Archive of Kirill's Paper of the Week - 2007

by Kirill Degtyarenko

Last modified: Fri Jan 11 09:18:07 GMT 2008

21 December 2007.

• Berg, A.K., Manokaran, S., Eiler, D., Kooren, J., Mallik, S. and Srivastava, D.K. (2008) Energetic rationale for an unexpected and abrupt reversal of guanidinium chloride-induced unfolding of peptide deformylase. Protein Science 17, 11-15.

14 December 2007.

• Basak, S., Roy, S. and Ghosh, T.C. (2007) On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes. FEBS Lett. 581, 5825-5830.

7 December 2007.

• Jones, A.K., Lichtenstein, B.R., Dutta, A., Gordon, G. and Dutton, P.L. (2007) Synthetic hydrogenases: incorporation of an iron carbonyl thiolate into a designed peptide. J. Am. Chem. Soc. 129, 14844-14845.

30 November 2007.

• Metcalfe, C.L., Daltrop, O., Ferguson, S.J. and Raven, E.L. (2007) Tuning the formation of a covalent haem-protein link by selection of reductive or oxidative conditions as exemplified by ascorbate peroxidase. Biochem. J. 408, 355-361.

23 November 2007.

• Sutherland, T.D., Weisman, S., Trueman, H.E., Sriskantha, A., Trueman, J.W.H. and Haritos, V.S. (2007) Conservation of essential design features in coiled coil silks. Mol. Biol. Evol. 24, 2424-2432.

16 November 2007.

• Rasmussen, S.G.F., Choi, H.-J., Rosenbaum, D.M., Kobilka, T.S., Thian, F.S., Edwards, P.C., Burghammer, M., Ratnala, V.RP.., Sanishvili, R., Fischetti, R.F., Schertler, G.F.X., Weis, W.I. and Kobilka, B.K. (2007) Crystal structure of the human β₂ adrenergic G-protein-coupled receptor. Nature 450, 383-387.

9 November 2007.

• Hayashi, M. and Harada, Y. (2007) Direct observation of the reversible unwinding of a single DNA molecule caused by the intercalation of ethidium bromide. Nucleic Acids Res. 35, e125.

2 November 2007.

• Colletier, J.-P., Royant, A., Specht, A., Sanson, B., Nachon, F., Masson, P., Zaccai, G., Sussman, J.L., Goeldner, M., Silman, I., Bourgeois, D. and Weik, M. (2007) Use of a 'caged' analogue to study the traffic of choline within acetylcholinesterase by kinetic crystallography. Acta Crystallogr. D63, 1115-1128.

26 October 2007.

• Oren, E.E., Tamerler, C., Sahin, D., Hnilova, M., Seke, U.O.S., Sarikaya, M. and Samudrala, R. (2007) A novel knowledge-based approach to design inorganic binding peptides. Bioinformatics 23, 2816-2822.

19 October 2007.

• Sawa, T., Zaki, M.H., Okamoto, T., Akuta, T., Tokutomi, Y., Kim-Mitsuyama, S., Ihara, H., Kobayashi, A., Yamamoto, M., Fujii, S., Arimoto, H. and Akaike, T. (2007) Protein S-guanylation by the biological signal 8-nitroguanosine 3',5'-cyclic monophosphate. Nature Chem. Biol. 3, 727-735.

12 October 2007.

• Pereira, M.M., Refojo, P.N., Hreggvidsson, G.O., Hjorleifsdottir, S. and Teixeira, M. (2007) The alternative complex III from Rhodothermus marinus - A prototype of a new family of quinol:electron acceptor oxidoreductases. FEBS Lett. 581, 4831-4835.

5 October 2007.

• Lessner, D.J. and Ferry, J.G. (2007) The archaeon Methanosarcina acetivorans contains a protein disulfide reductase with an iron-sulfur cluster. J. Bacteriol. 189, 7475-7484.

28 September 2007.

• Loftin, I.R., Franke, S., Blackburn, N.J. and McEvoy, M.M. (2007) Unusual Cu(I)/Ag(I) coordination of Escherichia coli CusF as revealed by atomic resolution crystallography and X-ray absorption spectroscopy. Protein Science 16, 2287-2293.

14 September 2007.

• Klinge, S., Hirst, J., Maman, J.D., Krude, T. and Pellegrini, L. (2007) An iron-sulfur domain of the eukaryotic primase is essential for RNA primer synthesis. Nature Struct. Mol. Biol. 14, 875-877.

