Archive of Kirill's Paper of the Week

Archive of Kirill's Paper of the Week - 1999

By Kirill Degtyarenko

Last modified: Thu Apr 15 15:59:54 BST 2004

24 December 1999.

Hasegawa, J., Shimahara, H., Mizutani, M., Uchiyama, S., Arai, H., Ishii, M., Kobayashi, Y., Ferguson, S.J., Sambongi, Y. and Igarashi, Y. (1999) Stabilization of Pseudomonas aeruginosa cytochrome c₅₅₁ by systematic amino acid substitutions based on the structure of thermophilic Hydrogenobacter thermophilus cytochrome c₅₅₂. J. Biol. Chem. 274, 37533-37537.

Merry Christmas and a Happy Year 2000

17 December 1999.

Liu, Z., Reches, M. and Engelberg-Kulka, H. (1999) A sequence in the Escherichia coli fdhF "selenocysteine insertion sequence" (SECIS) operates in the absence of selenium. J. Mol. Biol. 294, 1073-1086.

10 December 1999.

Forst, C.V. and Schulten, K. (1999) Evolution of metabolisms: a new method for the comparison of metabolic pathways using genomics information. J. Comput. Biol. 6, 343-360.

This paper appears in Special Double Issue Journal of Computational Biology, vol. 6, no. 3-4, 1999: Selected Papers from RECOMB'99 (Istrail, S., Pevzner, P.A. and Waterman, M.S., Eds.)

2 December 1999.

Somewhat predictably, the paper of this week is...

Dunham, I. et al. (1999) The DNA sequence of human chromosome 22. Nature 402, 489-495.
The complete sequence and analysis is available @ http://www.sanger.ac.uk/HGP/Chr22/

And by the way, have a look at the Figure 3 (Intrachromosomal repeats on human chromosome 22). I have modified the figure encircling the cluster of CYP2D genes and placed it here.

26 November 1999.

Lancaster, C.R.D., Kröger, A., Auer, M. and Michel, H. (1999) Structure of fumarate reductase from Wolinella succinogenes at 2.2 Å resolution. Nature 402, 377-385.

19 November 1999.

Woycechowsky, K.J., Wittrup, K.D. and Raines, R.T. (1999) A small-molecule catalyst of protein folding in vitro and in vivo. Chemistry & Biology 6, 871-879.

A synthetic small-molecule dithiol, (±)-trans-1,2-bis(2-mercapto-acetamido)cyclohexane (BMC), has a pK_a value of 8.3 and an E°' value of -0.24 V. These values are similar to those of the protein disulfide isomerase active sites. BMC catalyses the activation of scrambled ribonuclease A, an inactive enzyme with non-native disulfide bonds, and doubles the yield of active enzyme.

12 November 1999.

Forgo, P. and D'Souza, V.T. (1999) The use of high-resolution NMR spectroscopy in supramolecular systems. Org. Lett. 1, 1543-1545.

5 November 1999.

Brown, D.R., Wong, B.-S., Hafiz, F., Clive, C., Haswell, S.J. and Jones, I.M. (1999) Normal prion protein has an activity like that of superoxide dismutase. Biochem. J. 344, 1-5.

29 October 1999.

Weiner, H. and Finke, R.G. (1999) An all-inorganic, polyoxometalate-based catechol dioxygenase that exhibits >100 000 catalytic turnovers. J. Am. Chem. Soc. 121, 9831-9842. [Supplementary Material]

22 October 1999.

van Aalten, D.M.F., Erlanson, D.A., Verdine, G.L. and Joshua-Tor, L. (1999) A structural snapshot of base-pair opening in DNA. Proc. Natl. Acad. Sci. USA 96, 11809-11814.

15 October 1999.

May, A.C.W. (1999) Towards more meaningful hierarchical classification of amino acid scoring matrices. Protein Engineering 12, 707-712.

8 October 1999.

Nimri, S. and Keinan, E. (1999) Antibody-metalloporphyrin catalytic assembly mimics natural oxidation enzymes. J. Am. Chem. Soc. 121, 9235-9236. [Supplementary Material]

1 October 1999.

Carrion-Vazquez, M., Marszalek, P.E., Oberhauser, A.F. and Fernandez, J.M. (1999) Atomic force microscopy captures length phenotypes in single proteins. Proc. Natl. Acad. Sci. USA 96, 11288-11292.

24 September 1999.

Kuciauskas, D., Liddell, P.A., Lin, S., Johnson, T.E., Weghorn, S.J., Lindsey, J.S., Moore, A.L., Moore, T.A. and Gust, D. (1999) An artificial photosynthetic antenna-reaction center complex. J. Am. Chem. Soc. 121, 8604-8614.

