Archive of Kirill's Paper of the Week

Archive of Kirill's Paper of the Week - 2001

By Kirill Degtyarenko

Last modified: Mon Aug 2 10:03:22 BST 2004

14 December 2001.

Krantz, B.A. and Sosnick, T.R. (2001) Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil. Nature Struct. Biol. 8, 1042-1047.

7 December 2001.

Eggers, D.K. and Valentine, J.S. (2001) Crowding and hydration effects on protein conformation: A study with sol-gel encapsulated proteins. J. Mol. Biol. 314, 911-922.

30 November 2001.

Datta, S., Mori, Y., Takagi, K., Kawaguchi, K., Chen, Z.-W., Okajima, T., Kuroda, S., Ikeda, T., Kano, K., Tanizawa, K. and Mathews, F.S. (2001) Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking. Proc. Natl. Acad. Sci. USA 98, 14268-14273.

23 November 2001.

Kindt, J., Tzlil, S., Ben-Shaul, A. and Gelbart, W.M. (2001) DNA packaging and ejection forces in bacteriophage. Proc. Natl. Acad. Sci. USA 98, 13671-13674.

16 November 2001.

McCloskey, J.A., Graham, D.E., Zhou, S., Crain, P.F., Ibba, M., Konisky, J., Söll, D. and Olsen, G.J. (2001) Post-transcriptional modification in archaeal tRNAs: identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales. Nucleic Acids Res. 29, 4699-4706.

9 November 2001.

Martin, P., DeMel, S., Shi, J., Gladysheva, T., Gatti, D.L., Rosen, B.P. and Edwards, B.F.P. (2001) Insights into the structure, solvation, and mechanism of ArsC arsenate reductase, a novel arsenic detoxification enzyme. Structure 9, 1071-1081.

2 November 2001.

Østergaard, H., Henriksen, A., Hansen, F.G. and Winther, J.R. (2001) Shedding light on disulfide bond formation: engineering a redox switch in green fluorescent protein. EMBO J. 20, 5853-5862.

26 October 2001.

Pradines, J.R., Hasty, J. and Pakdaman, K. (2001) Complex ligand-protein systems: a globally convergent iterative method for the n × m case. J. Math. Biol. 43, 313-324.

19 October 2001.

Bald, D., Noji, H., Yoshida, M., Hirono-Hara, Y. and Hisabori, T. (2001) Redox regulation of the rotation of F₁-ATP synthase. J. Biol. Chem. 276, 39505-39507.

12 October 2001.

Finkel, S.E. and Kolter, R. (2001) DNA as a nutrient: novel role for bacterial competence gene homologs. J. Bacteriol. 183, 6288-6293.

5 October 2001.

Burkhardt, C. and Zacharias, M. (2001) Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation. Nucleic Acids Res. 29, 3910-3918.

28 September 2001.

Oh, D.H., King, B.A., Boxer, S.G. and Hanawalt, P.C. (2001) Spatially localized generation of nucleotide sequence-specific DNA damage. Proc. Natl. Acad. Sci. USA 98, 11271-11276.

21 September 2001.

Bell , P.J.L. (2001) Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus? J. Mol. Evol. 53, 251-256.

14 September 2001.

Kurz, M., Gu, K., Al-Gawari, A. and Lohse, P.A. (2001) cDNA-protein fusions: covalent protein-gene conjugates for the in vitro selection of peptides and protein. ChemBioChem 2, 666-672.

7 September 2001.

Taguchi, H., Ueno, T., Tadakuma, H., Yoshida, M. and Funatsu, T. (2001) Single-molecule observation of protein-protein interactions in the chaperonin system. Nature Biotechnol. 19, 861-865. [Supplementary Material]

31 August 2001.

Watts, R.A., Hunt, P.W., Hvitved, A.N., Hargrove, M.S., Peacock, W.J. and Dennis, E.S. (2001) A hemoglobin from plants homologous to truncated hemoglobins of microorganisms. Proc. Natl. Acad. Sci. USA 98, 10119-10124.

17 August 2001.

Nelson, G., Hoon, M.A., Chandrashekar, J., Zhang, Y., Ryba, N.J.P. and Zuker, C.S. (2001) Mammalian sweet taste receptors. Cell 106, 381-390.

