Archive of Kirill's Paper of the Week - 1997

Last modified: Thu Apr 15 14:03:42 BST 2004

26 December 1997.

• Snyder, J.P., Nevins, N., Tardif, S.L. and Harpp, D.N. (1997) Inherently hindered rotation about a disulfide bond. J. Am. Chem. Soc. 119, 12685-12686.

19 December 1997.

• Nyanguile, O., Uesugi, M., Austin, D.J. and L. Verdine, G.L. (1997) A nonnatural transcriptional coactivator. Proc. Natl. Acad. Sci. USA 94, 13402-13406.

12 December 1997.

• Lee, D.H., Severin, K., Yokobayashi, Y. and Ghadiri, M.R. (1997) Emergence of symbiosis in peptide self-replication through a hypercyclic network. Nature 390, 591-594.

5 December 1997.

• Gerstein, M. (1997) A structural census of genomes: Comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure. J. Mol. Biol. 274, 562-576.

28 November 1997.

• Kim, Y.-G., Kim, P.S., Herbert, A. and Rich, A. (1997) Construction of a Z-DNA-specific restriction endonuclease. Proc. Natl. Acad. Sci. USA 94, 12875-12879.

21 November 1997.

• Ermler, U., Grabarse, W., Shima, S., Goubeaud, M. and Thauer, R.K. (1997) Crystal structure of methyl-coenzyme M reductase: The key enzyme of biological methane formation. Science 278, 1457-1462.

14 November 1997.

• Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K., Harrison, D., Hoang, L., Keagle, P., Lumm, W., Pothier, B., Qiu, D., Spadafora, R., Vicaire, R., Wang, Y., Wierzbowski, J., Gibson, R., Jiwani, N., Caruso, A., Bush, D., Safer, H., Patwell, D., Prabhakar, S., McDougall, S., Shimer, G., Goyal, A., Pietrokovski, S., Church, G.M., Daniels, C.J., Mao, J.-i., Rice, P., Nölling, J. and Reeve, J.N. (1997) Complete genome sequence of Methanobacterium thermoautotrophicum H: Functional analysis and comparative genomics. J. Bacteriol. 179, 7135-7155.

7 November 1997.

• García, A.E., Krumhansl, J.A. and Frauenfelder, H. (1997) Variations on a theme by Debye and Waller: From simple crystals to proteins. Proteins 29, 153-160.

31 October 1997.

• Yao, S., Ghosh, I., Zutshi, R. and Chmielewski, J. (1997) A pH-modulated, self-replicating peptide. J. Am. Chem. Soc. 119, 10559-10560.

24 October 1997.

• Kleywegt, G.J. (1997) Validation of protein models from C coordinates alone. J. Mol. Biol. 273, 371-376.

17 October 1997.

• Bruggeman, Y.E., Honegger, A., Kreuwel, H., Visser, A.J.W.G., Laane, C., Schots, A. and Hilhorst, R. (1997) Regulation of the flavin redox potential by flavin-binding antibodies. Eur. J. Biochem. 249, 393-400.

10 October 1997.

• Ostermeier, C., Harrenga, A., Ermler, U. and Michel, H. (1997) Structure at 2.7 Å resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody F_V fragment. Proc. Natl. Acad. Sci. USA 94, 10547-10553.

3 October 1997.

• Pfeil, W., Gesierich, U., Kleemann, G.R. and Sterner, R. (1997) Ferredoxin from the hyperthermophile Thermotoga maritima is stable beyond the boiling point of water. J. Mol. Biol. 272, 591-596.

26 September 1997.

• Moore, J.C., Jin, H.-M., Kuchner, O. and Arnold, F.H. (1997) Strategies for the in vitro evolution of protein function: Enzyme evolution by random recombination of improved sequences. J. Mol. Biol. 272, 336-347.

19 September 1997.

• Luger, K., Mäder, A.W., Richmond, R.K., Sargent, D.F. and Richmond, T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251-260.

12 September 1997.

• Jespersen, H.M., Kjærsgård, I.V.H., Østergaard, L. and Welinder, K.G. (1997) From sequence analysis of three novel ascorbate peroxidases from Arabidopsis thaliana to structure, function and evolution of seven types of ascorbate peroxidase. Biochem. J. 326, 305-310.

5 September 1997.

• Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.

