Archive of Kirill's Paper of the Week - 2004

Last modified: Fri Jan 7 17:10:55 GMT 2005

24 December 2004.

Matsumoto, A., Tobias, I. and Olson, W.K. (2004a) Normal-mode analysis of circular DNA at the base-pair level. 1. Comparison of computed motions with the predicted behavior of an ideal elastic rod. J. Chem. Theory Comput., in press. [Supplementary Material]
Matsumoto, A., Tobias, I. and Olson, W.K. (2004b) Normal-mode analysis of circular DNA at the base-pair level. 2. Large-scale configurational transformation of a naturally curved molecule. J. Chem. Theory Comput., in press. [Supplementary Material]

17 December 2004.

Mangold, U. and Leberer, E. (2005) Regulation of all members of the antizyme family by antizyme inhibitor. Biochem. J. 385, 21-28.

10 December 2004.

Agah, A., Aghajan, M., Mashayekhi, F., Amini, S., Davis, R.W., Plummer, J.D., Ronaghi, M. and Griffin, P.B. (2004) A multi-enzyme model for pyrosequencing. Nucleic Acids Res. 32, e166.

The general principle of the Pyrosequencing reaction system

3 December 2004.

Misra, H.S., Khairnar, N.P., Barik, A., Indira Priyadarsini, K., Mohan, H. and Apte, S.K. (2004) Pyrroloquinoline-quinone: a reactive oxygen species scavenger in bacteria. FEBS Lett. 578, 26-30.

26 November 2004.

Finally, the function for rubrerythrin?

Weinberg, M.V., Jenney, F.E., Jr., Cui, X. and Adams, M.W.W. (2004) Rubrerythrin from the hyperthermophilic archaeon Pyrococcus furiosus is a rubredoxin-dependent, iron-containing peroxidase. J. Bacteriol. 186, 7888-7895.

19 November 2004.

Forum on Metalloprotein Folding

Inorganic Chemistry

12 November 2004.

Cobine, P.A., McKay, R.T., Zangger, K., Dameron, C.T. and Armitage, I.M. (2004) Solution structure of Cu₆ metallothionein from the fungus Neurospora crassa. Eur. J. Biochem. 271, 4213-4221.

5 November 2004.

Inouye, S. (2004) Blue fluorescent protein from the calcium-sensitive photoprotein aequorin is a heat resistant enzyme, catalyzing the oxidation of coelenterazine. FEBS Lett. 577, 105-110.

29 October 2004.

Samatey, F.A., Matsunami, H., Imada, K., Nagashima, S., Shaikh, T.R., Thomas, D.R., Chen, J.Z., Derosier, D.J., Kitao, A. and Namba, K. (2004) Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism. Nature 431, 1062-1068. [Supplementary Material]

22 October 2004.

Kehat, I., Khimovich, L., Caspi, O., Gepstein, A., Shofti, R., Arbel, G., Huber, I., Satin, J., Itskovitz-Eldor, J. and Gepstein, L. (2004) Electromechanical integration of cardiomyocytes derived from human embryonic stem cells. Nature Biotechnol. 22, 1282-1289. [Supplementary Material]

Electroanatomical mapping and pathological correlation of the new ectopic rhythm

15 October 2004.

Sessions, R.B., Thomas, G.L. and Parker, M.J. (2004) Water as a conformational editor in protein folding. J. Mol. Biol. 343, 1125-1133.

8 October 2004.

Kühner, F., Costa, L.T., Bisch, P.M., Thalhammer, S., Heckl, W.M. and Gaub, H.E. (2004) LexA-DNA bond strength by single molecule force spectroscopy. Biophys. J. 87, 2683-2690.

1 October 2004.

Pickett, C.J., Vincent, K.A., Ibrahim, S.K., Gormal, C.A., Smith, B.E., Fairhurst, S.A. and Best, S.P. (2004) Synergic binding of carbon monoxide and cyanide to the FeMo cofactor of nitrogenase: Relic chemistry of an ancient enzyme? Chem. Eur. J. 10, 4770-4776.

24 September 2004.

Mowat, C.G., Rothery, E., Miles, C.S., McIver, L., Doherty, M.K., Drewette, K., Taylor, P., Walkinshaw, M.D., Chapman, S.K. and Reid, G.A. (2004) Octaheme tetrathionate reductase is a respiratory enzyme with novel heme ligation. Nature Struct. Mol. Biol. 11, 1023-1024.

PDB reference: 1SP3

17 September 2004.

Giegerich, R., Voß, B. and Rehmsmeier, M. (2004) Abstract shapes of RNA. Nucleic Acids Res. 32, 4843-4851.

Representations of RNA secondary structure

Explore RNAshapes here!

