Archive of Kirill's Paper of the Week - 2003

by Kirill Degtyarenko

Last modified: Fri Jul 30 17:22:20 BST 2004

26 December 2003.

Atilgan, A.R., Akan, P. and Baysal, C. (2004) Small-world communication of residues and significance for protein dynamics. Biophys. J. 86, 85-91.

19 December 2003.

Ding, Y.-H.R. and Ferry, J.G. (2004) Flavin mononucleotide-binding flavoprotein family in the domain Archaea. J. Bacteriol. 186, 90-97.

12 December 2003.

Galijasevic, S., Saed, G.M., Diamond, M.P. and Abu-Soud, H.M. (2003) Myeloperoxidase up-regulates the catalytic activity of inducible nitric oxide synthase by preventing nitric oxide feedback inhibition. Proc. Natl. Acad. Sci. USA 100, 14766-14771.

influence of the MPO/H2O2 system on the formation of the iNOSnitrosyl complex

5 December 2003.

Jarvet, J., Damberg, P., Danielsson, J., Johansson, I., Eriksson, L.E.G. and Gräslund, A. (2003) A left-handed 3₁ helical conformation in the Alzheimer A(12-28) peptide. FEBS Lett. 555, 371-374.

28 November 2003.

Layer, G., Moser, J., Heinz, D.W., Jahn, D. and Schubert, W.-D. (2003) Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes. EMBO J. 22, 6214-6224.

21 November 2003.

Santoro, S.W., Anderson, J.C., Lakshman, V. and Schultz, P.G. (2003) An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli. Nucleic Acids Res. 31, 6700-6709. [Supplementary Material]

14 November 2003.

Kurisu, G., Zhang, H., Smith, J.L. and Cramer, W.A. (2003) Structure of the cytochrome b₆f complex of oxygenic photosynthesis: tuning the cavity. Science 302, 1009-1014. [Supplementary Material]

₆

7 November 2003.

Gromer, S., Johansson, L., Bauer, H., Arscott, L.D., Rauch, S., Ballou, D.P., Williams, C.H., Jr., Schirmer, R.H. and Arnér, E.S.J. (2003) Active sites of thioredoxin reductases: Why selenoproteins? Proc. Natl. Acad. Sci. USA 100, 12618-12623. [Supplementary Material]

31 October 2003.

Halloween special: glowing pumpkin!

Jovanic, B.R. and Dramicanin, M.D. (2003) In vivo monitoring of chlorophyll fluorescence response to low-dose -irradiation in pumpkin (Cucurbita pepo) leaves. Luminescence 18, 274-277.

24 October 2003.

Pang, H., Bartlam, M., Zeng, Q., Miyatake, H., Hisano, T., Miki, K., Wong, L.-L., Gao, G.F. and Rao, Z. (2003) Crystal structure of human Pirin: An iron binding nuclear protein and transcription cofactor. J. Biol. Chem. 279, 1491-1498.

17 October 2003.

Nakamura, K., Kawabata, T., Yura, K. and Go, N. (2003) Novel types of two-domain multi-copper oxidases: possible missing links in the evolution. FEBS Lett. 553, 239-244.

10 October 2003.

Koepke, J., Scharff, E.I., Lücke, C., Rüterjans, H. and Fritzsch, G. (2003) Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 Å resolution. Acta Crystallogr. D59, 1744-1754.
Overall structure of the squid-type diisopropylfluorophosphatase

3 October 2003.

Schreiter, E.R., Sintchak, M.D., Guo, Y., Chivers, P.T., Sauer, R.T. and Drennan, C.L. (2003) Crystal structure of the nickel-responsive transcription factor NikR. Nature Struct. Biol. 10, 794-799. [Supplementary Material]

26 September 2003.

Matsumura, S., Ikawa, Y. and Inoue, T.H. (2003) Biochemical characterization of the kink-turn RNA motif. Nucleic Acids Res. 31, 5544-5551.

19 September 2003.

Håkansson, K.O. (2003) The crystallographic structure of Na,K-ATPase N-domain at 2.6 Å resolution. J. Mol. Biol. 332, 1175-1182.

Structure is deposited (PDB:1Q3I).

12 September 2003.

Brekasis, D. and Paget, M.S.B. (2003) A novel sensor of NADH/NAD⁺ redox poise in Streptomyces coelicolor A3(2). EMBO J. 22, 4856-4865.