29 August 1997.

• Li, L., Hong, R. and Hastings, J.W. (1997) Three functional luciferase domains in a single polypeptide chain. Proc. Natl. Acad. Sci. USA 94, 8954-8958.

22 August 1997.

• Reeves, N.J. and Evans, J.S. (1997) Polypeptide interactions at ice and biomineral interfaces are defined by secondary structure-dependent chain orientations. J. Phys. Chem. B101, 6665-6669.

15 August 1997.

• Yeagle, P.L., Alderfer, J.L. and Albert, A.D. (1997) Three-dimensional structure of the cytoplasmic face of the G protein receptor rhodopsin. Biochemistry 36, 9649-9654.

8 August 1997.

• Tomb, J.­F., White, O., Kerlavage, A.R., Clayton, R.A., Sutton, G.G., Fleischmann, R.D., Ketchum, K.A., Klenk, H.P., Gill, S., Dougherty, B.A., Nelson, K., Quackenbush, J., Zhou, L., Kirkness, E.F., Peterson, S., Loftus, B., Richardson, D., Dodson, R., Khalak, H.G., Glodek, A., McKenney, K., Fitzegerald, L.M., Lee, N., Adams, M.D., Hickey, E.K., Berg, D.E., Gocayne, J.D., Utterback, T.R., Peterson, J.D., Kelley, J.M., Cotton, M.D., Weldman, J.M., Fujii, C., Bowman, C., Watthey, L., Wallin, E., Hayes, W.S., Borodovsky, M., Karp, P.D., Smith, H.O., Fraser, C.M. and Venter, J.C. (1997) The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 386, 539-548.

1 August 1997.

• Kierzek, A.M., Wolf, W.M. and Zielenkiewicz, P. (1997) Simulations of nucleation and early growth stages of protein crystals. Biophys. J. 73, 571-580.

25 July 1997.

• Berg, O.G. and Kurland, C.G. (1997) Growth rate-optimised tRNA abundance and codon usage. J. Mol. Biol. 270, 544-550.

18 July 1997.

• Billeter, M., Riek, R., Wider, G., Hornemann, S., Glockshuber, R. and Wüthrich, K. (1997) Prion protein NMR structure and species barrier for prion diseases. Proc. Natl. Acad. Sci. USA 94, 7281-7285.

11 July 1997.

• Cho, G. and Doolittle, R.F. (1997) Intron distribution in ancient paralogs supports random insertion and not random loss. J. Mol. Evol. 44, 573-584.

4 July 1997.

• Ng, J.D., Kuznetsov, Yu.G., Malkin, A.J., Keith, G., Giegé, R. and McPherson, A. (1997) Visualization of RNA crystal growth by atomic force microscopy. Nucleic Acids Res. 25, 2582-2588.

27 June 1997.

• Picard, M., Gross, J., Lübbert, E., Tölzer, S., Krauss, S., van Pée, K.-H. and Berkessel, A. (1997) Metal-free bacterial haloperoxidases as unusual hydrolases: Activation of H₂O₂ by the formation of peracetic acid. Angew. Chem. Int. Ed. Engl. 36, 1196-1199.

20 June 1997.

• Walsdordd, C., Saak, W. and Pohl, S. (1997) A new preorganized tridentate ligand bearing three indolethiolate groups. Preparation of 3:1 subsite-differentiated Fe₄S₄ clusters. J. Chem. Soc. Dalton Trans., No. 11, 1857-1861.

13 June 1997.

• Russell, R.B., Saqi, M.A.S., Sayle, R.A., Bates, P.A. and Sternberg, M.J.E. (1997) Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J. Mol. Biol. 269, 423-439.

6 June 1997.

• Huang, W., Jia, J., Cummings, J., Nelson, M., Schneider, G. and Lindqvist, Y. (1997) Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold. Structure 5, 691-699.

30 May 1997.

• Weber, A.L. (1997) Energy from redox disproportionation of sugar carbon drives biotic and abiotic synthesis. J. Mol. Evol. 44, 361-370.

23 May 1997.

• Lykke-Andersen, J., Garrett, R.A. and Kjems, J. (1997) Mapping metal ions at the catalytic centres of two intron-encoded endonucleases. EMBO J. 16, 3272-3281.

16 May 1997.

• Velarde, M.G., Nekorkin, V.I., Kazantsev, V.B. and Ross, J. (1997) The emergence of form by replication. Proc. Natl. Acad. Sci. USA 94, 5024-5027.

