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.
Merry Christmas and a Happy Year
- Hasegawa, J., Shimahara, H., Mizutani, M., Uchiyama, S., Arai, H.,
Ishii, M., Kobayashi, Y., Ferguson, S.J., Sambongi, Y. and Igarashi, Y.
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.
17 December 1999.
- Liu, Z., Reches, M. and Engelberg-Kulka, H. (1999)
A sequence in the Escherichia coli fdhF "selenocysteine
sequence" (SECIS) operates in the absence of selenium.
J. Mol. Biol. 294, 1073-1086.
10 December 1999.
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...
And by the way, have a look at the
(Intrachromosomal repeats on human chromosome 22).
I have modified the figure encircling the cluster of CYP2D genes and placed it
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
Nature 402, 377-385.
19 November 1999.
A synthetic small-molecule dithiol,
(±)-trans-1,2-bis(2-mercapto-acetamido)cyclohexane (BMC), has a
pKa 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.
- 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.
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.
22 October 1999.
15 October 1999.
8 October 1999.
1 October 1999.
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.
See also comment:
10 September 1999.
3 September 1999.
Luecke, H., Schobert, B., Richter, H.-T., Cartailler, J.-P. and Lanyi, J.K.
Structure of bacteriorhodopsin at 1.55 Å resolution.
J. Mol. Biol. 291, 899-911.
20 August 1999.
See also Gallery of
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.
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
AlIIIZnII and InIIIZnII active
sites, including the first example of an active aluminum enzyme.
J. Am. Chem. Soc. 121, 6683-6689.
16 July 1999.
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.
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.
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.
They are not, authors conclude.
25 June 1999.
"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--helical bundle protein".
- 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
Structure 7, 597-603.
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.
This is an ASAP publication from the new journal,
Organic Letters -
first issue appears July 1999.
28 May 1999.
This is how CuB centre of cytochrome c oxidase looks:
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
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.
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.
This paper was presented at the National Academy of Sciences colloquium on
Mineralogy, and Human Welfare held November 8-9, 1998 at the Arnold and
Mabel Beckman Center in Irvine, CA.
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
Proc. Natl. Acad. Sci. USA 96, 3479-3485.
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.
19 March 1999.
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
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
EMBO J. 18, 534-542.
29 January 1999.
- Wilker, J.J., Dmochowski, I.J., Dawson, J.H., Winkler, J.R. and Gray, H.B.
Substrates for rapid delivery of electrons and holes to buried active sites in
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.
8 January 1999.
1 January 1999.
- Barnes, N.R. and Schreiner, A.F. (1998)
B-DNA binding with cobalt(III) and vanadyl(2+) derivatives of tetracationic
Combined CD, optical, and electronic MCD Spectra.
Inorg. Chem. 37, 6935-6938.
Kirill's Paper of the Week
Kirill's Paper of the Week - 2000
Kirill's Paper of the Week - 1998
Kirill's Paper of the Week - 1997
Kirill's Paper of the Week - 1996
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