NADH, but not NAD+, actively dissociates a Rex-ROP complex

5 September 2003.

Gregory, T.R. and Shorthouse, D.P. (2003) Genome sizes of spiders. J. Hered. 94, 285-290.

See also the Animal Genome Size Database.

29 August 2003.

Serafini, M., Bugianesi, R., Maiani, G., Valtuena, S., De Santis, S. and Crozier, A. (2003) Plasma antioxidants from chocolate. Nature 424, 1013.

Finally, a bit of useful news from Nature! "Here we show that consumption of plain, dark chocolate results in an increase in both the total antioxidant capacity and the (-)epicatechin content of blood plasma, but that these effects are markedly reduced when the chocolate is consumed with milk or if milk is incorporated as milk chocolate."

22 August 2003.

Kashefi, K. and Lovley, D R. (2003) Extending the upper temperature limit for life. Science 301, 934.

This Archaea ("Strain 121") grows at temperatures between 85° and 121°C.

15 August 2003.

Contreras-Zentella, M., Mendoza, G., Membrillo-Hernández, J. and Escamilla, J.E. (2003) A novel double heme substitutions produce a functional bo₃ variant of the quinol oxidase aa₃ of Bacillus cereus: Purification and partial characterization. J. Biol. Chem. 278, 31473-31478.

8 August 2003.

Chantalat, L., Nicholson, J.M., Lambert, S.J., Reid, A.J., Donovan, M.J., Reynolds, C.D., Wood, C.M. and Baldwin, J.P. (2003) Structure of the histone-core octamer in KCl/phosphate crystals at 2.15 Å resolution. Acta Crystallogr. D59, 1395-1407.

The packing diagram for histone octamers in crystals...

1 August 2003.

Zhou, H.-X. (2003) Effect of catenation on protein folding stability. J. Am. Chem. Soc. 125, 9280-9281. [Supplementary Material]

Folding equilibria of a linear dimeric protein and a catenated protein

25 July 2003.

Ma, H.-W. and Zeng, A.-P. (2003) The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 19, 1423-1430.

27 June 2003.

Hiraga, K. and Arnold, F.H. (2003) General method for sequence-independent site-directed chimeragenesis. J. Mol. Biol. 330, 287-296.

20 June 2003.

Renshaw, J.C., Halliday, V., Robson, G.D., Trinci, A.P.J., Wiebe, M.G., Livens, F.R., Collison, D. and Taylor, R.J. (2003) Development and application of an assay for uranyl complexation by fungal metabolites, including siderophores. Appl. Environ. Microbiol. 69, 3600-3606.

Comparison of (UO2)2+ and Fe3+ complexation

13 June 2003.

Lorenzen, S., Gille, C., Preissner, R. and Frömmel, C. (2003) Inverse sequence similarity of proteins does not imply structural similarity. FEBS Lett. 545, 105-109.

Inverse similarity of aldolase and glycerol dehydrogenase

6 June 2003.

Miele, A.E., Federici, L., Sciara, G., Draghi, F., Brunori, M. and Vallone, B. (2003) Analysis of the effect of microgravity on protein crystal quality: the case of a myoglobin triple mutant. Acta Crystallogr. D59, 982-988.

23 May 2003.

Dmitriev, B.A., Toukach, F.V., Schaper, K.-J., Holst, O., Rietschel, E.T. and Ehlers, S. (2003) Tertiary structure of bacterial murein: the scaffold model. J. Bacteriol. 185, 3458-3468.

16 May 2003.

Ennifar, E., Walter, P. and Dumas, P. (2003) A crystallographic study of the binding of 13 metal ions to two related RNA duplexes. Nucleic Acids Res. 31, 2671-2682.

9 May 2003.

Escaja, N., Gelpí, J.L., Orozco, M., Rico, M., Pedroso, E. and González, C. (2003) Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad. J. Am. Chem. Soc. 125, 5654-5662.

2 May 2003.

Jiang, Y., Lee, A., Chen, J., Ruta, V., Cadene, M., Chait, B.T. and MacKinnon, R. (2003) X-ray structure of a voltage-dependent K⁺ channel. Nature 423, 33-41.
Jiang, Y., Ruta, V., Chen, J., Lee, A. and MacKinnon, R. (2003) The principle of gating charge movement in a voltage-dependent K⁺ channel. Nature 423, 42-48.
See also: Nature web focus: Ion channels: structure and function

25 April 2003.

Wollenberg, M., Berndt, C., Bill, E., Schwenn, J.D. and Seidler, A. (2003) A dimer of the FeS cluster biosynthesis protein IscA from cyanobacteria binds a [2Fe2S] cluster between two protomers and transfers it to [2Fe2S] and [4Fe4S] apo proteins. Eur. J. Biochem. 270, 1662-1671.

