacing. Biophys. J. 82, 1756-1772.

29 March 2002.

Ho, B.K. and Curmi, P.M.G. (2002) Twist and shear in beta -sheets and beta -ribbons. J. Mol. Biol. 317, 291-308.

22 March 2002.

Sawasaki, T., Hasegawa, Y., Tsuchimochi, M., Kamura, N., Ogasawara, T., Kuroita, T. and Endo, Y. (2002) A bilayer cell-free protein synthesis system for high-throughput screening of gene products. FEBS Lett. 514, 102-105.

This paper appears in the special issue of FEBS Letters on Protein Biosynthesis (FEBS Letters vol. 514, no. 1, 2002).

15 March 2002.

Bucka, A. and Stasiak, A. (2002) Construction and electrophoretic migration of single-stranded DNA knots and catenanes. Nucleic Acids Res. 30, e24.

8 March 2002.

Peier, A.M., Moqrich, A., Hergarden, A.C., Reeve, A.J., Andersson, D.A., Story, G.M., Earley, T.J., Dragoni, I., McIntyre, P., Bevan, S. and Patapoutian, A. (2002) A TRP channel that senses cold stimuli and menthol. Cell 108, 705-715.

1 March 2002.

He, Q.-C., Zhou, J.-M., Zhou, D.-M., Nakamatsu, Y., Baba, T. and Taira, K. (2002) Comparison of metal-ion-dependent cleavages of RNA by a DNA enzyme and a hammerhead ribozyme. Biomacromolecules 3, 69-83.

The proposed mechanisms for the RNA cleavage

22 February 2002.

Griffiths, C., Yamini, B., Hall, C. and Garthwaite, J. (2002) Nitric oxide inactivation in brain by a novel O₂-dependent mechanism resulting in the formation of nitrate ions. Biochem. J. 362, 459-464.

15 February 2002.

Faham, S. and Bowie, J.U. (2002) Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure. J. Mol. Biol. 316, 1-6.

8 February 2002.

Vogler, R. and Vahrenkamp, H. (2002) Dipeptides made up solely from histidine: solution behaviour and zinc complexation. Eur. J. Inorg. Chem., 761-766.

1 February 2002.

Helling, R.B. (2002) Speed versus efficiency in microbial growth and the role of parallel pathways. J. Bacteriol. 184, 1041-1045.

25 January 2002.

Schneider, T.R. (2002) A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta Crystallogr. D58, 341-342.

18 January 2002.

Bernadó, P., Barbieri, R., Padrós, E., Luchinat, C. and Pons, M. (2002) Lanthanide modulation of the orientation of macromolecules induced by purple membrane. J. Am. Chem. Soc. 124, 374-375. [Supplementary Material]

11 January 2002.

Geremia, S., Garau, G., Vaccari, L., Sgarra, R., Viezzoli, M.S., Calligaris, M. and Randaccio, L. (2002) Cleavage of the iron-methionine bond in c-type cytochromes: Crystal structure of oxidized and reduced cytochrome c₂ from Rhodopseudomonas palustris and its ammonia complex. Protein Science 11, 6-17.

NH3 exogenous ligand coordinated to the haem iron

4 January 2002.

Watson, J.D. and Milner-White, E.J. (2002) A novel main-chain anion-binding site in proteins: the nest. A particular combination of , values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions. J. Mol. Biol. 315, 171-182.

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