10 August 2001.

Riccio, A., Vitagliano, L., di Prisco, G., Zagari, A. and Mazzarella, L. (2001) Liganded and unliganded forms of Antarctic fish haemoglobins in polyethylene glycol: crystallization of an R-state haemichrome intermediate. Acta Crystallogr. D57, 1144-1146.
"This is the first crystallization of a haemichrome intermediate of a vertebrate haemoglobin."

3 August 2001.

Subramaniam, R., Desveaux, D., Spickler, C., Michnick, S.W. and Brisson, N. (2001) Direct visualization of protein interactions in plant cells. Nature Biotechnol. 8, 769-772.

27 July 2001.

Kuhn, C. (2001) Computer-modeling origin of a simple genetic apparatus. Proc. Natl. Acad. Sci. USA 98, 8620-8625.

20 July 2001.

White, M.C., Doyle, A.G. and Jacobsen, E.N. (2001) A synthetically useful, self-assembling MMO mimic system for catalytic alkene epoxidation with aqueous H₂O₂. J. Am. Chem. Soc. 123, 7194-7195. [Supplementary Material]

13 July 2001.

Apic, G., Gough, J. and Teichmann, S.A. (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 310, 311-325.

6 July 2001.

Garforth, S.J., Patel, D., Feng, M. and Sayers, J.R. (2001) Unusually wide co-factor tolerance in a metalloenzyme; divalent metal ions modulate endo-exonuclease activity in T5 exonuclease. Nucleic Acids Res. 29, 2772-2779.

29 June 2001.

Cortés, A., Cascante, M., Cárdenas, M.L. and Cornish-Bowden, A. (2001) Relationships between inhibition constants, inhibitor concentrations for 50% inhibition and types of inhibition: new ways of analysing data. Biochem. J. 357, 263-268.

Looks simple, isn't it? So it is.

22 June 2001.

Ursing, B.M., van Enckevort, F.H.J., Leunissen, J.A.M. and Siezen, R.J. (2001) EXProt - a database for EXPerimentally verified Protein functions. In Silico Biology 2, 010201.

Visit EXProt at http://www.cmbi.kun.nl/EXProt/

15 June 2001.

Rau, H.K., Snigula, H., Struck, A., Robert, B., Scheer, H. and Haehnel, W. (2001) Design, synthesis and properties of synthetic chlorophyll proteins. Eur. J. Biochem. 268, 3284-3295.

8 June 2001.

Tieleman, D.P., Shrivastava, I.H., Ulmschneider, M.R. and Sansom, M.S.P. (2001) Proline-induced hinges in transmembrane helices: Possible roles in ion channel gating. Proteins 44, 63-72.

1 June 2001.

Ko, T.-P., Kuznetsov, Y.G., Malkin, A.J., Day, J. and McPherson, A. (2001) X-ray diffraction and atomic force microscopy analysis of twinned crystals: rhombohedral canavalin. Acta Crystallogr. D57, 829-839.

25 May 2001.

Gomes, C.M., Backgren, C., Teixeira, M., Puustinen, A., Verkhovskaya, M.L., Wikström, M. and Verkhovsky, M.I. (2001) Heme-copper oxidases with modified D- and K-pathways are yet efficient proton pumps. FEBS Lett. 497, 159-164.

18 May 2001.

Odom, D.T., Dill, E.A. and Barton, J.K. (2001) Charge transport through DNA four-way junctions. Nucleic Acids Res. 29, 2026-2033.

11 May 2001.

Raymo, F.M. and Giordani, S. (2001) Signal processing at the molecular level. J. Am. Chem. Soc. 123, 4651-4652. [Supplementary Material]

4 May 2001.

Fiorini, M., McKendry, R., Cooper, M.A., Rayment, T. and Abell, C. (2001) Chemical force microscopy with active enzymes. Biophys. J. 80, 2471-2476.

27 April 2001.

Ponsard, I., Galleni, M., Soumillion, P. and Fastrez, J. (2001) Selection of metalloenzymes by catalytic activity using phage display and catalytic elution. ChemBioChem 2, 253-259.

20 April 2001.

Tompa, P., Tusnády, G.E., Cserzõ, M. and Simon, I. (2001) Prion protein: Evolution caught en route. Proc. Natl. Acad. Sci. USA 98, 4431-4436.

6 April 2001.

Andrew, C.R., Green, E.L., Lawson, D.M. and Eady, R.E. (2001) Resonance Raman studies of cytochrome c' support the binding of NO and CO to opposite sides of the heme: Implications for ligand discrimination in heme-based sensors. Biochemistry 40, 4115-4122.