10 September 2004.

Aksimentiev, A., Heng, J.B., Timp, G. and Schulten, K. (2004) Microscopic kinetics of DNA translocation through synthetic nanopores. Biophys. J. 87, 2086-2097. [Supplementary Material]

3 September 2004.

Ye, J. and van den Berg, B. (2004) Crystal structure of the bacterial nucleoside transporter Tsx. EMBO J. 23, 3187-3195.

PDB references: 1TLW, 1TLY and 1TLZ.

27 August 2004.

Li, K., Pasternak, C., Härtig, E., Haberzettl, K., Maxwell, A. and Klug, G. (2004) Thioredoxin can influence gene expression by affecting gyrase activity. Nucleic Acids Res. 32, 4563-4575.

20 August 2004.

Jeong, J., Rouault, T.A. and Levine, R.L. (2004) Identification of a heme sensing domain in iron-regulatory protein 2. J. Biol. Chem. 279, 45450-45454.

6 August 2004.

Passerini, A. and Frasconi, P. (2004) Learning to discriminate between ligand-bound and disulfide-bound cysteines. Protein Eng. Des. Sel. 17, 367-373.

30 July 2004.

Schüttelkopf, A.W. and van Aalten, D.M.F. (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D60, 1355-1363.

16 July 2004.

Rugar, D., Budakian, R., Mamin, H.J. and Chui, B.W. (2004) Single spin detection by magnetic resonance force microscopy. Nature 430, 329-332. [Supplementary Material]

9 July 2004.

Dias, J.M., Alves, T., Bonifácio, C., Pereira, A.S., Trincão, J., Bourgeois, D., Moura, I. and Romão, M.A. (2004) Structural basis for the mechanism of Ca²⁺ activation of the di-heme cytochrome c peroxidase from Pseudomonas nautica 617. Structure 12, 961-973.

2 July 2004.

Ose, T., Watanabe, K., Yao, M., Honma, M., Oikawa, H. and Tanaka, I. (2004) Structure of macrophomate synthase. Acta Crystallogr. D60, 1187-1197.

Comparison of the trimeric structures of MPS and DDG aldolase

25 June 2004.

Korhonen, J.A., Pham, X.H., Pellegrini, M. and Falkenberg, M. (2004) Reconstitution of a minimal mtDNA replisome in vitro. EMBO J. 23, 2423-2429. [Supplementary Material]

18 June 2004.

Giordani, R. and Buc, J. (2004) Evidence for two different electron transfer pathways in the same enzyme, nitrate reductase A from Escherichia coli. Eur. J. Biochem. 271, 2400-2407.

Proposed mechanism for electron transfer in nitrate reductase

11 June 2004.

De Rosa, M.C., Castagnola, M., Bertonati, C., Galtieri, A. and Giardina, B. (2004) From the Arctic to fetal life: physiological importance and structural basis of an 'additional' chloride-binding site in haemoglobin. Biochem. J. 380, 889-896.

4 June 2004.

Shouldice, S.R., Skene, R.J., Dougan, D.R., Snell, G., McRee, D.E., Schryvers, A.B. and Tari, L.W. (2004) Structural basis for iron binding and release by a novel class of periplasmic iron-binding proteins found in gram-negative pathogens. J. Bacteriol. 86, 3903-3910.

28 May 2004.

Vlassov, A.V., Johnston, B.H., Landweber, L.F. and Kazakov, S.A. (2004) Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world. Nucleic Acids Res. 32, 2966-2974.

21 May 2004.

Fischer, T.M. (2004) Shape memory of human red blood cells. Biophys. J. 86, 3304-3313.

14 May 2004.

De Napoli, M., Nardis, S., Paolesse, R., Vicente, M.G., Lauceri, R. and Purrello, R. (2004) Hierarchical porphyrin self-assembly in aqueous solution. J. Am. Chem. Soc. 26, 5934-5935. [Supplementary Material]

Hierarchical porphyrin self-assembly in aqueous solution

7 May 2004.

Bertini, I., Del Bianco, C., Gelis, I., Katsaros, N., Luchinat, C., Parigi, G., Peana, M., Provenzani, A. and Zoroddu, M.A. (2004) Experimentally exploring the conformational space sampled by domain reorientation in calmodulin. Proc. Natl. Acad. Sci. USA 101, 6841-6846. [Supplementary Material]
PDB reference: 1SW8

30 April 2004.

Ueno, T., Ohashi, M., Kono, M., Kondo, K., Suzuki, A., Yamane, T. and Watanabe, Y. (2004) Crystal structures of artificial metalloproteins: Tight binding of Fe^III(Schiff-base) by mutation of Ala71 to Gly in apo-myoglobin. Inorg. Chem. 43, 2852-2858.
Structure of myoglobin-based artificial metalloprotein