7 September 2007.

• Cappitelli, F., Toniolo, L., Sansonetti, A., Gulotta, D., Ranalli, G., Zanardini, E., and Sorlini, C. (2007) Advantages of using microbial technology over traditional chemical technology in removal of black crusts from stone surfaces of historical monuments. Appl. Environ. Microbiol. 73, 5671-5675.

24 August 2007.

• Ishikawa, T., Morita, T. and Kimura, S. (2007) Unique helical triangle molecular geometry induced by dipole-dipole interactions. Bulletin of the Chemical Society of Japan 80, 1483-1491.

17 August 2007.

• Hu, J., Zhong, C., Ding, C., Chi, Q., Walz, A., Mombaerts, P., Matsunami, H. and Luo, M. (2007) Detection of near-atmospheric concentrations of CO₂ by an olfactory subsystem in the mouse. Science 317, 953-957.

10 August 2007.

• Cristina Stanca-Kaposta, E., Gamblin, D.P., Screen, J., Liu, B., Snoek, L.C., Davis, B.G. and Simons, J.P. (2007) Carbohydrate molecular recognition: a spectroscopic investigation of carbohydrate-aromatic interactions. Phys. Chem. Chem. Phys. 9, 4444-4451.

3 August 2007.

Continuing with multihaem cytochromes...

• Atkinson, S.J., Mowat, C.G., Reid, G.A. and Chapman, S.K. (2007) An octaheme c-type cytochrome from Shewanella oneidensis can reduce nitrite and hydroxylamine. FEBS Lett. 581, 3805-3808.

27 July 2007.

• Clarke, T.A., Cole, J.A., Richardson, D.J. and Hemmings, A.M. (2007) The crystal structure of the pentahaem c-type cytochrome NrfB and characterization of its solution-state interaction with the pentahaem nitrite reductase NrfA. Biochem. J. 406, 19-30.

20 July 2007.

• Hansen, D., Macedo-Ribeiro, S., Ver¡ssimo, P., Yoo Im, S., Sampaio, M.U. and Oliva, M.L.V. (2007) Crystal structure of a novel cysteinless plant Kunitz-type protease inhibitor. Biochem. Biophys. Res. Commun. 46, 735-740.

13 July 2007.

• Pearson, A.R., Elmore, B.O., Yang, C., Ferrara, J.D., Hooper, A.B. and Wilmot, C.M. (2007) The crystal structure of cytochrome P460 of Nitrosomonas europaea reveals a novel cytochrome fold and heme-protein cross-link. Biochemistry 46, 8340-8349.

6 July 2007.

• Piccinelli, P. and Samuelsson, T. (2007) Evolution of the iron-responsive element. RNA 13, 952-966.

29 June 2007.

• Blankenship, J.W. and Dawson, P.E. (2007) Threading a peptide through a peptide: Protein loops, rotaxanes, and knots. Protein Science 16, 1249-1256.

22 June 2007.

• Franklin, E., Browne, S., Hayes, J., Boland, C., Dunne, A., Elliot, G. and Mantle, T.J. (2007) Activation of biliverdin-IXα reductase by inorganic phosphate and related anions. Biochem. J. 405, 61-67.

15 June 2007.

• Butcher, R.A., Fujita, M., Schroeder, F.C. and Clardy, J. (2007) Small-molecule pheromones that control dauer development in Caenorhabditis elegans. Nature Chem. Biol. 3, 420-422.

8 June 2007.

• Shaw, R.S., Packard, N., Schröter, M. and Swinney, H.L. (2007) Geometry-induced asymmetric diffusion. Proc. Natl. Acad. Sci. USA 104, 9580-9584.

1 June 2007.

• Alonso-Lomillo, M.A., Rüdiger, O., Maroto-Valiente, A., Velez, M., Rodríguez-Ramos, I., Muñoz, F.J., Fernandez, V.M. and de Lacey, A.L. (2007) Hydrogenase-coated carbon nanotubes for efficient H₂ oxidation. Nano Lett. 7, 1603-1608.

25 May 2007.

• Kawasaki, S., Ono, M., Watamura, Y., Sakai, Y., Satoh, T., Arai, T., Satoh, J. and Niimura Y. (2007) An O₂-inducible rubrerythrin-like protein, rubperoxin, is functional as a H₂O₂ reductase in an obligatory anaerobe Clostridium acetobutylicum. FEBS Lett. 581, 2460-2464.