"Parallels between certain physicochemical properties of cytochrome c' and those of heme-based sensor proteins raise the possibility that the latter may also utilize both sides of their hemes to discriminate between NO and CO binding."

30 March 2001.

Chevalier, B.S., Monnat, R.J., Jr. and Stoddard, B.L. (2001) The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites. Nature Struct. Biol. 8, 312-316.

23 March 2001.

Lee, S.E., Sidorov, A., Gourlain, T., Mignet, N., Thorpe, S.J., Brazier, J.A., Dickman, M.J., Hornby, D.P., Grasby, J.A. and Williams, D.M. (2001) Enhancing the catalytic repertoire of nucleic acids: a systematic study of linker length and rigidity. Nucleic Acids Res. 29, 1565-1573.

16 March 2001.

Vajda, T. and Hollósi, M. (2001) Cryo-bioorganic chemistry: freezing effect on stereoselection of L- and DL-leucine cooligomerization in aqueous solution. Cell. Mol. Life Sci. 58, 343-346.

"This is the first recorded example of the effect of freezing on stereoselection".

9 March 2001.

Frauenfelder, H., McMahon, B.H., Austin, R.H., Chu, K. and Groves, J.T. (2001) The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin. Proc. Natl. Acad. Sci. USA 98, 2370-2374.

"Described as only a passive dioxygen storage protein in texts, we argue here that Mb is actually an allosteric enzyme that can catalyze reactions among small molecules."

2 March 2001.

Harding, M.M. (2001) Geometry of metal-ligand interactions in proteins. Acta Crystallogr. D57, 401-411.

23 February 2001.

Strasdeit, H., Büsching, I., Behrends, S. Saak, W. and Barklage, W. (2001) Syntheses and properties of zinc and calcium complexes of valinate and isovalinate: metal -amino acidates as possible constituents of the early Earth's chemical inventory. Chem. Eur. J. 7, 1133-1142.

16 February 2001.

Ellis, P.J., Conrads, T., Hille, R. and Kuhn, P. (2001) Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 Å and 2.03 Å. Structure 9, 125-132.

"The large subunit of arsenite oxidase is similar to other members of the dimethylsulfoxide (DMSO) reductase family of molybdenum enzymes, particularly the dissimilatory periplasmic nitrate reductase from Desulfovibrio desulfuricans, but is unique in having no covalent bond between the polypeptide and the Mo atom. The small subunit has no counterpart among known Mo protein structures but is homologous to the Rieske [2Fe-2S] protein domain of the cytochrome bc₁ and cytochrome b₆f complexes and to the Rieske domain of naphthalene 1,2-dioxygenase".

9 February 2001.

Andrec, M., Du, P. and Levy, R.M. (2001) Protein structural motif recognition via NMR residual dipolar couplings. J. Am. Chem. Soc. 123, 1222-1229.

2 February 2001.

Maccarrone, M. and Finazzi-Agrò, A. (2001) Microgravity increases the affinity of lipoxygenases for free fatty acids. FEBS Lett. 489, 283.

The catalytic efficiency of soybean lipoxygenase-1 (k_cat/K_m) was found to be ~ 4-fold higher in flight than on ground.

26 January 2001.

Armengaud, J., Sainz, G., Jouanneau, Y. and Sieker, L.C. (2001) Crystallization and preliminary X-ray diffraction analysis of a [2Fe-2S] ferredoxin (FdVI) from Rhodobacter capsulatus. Acta Crystallogr. D57, 301-303.

A bacterial [Fe₂S₂] ferredoxin possibly involved in iron-sulfur cluster biosynthesis has been crystallized for the first time.

19 January 2001.

Newman, M.E.J. (2001) The structure of scientific collaboration networks. Proc. Natl. Acad. Sci. USA 98, 404-409.

12 January 2001.

Korbel, G.A., Lalic, G. and Shair, M.D. (2001) Reaction microarrays: a method for rapidly determining the enantiomeric excess of thousands of samples. J. Am. Chem. Soc. 123, 269-278. [Electronic Supplementary Material]

5 January 2001.

Bachand, G.D., Soong, R.K., Neves, H.P. Olkhovets, A., Craighead, H.G. and Montemagno, C.D. (2000) Precision attachment of individual F₁-ATPase biomolecular motors on nanofabricated substrates. Nano Letters 1, 42-44.

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