9 May 1997.

• Sykora, M. and Kincaid, J.R. (1997) Photochemical energy storage in a spatially organized zeolite-based photoredox system. Nature 387, 162-164.

2 May 1997.

• Moats, R.A., Fraser, S.E. and Meade, T.J. (1997) A "smart" magnetic resonance imaging agent that reports on specific enzymatic activity. Angew. Chem. Int. Ed. Engl. 36, 726-728.

25 April 1997.

• Neuwald, A.F., Liu, J.S., Lipman, D.J. and Lawrence, C.E. (1997) Extracting protein alignment models from the sequence database. Nucleic Acids Res. 25, 1665-1677.

18 April 1997.

• Kurzynski, M. (1997) Protein machine model of enzymatic reactions gated by enzyme internal dynamics. Biophys. Chem. 65, 1-28.

11 April 1997.

• Koshi, J.M. and Goldstein, R.A. (1997) Mutation matrices and physical-chemical properties: correlations and implications. Proteins 27, 336-344.

4 April 1997.

• Zhang, C., Vasmatzis, G., Cornette, J.L. and DeLisi, C. (1997) Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol. 267, 707-726.

28 March 1997.

• Busch, J.L.H., Breton, J.L., Bartlett, B.M., Armstrong, F.A., James, R. and Thomson, A.J. (1997) [3Fe-4S] [4Fe-4S] cluster interconversion in Desulfovibrio africanus ferredoxin III: properties of an Asp¹⁴Cys mutant. Biochem. J. 323, 95-102.

21 March 1997.

• Gohlke, U., Warne, A. and Saraste, M. (1997) Projection structure of the cytochrome bo ubiquinol oxidase from Escherichia coli at 6 Å resolution. EMBO J. 16, 1181-1188.

14 March 1997.

• Puente, X.S. and López-Otín, C. (1997) The PLEES proteins: a family of structurally related enzymes widely distributed from bacteria to humans. Biochem. J. 322, 947-949.

7 March 1997.

• Skourtis, S.S. and Beratan, D.N. (1997) Electron transfer contact maps. J. Phys. Chem. B 101, 1215-1234.

28 February 1997.

• Mestre, B., Pitié, M., Loup, C., Claparols, C., Pratviel, G. and Meunier, B. (1997) Influence of the nature of the porphyrin ligand on the nuclease activity of metalloporphyrin-oligonucleotide conjugates designed with cationic, hydrophobic or anionic metalloporphyrins. Nucleic Acids Res. 25, 1022-1027.

14 February 1997.

• Schmidt, R.B., Gerstein M., and Altman, R.B. (1997) LPFC: An Internet library of protein family core structures. Protein Science 6, 246-248.

7 February 1997.

• Shu, L., Nesheim, J.C., Kauffmann, K., Münck, E., Lipscomb, J.D. and Que, L., Jr. (1997) An Fe^IV₂O₂ diamond core structure for the key intermediate Q of methane monooxygenase. Science 275, 515-518.

31 January 1997.

• Riera, J., Robb, F.T., Weiss, R. and Fontecave, M. (1997) Ribonucleotide reductase in the archaeon Pyrococcus furiosus: A critical enzyme in the evolution of DNA genomes? Proc. Natl. Acad. Sci. USA 94, 475-478.

24 January 1997.

• Swartz, P.D., Beck, B.W. and Ichiye, T. (1996) Structural origins of redox potentials in Fe-S proteins: Electrostatic potentials of crystal structures. Biophys. J. 71, 2958-2969.

17 January 1997.

• Steinberg-Yfrach, G., Liddell, P.A., Hung, S.-H., Moore, A.L., Gust, D. and Moore, T.A. (1997) Conversion of light energy to proton potential in liposomes by artificial photosynthetic reaction centres. Nature 385, 239-241.

10 January 1997.

• Hoover, D.M., Jarrett, J.T., Sands, R.H., Dunham, W.R., Ludwig, M.L. and Matthews, R.G. (1997) Interaction of Escherichia coli cobalamin-dependent methionine synthase and its physiological partner flavodoxin: Binding of flavodoxin leads to axial ligand dissociation from the cobalamin cofactor. Biochemistry 36, 127-138.

3 January 1997.

• Gotoh, O. (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol. 264, 823-838.

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