18 May 2007.

• Barros, L.F. and Martínez, C. (2007) An enquiry into metabolite domains. Biophys. J. 92, 3878-3884.

4 May 2007.

• Carrico, I.S., Carlson, B.L. and Bertozzi, C.R. (2007) Introducing genetically encoded aldehydes into proteins. Nature Chem. Biol. 3, 321-322.

27 April 2007.

• Nicola, G. and Vakser, I.A. (2007) A simple shape characteristic of protein-protein recognition. Bioinformatics 23, 789-792.

20 April 2007.

• Stout, J., Van Driessche, G., Savvides, S.N. and Van Beeumen, J. (2007) X-ray crystallographic analysis of the sulfur carrier protein SoxY from Chlorobium limicola f. thiosulfatophilum reveals a tetrameric structure. Protein Science 16, 589-601.

30 March 2007.

• Davies, R.J.H., Malone, J.F., Gan, Y., Cardin, C.J., Lee, M.P.H. and Neidle, S. (2007) High-resolution crystal structure of the intramolecular d(TpA) thymine-adenine photoadduct and its mechanistic implications. Nucleic Acids Res. 35, 1048-1053.

23 March 2007.

• Shinzawa-Itoh, K., Aoyama, H., Muramoto, K., Terada, H., Kurauchi, T., Tadehara, Y., Yamasaki, A., Sugimura, T., Kurono, S., Tsujimoto, K., Mizushima, T., Yamashita, E., Tsukihara, T. and Yoshikawa, S. (2007) Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase. EMBO J. 26, 1713-1725.

16 March 2007.

• Brindefalk, B., Viklund, J., Larsson, D., Thollesson, M. and Andersson, S.G.E. (2007) Origin and evolution of the mitochondrial aminoacyl-tRNA synthetases. Mol. Biol. Evol. 24, 743-756.

9 March 2007.

• Ederer, M. and Gilles, E.D. (2007) Thermodynamically feasible kinetic models of reaction networks. Biophys. J. 92, 1846-1857.

2 March 2007.

• Inoue, Y., Nomura, W., Takeuchi, Y., Ohdate, T., Tamasu, S., Kitaoka, A., Kiyokawa, Y., Masutani, H., Murata, K., Wakai, Y., Izawa, S. and Yodoi, J. (2007) Efficient extraction of thioreodoxin from Saccharomyces cerevisiae by ethanol. Appl. Environ. Microbiol. 73, 1672-1675.

23 February 2007.

• Balamurugan, K., Egli, D., Hua, H., Rajaram, R., Seisenbacher, G., Georgiev, O. and Schaffner, W. (2007) Copper homeostasis in Drosophila by complex interplay of import, storage and behavioral avoidance. EMBO J. 26, 1035-1044.

16 February 2007.

• Andreini, C., Banci, L., Bertini, I., Elmi, S. and Rosato, A.(2007) Non-heme iron through the three domains of life. Proteins 67, 317-324.

9 February 2007.

• McCarney, E.R., Armstrong, B.D., Lingwood, M.D. and Han, S. (2007) Hyperpolarized water as an authentic magnetic resonance imaging contrast agent. Proc. Natl. Acad. Sci. USA 104, 1754-1759.

2 February 2007.

• Bento, I., Peixoto, C., Zaitsev, V.N. and Lindley, P.F. (2007) Ceruloplasmin revisited: structural and functional roles of various metal cation-binding sites. Acta Crystallogr. D 63, 240-248.

25 January 2007.

• Vergassola, M., Villermaux, E. and Shraiman, B.I. (2007) 'Infotaxis' as a strategy for searching without gradients. Nature 445, 406-409.

19 January 2007.

• Grossmann, G., Opekarová, M., Malinsky, J., Weig-Meckl, I. and Tanner, W. (2007) Membrane potential governs lateral segregation of plasma membrane proteins and lipids in yeast. EMBO J. 26, 1-8.

12 January 2007.

• Chinnapen, D.J.-F. and Sen, D. (2007) Towards elucidation of the mechanism of UV1C, a deoxyribozyme with photolyase activity. J. Mol. Biol. 365, 1326-1336.

5 January 2007.

• Chopra, P. and Bender, A. (2006) Evolved cellular automata for protein secondary structure prediction imitate the determinants for folding observed in nature. In Silico Biology 7, 0007.

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