17 September 1999.

Zengler, K., Richnow, H.H., Rossells-Mora, R., Michaelis, W. and Widdel, F. (1999) Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401, 266-269.

See also Gallery of Cation-

Interactions

13 August 1999.

Caylor, C.L., Dobrianov, I., Lemay, S.G., Kimmer, C., Kriminski, S., Finkelstein, K.D., Zipfel, W., Webb, W.W., Thomas, B.R., Chernov, A.A. and Thorne, R.E. (1999) Macromolecular impurities and disorder in protein crystals. Proteins 36, 270-281.

6 August 1999.

Campbell, S., Mrázek, J. and Karlin, S. (1999) Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proc. Natl. Acad. Sci. USA 96, 9184-9189.

30 July 1999.

Shchepinov, M.S., Mir, K.U., Elder, J.K., Frank-Kamenetskii, M.D. and Southern, E.M. (1999) Oligonucleotide dendrimers: stable nano-structures. Nucleic Acids Res. 27, 3035-3041.

23 July 1999.

Welcome to the world of aluminium enzymology:

Merkx, M. and Averill, B.A. (1999) Probing the role of the trivalent metal in phosphate ester hydrolysis: Preparation and vharacterization of purple acid phosphatases containing Al^IIIZn^II and In^IIIZn^II active sites, including the first example of an active aluminum enzyme. J. Am. Chem. Soc. 121, 6683-6689. [Supplementary Material]

16 July 1999.

Solbiati, J., Chapman-Smith, A., Miller, J.L., Miller, C.G. and Cronan, J.E., Jr. (1999) Processing of the N termini of nascent polypeptide chains requires deformylation prior to methionine removal. J. Mol. Biol. 290, 607-614.

Salmonella typhimurium methionine aminopeptidase is totally inactive on an N-formyl-methionyl peptide in vitro. A reporter protein expresssed in a strain lacking peptide deformylase was shown to retain the formyl group.

9 July 1999.

Eswar, N. and Ramakrishnan, C. (1999) Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures. Protein Engineering 12, 447-455.

2 July 1999.

Stevens, T.J. and Arkin, I.T. (1999) Are membrane proteins "inside-out" proteins? Proteins 36, 135-143.

They are not, authors conclude.

25 June 1999.

Glykos, N.M., Cesareni, G. and Kokkinidis, M. (1999) Protein plasticity to the extreme: Changing the topology of a 4--helical bundle with a single amino acid substitution. Structure 7, 597-603.

"Conventional wisdom has it that two proteins sharing 98.4% sequence identity have nearly identical three-dimensional structures. Here we provide a counter-example to this statement by showing that a single amino acid substitution can change the topology of a homodimeric 4- alpha

-helical bundle protein".

18 June 1999.

Arnoux, P., Haser, R., Izadi, N., Lecroisey, A., Delepierre, M., Wandersman, C. and Czjzek, M. (1999) The crystal structure of HasA, a hemophore secreted by Serratia marcescens. Nature Struct. Biol. 6, 516-520.

11 June 1999.

de la Fuente, I.M., Benitez, N., Santamaria, A., Aguirregabiria, J.M. and Veguillas, J. (1999) Persistence in metabolic nets. Bull. Math. Biol. 61, 573-595.

4 June 1999.

Baures, P.W. (1999) Heterocyclic HIV-1 protease inhibitors. Org. Lett. 1, 249-252.

This is an ASAP publication from the new journal, Organic Letters - first issue appears July 1999.

28 May 1999.

Buse, G., Soulimane, T., Dewor, M., Meyer, H.E. and Blüggel, M. (1999) Evidence for a copper-coordinated histidine-tyrosine cross-link in the active site of cytochrome oxidase. Protein Science 8, 985-990.

This is how Cu_B centre of cytochrome c oxidase looks: CuB centre

14 May 1999.

Vlad, M.O., Moran, F. and Ross, J. (1999) Transit time distribution for biochemical networks far from equilibrium: Amplification of the probability of net transformation due to multiple reflections. J. Phys. Chem. B103, 3965-3974.

7 May 1999.

Foster, M.W. and Cowan, J.A. (1999) Chemistry of nitric oxide with proteinbound iron sulfur centers. Insights on physiological reactivity. J. Am. Chem. Soc. 121, 4093-4100.

30 April 1999.

Liu, D.R. and Schultz, P.G. (1999) Progress toward the evolution of an organism with an expanded genetic code. Proc. Natl. Acad. Sci. USA 96, 4780-4785.

23 April 1999.

Düring, K., Porsch, P., Mahn, A., Brinkmann, O. and Gieffers, W. (1999) The non-enzymatic microbicidal activity of lysozymes. FEBS Lett. 449, 93-100.