23 April 2004.

Hino, T., Kanamori, E., Shen, J.-R. and Kouyama, T. (2004) An icosahedral assembly of the light-harvesting chlorophyll a/b protein complex from pea chloroplast thylakoid membranes. Acta Crystallogr. D60, 803-809.
PDB reference: 1VCR

16 April 2004.

Wolf, L.K., Gao, Y. and Georgiadis, R.M. (2004) Sequence-dependent DNA immobilization: specific versus nonspecific contributions. Langmuir 20, 3357-3361. [Supplementary Material]

9 April 2004.

Tachibana, H., Koga, K., Fujimura, Y. and Yamada, K. (2004) A receptor for green tea polyphenol EGCG. Nature Struct. Mol. Biol. 11, 380-381. [Supplementary Material]

2 April 2004.

Rat Genome Sequencing Project Consortium (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493-521.

26 March 2004.

Cobine, P.A., Ojeda, L.D., Rigby, K.M. and Winge, D.R. (2004) Yeast contain a non-proteinacious pool of copper in the mitochondrial matrix. J. Biol. Chem. 279, 14447-14455.

19 March 2004.

Vetting, M.W., Wackett, L.P., Que, L., Jr., Lipscomb, J.D. and Ohlendorf, D.H. (2004) Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases. J. Bacteriol. 186, 1945-1958.

12 March 2004.

Schneider, B., Morávek, Z. and Berman, H.M. (2004) RNA conformational classes. Nucleic Acids Res. 32, 1666-1677.

A chemical diagram of a dinucleotide fragment shows definitions of the backbone torsions

5 March 2004.

Darnton, N., Turner, L., Breuer, K. and Berg, H.C. (2004) Moving fluid with bacterial carpets. Biophys. J. 86, 1863-1870.

27 February 2004.

Maes, D., Gonzalez-Ramirez, L.A., Lopez-Jaramillo, J., Yu, B., De Bondt, H., Zegers, I., Afonina, E., Garcia-Ruiz, J.M. and Gulnik, S. (2004) Structural study of the type II 3-dehydroquinate dehydratase from Actinobacillus pleuropneumoniae. Acta Crystallogr. D60, 463-471.

Crystals from type II 3-dehydroquinate dehydratase (DHQase) from Actinobacillus pleuropneumoniae in a 0.7 mm capillary of the Granada Crystallization Box. The crystals were obtained in the International Space Station (ISS) during the Andromeda mission

20 February 2004.

Ouyang, L., Rulis, P., Ching, W.Y., Nardin, G. and Randaccio, L. (2004) Accurate redetermination of the X-ray structure and electronic bonding in adenosylcobalamin. Inorg. Chem. 43, 1235-1241. [Supplementary Material]

13 February 2004.

Ambroggio, X.I., Rees, D.C. and Deshaies, R.J. (2004) JAMM: a metalloprotease-like zinc site in the proteasome and signalosome. PLoS Biology 2, 0113-0119.
The structure is available at PDB:1R5X. See also the comment:

Structure and implications of JAMM, a novel metalloprotease. PLoS Biology 2, 0008.
The active site of JAMM

6 February 2004.

Gadewar, S.B., Hofmann, H.M. and Doherty, M.F. (2004) Evolution of crystal shape. Crystal Growth & Design 4, 109-112.

30 January 2004.

Peak, D., West, J.D., Messinger, S.M. and Mott, K.A. (2004) Evidence for complex, collective dynamics and emergent, distributed computation in plants. Proc. Natl. Acad. Sci. USA 101, 918-922.

Stomatal aperture is inversely correlated with chlorophyll fluorescence

23 January 2004.

Petrescu, A.-J., Milac, A.-L., Petrescu, S.M., Dwek, R.A. and Wormald, M.R. (2004) Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure and folding. Glycobiology 14, 103-114.

16 January 2004.

Sinha, S.C., Chaudhuri, B.N., Burgner, J.W., Yakovleva, G., Davisson, V.J. and Smith, J.L. (2004) Crystal structure of imidazole glycerol phosphate dehydratase: Duplication of an unusual fold. J. Biol. Chem. 279, 15491-15498.

9 January 2004.

Vallazza, M., Perbandt, M., Klussmann, S., Rypniewski, W., Einspahr, H.M., Erdmann, V.A. and Betzel, Ch. (2004) First look at RNA in L-configuration. Acta Crystallogr. D60, 1-7.

2 January 2004.

Berkovitch, F., Nicolet, Y., Wan, J.T., Jarrett, J.T. and Drennan, C.L. (2004) Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme. Science 303, 76-79. [Supplementary Material]

Structure of BioB, FeS clusters, and bound AdoMet and DTB

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