11 April 2003.

Bhaskar, B., Immoos, C.E., Shimizu, H., Sulc, F., Farmer, P.J. and Poulos, T.L. (2003) A novel heme and peroxide-dependent tryptophan-tyrosine cross-link in a mutant of cytochrome c peroxidase. J. Mol. Biol. 328, 157-166.

4 April 2003.

Zborowski, M., Ostera, G.R., Moore, L.R., Milliron, S., Chalmers, J.J. and Schechter, A.N. (2003) Red blood cell magnetophoresis. Biophys. J. 84, 2638-2645.

28 March 2003.

Macedo, S., Romão, C.V., Mitchell, E., Matias, P.M., Liu, M.-Y., Xavier, A.V., LeGall, J., Teixeira, M., Lindley, P. and Carrondo, M.A. (2003) The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans. Nature Struct. Biol. 10, 285-290.

21 March 2003.

Brüser, T., Yano, T., Brune, D.C. and Daldal, F. (2003) Membrane targeting of a folded and cofactor-containing protein. Eur. J. Biochem. 270, 1211-1221.

14 March 2003.

Shall we call this "metallomics"?

Herald V.L., Heazlewood, J.L., Day, D.A. and Millar, A.H. (2003) Proteomic identification of divalent metal cation binding proteins in plant mitochondria. FEBS Lett. 537, 96-100.

7 March 2003.

Blankenship, J.W. and Dawson, P.E. (2003) Thermodynamics of a designed protein catenane. J. Mol. Biol. 327, 537-548.

28 February 2003.

Smith, G.D., Pangborn, W.A. and Blessing, R.H. (2003) The structure of T₆ human insulin at 1.0 Å resolution. Acta Crystallogr. D59, 474-482.

water in the central core of the T6 human insulin hexamer

21 February 2003.

Tanaka, K., Tengeiji, A., Kato, T., Toyama, N. and Shionoya, M. (2003) A discrete self-assembled metal array in artificial DNA. Science 299, 1212-1213. [Supplementary Material]

14 February 2003.

Nilsson, K., Lecerof, D., Sigfridsson, E. and Ryde, U. (2003) An automatic method to generate force-field parameters for hetero-compounds. Acta Crystallogr. D59, 274-289. [Supplementary Material]

7 February 2003.

Jaffe, E.K. (2003) An unusual phylogenetic variation in the metal ion binding sites of porphobilinogen synthase. Chemistry & Biology 10, 25-34.

31 January 2003.

Huang, F. (2003) Efficient incorporation of CoA, NAD and FAD into RNA by in vitro transcription. Nucleic Acids Res. 31, e8.

24 January 2003.

Chatake, T., Ostermann, A., Kurihara, K., Parak, F.G. and Niimura, N. (2003) Hydration in proteins observed by high-resolution neutron crystallography. Proteins 50, 516-523.

Classification of hydration water molecules

17 January 2003.

Islam, M., Khanin, M. and Sadik, O.A. (2003) Fluorescent chelates for monitoring metal binding with macromolecules. Biomacromolecules 4, 114-121.

Structures of PAR derivatives and the new fluorescent conjugates

10 January 2003.

Müller, P., Köpke, S. and Sheldrick, G.M. (2003) Is the bond-valence method able to identify metal atoms in protein structures? Acta Crystallogr. D59, 32-37.

The VECSUM for the case of trigonal bipyramidal geometry

3 January 2003.

Hanson, G.T., McAnaney, T.B., Park, E.S., Rendell, M.E., Yarbrough, D.K., Chu, S., Xi, L., Boxer, S.G., Montrose, M.H. and Remington, S.J. (2002) Green fluorescent protein variants as ratiometric dual emission pH sensors. 1. Structural characterization and preliminary application. Biochemistry 41, 15477-15488.
McAnaney, T.B., Park, E.S., Hanson, G.T., Remington, S.J. and Boxer, S.G. (2002) Green fluorescent protein variants as ratiometric dual emission pH sensors. 2. Excited-state dynamics. Biochemistry 41, 15489-15494.

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