16 April 1999.

Cherry, J.R., Lamsa, M.H., Schneider, P., Vind, J., Svendsen, A., Jones, A. and Pedersen, A.H. (1999) Directed evolution of a fungal peroxidase. Nature Struct. Biol. 17, 379-384.

9 April 1999.

Smith, J.V., Arnold, F.P., Jr., Parsons, I. and Lee, M.R. (1999) Biochemical evolution III: Polymerization on organophilic silica-rich surfaces, crystal-chemical modeling, formation of first cells, and geological clues. Proc. Natl. Acad. Sci. USA 96, 3479-3485.

This paper was presented at the National Academy of Sciences colloquium on Geology, Mineralogy, and Human Welfare held November 8-9, 1998 at the Arnold and Mabel Beckman Center in Irvine, CA.
Parts I and II were published last year:

Smith, J.V. (1998) Biochemical evolution I: Polymerization on internal, organophilic silica surfaces of dealuminated zeolites and feldspars. Proc. Natl. Acad. Sci. USA 95, 3370-3375.
Parsons, I., Lee, M.R. and Smith, J.V. (1998) Biochemical evolution II: Origin of life in tubular microstructures on weathered feldspar surfaces. Proc. Natl. Acad. Sci. USA 95, 15173-15176.

1 April 1999.

Itoh, T., Takemoto, K., Mori, H. and Gojobori, T. (1999) Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol. Biol. Evol. 16, 332-346.

26 March 1999.

Yang, D. and Kay, L.E. (1999) TROSY triple-resonance four-dimensional NMR spectroscopy of a 46 ns tumbling protein. J. Am. Chem. Soc. 121, 2571-2575.

19 March 1999.

Duke, T.A.J. (1999) Molecular model of muscle contraction. Proc. Natl. Acad. Sci. USA 96, 2770-2775.

12 March 1999.

Subramaniam, S., Lindahl, M., Bullough, P., Faruqi, A.R., Tittor, J., Oesterhelt, D., Brown, L., Lanyi, J. and Henderson, R. (1999) Protein conformational changes in the bacteriorhodopsin photocycle. J. Mol. Biol. 287, 145-161.

5 March 1999.

Georgalis, Y., Umbach, P., Saenger, W., Ihmels, B. and Soumpasis, D.M. (1999) Ordering of fractal clusters in crystallizing lysozyme solutions. J. Am. Chem. Soc. 121, 1627-1635.

26 February 1999.

Sogo, J.M., Stasiak, A., Martínez-Robles, M.L., Krimer, D.B., Hernández, P. and Schvartzman, J.B. (1999) Formation of knots in partially replicated DNA molecules. J. Mol. Biol. 286, 637-643.

19 February 1999.

Pfannschmidt, T., Nilsson, A. and Allen, J.F. (1999) Photosynthetic control of chloroplast gene expression. Nature 397, 625-628.

12 February 1999.

Wendt, K.U., Lenhart, A. and Schulz, G.E. (1999) The structure of the membrane protein squalene-hopene cyclase at 2.0 Å resolution. J. Mol. Biol. 286, 175-187.

5 February 1999.

Jungas, C., Ranck, J.L., Rigaud, J.L., Joliot, P. and Verméglio, A. (1999) Supramolecular organization of the photosynthetic apparatus of Rhodobacter sphaeroides. EMBO J. 18, 534-542.

29 January 1999.

Wilker, J.J., Dmochowski, I.J., Dawson, J.H., Winkler, J.R. and Gray, H.B. (1999) Substrates for rapid delivery of electrons and holes to buried active sites in proteins. Angew. Chem. Int. Ed. 38, 89-92.

22 January 1999.

Kubiak, R.J., Hondal, R.J., Yue, X., Tsai, M.-D. and Bruzik, K.S. (1999) Identification of a novel catalytic triad with dual functions in enzymatic cleavage of the P-O bond. J. Am. Chem. Soc. 121, 488-489.

15 January 1999.

Almholt, K., Arkhammar, P.O.G., Thastrup, O. and Tullin, S. (1999) Simultaneous visualization of the translocation of protein kinase C-green fluorescent protein hybrids and intracellular calcium concentrations. Biochem. J. 337, 211-218.
For Multimedia presentation, click here.

8 January 1999.

Chou, H.-P., Spence, C., Scherer, A. and Quake, S. (1999) A microfabricated device for sizing and sorting DNA molecules. Proc. Natl. Acad. Sci. USA 96, 11-13.

1 January 1999.

Barnes, N.R. and Schreiner, A.F. (1998) B-DNA binding with cobalt(III) and vanadyl(2+) derivatives of tetracationic 5,10,15,20-tetrakis(4-N-methylpyridyl)porphine: Combined CD, optical, and electronic MCD Spectra. Inorg. Chem. 37, 6935-6938.

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