Archive of Kirill's Paper of the Week

Archive of Kirill's Paper of the Week - 1996

By Kirill Degtyarenko

Last modified: Thu Apr 15 14:04:08 BST 2004

27 December 1996.

Kleywegt, G.J. and Jones, T.A. (1996) Phi/Psi-chology: Ramachandran revisited. Structure 4, 1395-1400.

20 December 1996.

Chayen, N.E., Boggon, T.J., Cassetta, A., Deacon, A., Gleichmann, T., Habash, J., Harrop, S.J., Helliwell, J.R., Nieh, Y.P., Peterson, M.R., Raftery, J., Snell, E.H., Hädener, A., Niemann, A.C., Siddons, D.P., Stojanoff, V., Thompson, A.W., Ursby, T. and Wulff, M. (1996) Trends and challenges in experimental macromolecular crystallography. Q. Rev. Biophys. 29, 227-278.

13 December 1996.

Miller, M.A. (1996) A complete mechanism for steady-state oxidation of yeast cytochrome c by yeast cytochrome c peroxidase. Biochemistry 35, 15791-15799.

6 December 1996.

Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B.-C. and Herrmann, R. (1996) Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24, 4420-4450.

29 November 1996.

Eaton, S., Bartlett, K. and Pourfarzam, M. (1996) Mammalian mitochondrial ß-oxidation. Biochem. J. 320, 345-357.

22 November 1996.

Wang, L. and Di Cera, E. (1996) Systematic derivation of partition functions for ligand binding to two-dimensional lattices. Proc. Natl. Acad. Sci. USA 93, 12953-12958.

15 November 1996.

Krauß, N., Schubert, W.-D., Klukas, O., Fromme, P., Witt, H.T. and Saenger, W. (1996) Photosystem I at 4 Å resolution represents the first structural model of a joint photosynthetic reaction centre and core antenna system. Nature Struct. Biol. 3, 965-973.

8 November 1996.

Garcia-Higuera, I., Fenoglio, J., Li, Y., Lewis, C., Panchenko, M.P., Reiner, O., Smith, T.F. and Neer, E.J. (1996) Folding of proteins with WD-repeats: comparison of six members of the WD-repeat superfamily to the G protein ß subunit. Biochemistry 35, 13985-13994.

1 November 1996.

Fontecilla-Camps, J.C., Volbeda, A. and Frey, M. (1996) Hydrogen biocatalysis: a tale of two metals. Trends Biotechnol. 14, 417-420.

25 October 1996.

Thanaraj, T.A. and Argos, P. (1996) Protein secondary structural types are differentially coded on messenger RNA. Protein Science 5, 1973-1983.

18 October 1996.

Scrutton, N.S. and Raine, A.R.C. (1996) Cation- bonding and amino-aromatic interactions in the biomolecular recognition of substituted ammonium ligands. Biochem. J. 319, 1-8.

11 October 1996.

Kanyo, Z.F., Scolnick, L.R., Ash, D.E. and Christianson, D.W. (1996) Structure of a unique binuclear manganese cluster in arginase. Nature 382, 554-557.

4 October 1996.

Something really amazing:

Takusagawa, F. and Kamitori, S. (1996) A real knot in protein. J. Am. Chem. Soc. 118, 8945-8946.

Authors have revealed a polypeptide chain knot in the previously published structure:

Takusagawa, F., Kamitori, S. and Markham, G.D. (1996) Structure and function of S-adenosylmethionine synthetase: crystal structures of S-adenosylmethionine synthetase with ADP, BrADP, and PP_i at 2.8 Å resolution. Biochemistry 35, 2586-2596.

27 September 1996.

Schenning, A.P.H.J., Benneker, F.B.G., Geurts, H.P.M., Liu, X.Y. and Nolte, R.J.M. (1996) Porphyrin wheels. J. Am. Chem. Soc. 118, 8549-8552.

20 September 1996.

Weber, G. (1996) Persistent confusion of total entropy and chemical system entropy in chemical thermodynamics. Proc. Natl. Acad. Sci. USA 93, 7452-7453.

13 September 1996.

Wallqvist, A. and Covell, D.G. (1996) Docking enzyme-inhibitor complexes using a preference-based free-energy surface. Proteins 25, 403-419.

6 September 1996. Attend the Felix Hoppe-Seyler Lecture 1996:

Rothman, J.E. (1996) Mechanisms of intracellular protein transport. Biol. Chem. 377, 407-410.

Note the change of the journal's name (formerly Biological Chemistry Hoppe-Seyler).

30 August 1996.

Jorgensen, W.L. and Tirado-Rives, J. (1996) Monte Carlo vs molecular dynamics for conformational sampling. J. Phys. Chem. 100, 14508-14513.

23 August 1996.

Flower, D.R. (1996) The lipocalin protein family: structure and function. Biochem. J. 318, 1-14.

16 August 1996.

Mines, G.A., Pascher, T., Lee, S.C., Winkler, J.R. and Gray, H.B. (1996) Cytochrome c folding triggered by electron transfer. Chemistry & Biology 3, 491-497.

9 August 1996.

Eisenberg, R.S. (1996) Intellectual property issues in genomics. Trends Biotechnol. 14, 302-307.

This paper appears in very interesting special issue of TIBTECH called Bioinformatics in the Biopharmaceutical Industry (Trends in Biotechnology vol. 14, no. 8 (151), 1996).

2 August 1996.

Hanson, R.S. and Hanson, T.E. (1996) Methanotrophic bacteria. Microbiol. Rev. 60, 439-471.

26 July 1996.

Fields, B.A. and Mariuzza, R.A. (1996) Structure and function of the T-cell receptor: insights from X-ray crystallography. Immunol. Today 17, 330-336.

19 July 1996.

Ballew, R.M., Sabelko, J. and Gruebele, M. (1996) Direct observation of fast protein folding: The initial collapse of apomyoglobin. Proc. Natl. Acad. Sci. USA 93, 5759-5764.

12 July 1996.

Ribas de Pouplana, L., Auld, D.S., Kim, S. and Schimmel, P. (1996) A mechanism for reducing entropic cost of induced fit in protein-RNA recognition. Biochemistry 35, 8095-8102.

5 July 1996.

Murzin, A.G. (1996) Structural classification of proteins: new superfamilies. Curr. Opin. Struct. Biol. 6, 386-394.

This paper appears in the June issue of Current Opinion in Structural Biology (Sequences and Topology section) full of wonderful stuff.

28 June 1996.

Schulten, K., Humphrey, W., Logunov, I., Sheves, M. and Xu, D. (1995) Molecular dynamics studies of bacteriorhodopsin's cycles. Isr. J. Chem. 35, 447-464.

This paper appears in the special issue of Israel Journal of Chemistry on Photophysics and Photochemistry of Retinal Proteins (Isr. J. Chem. vol. 35, no. 3-4, 1995).

21 June 1996. Actually there are even two papers, you may choose the better one:

Finkelstein, A.V. and Reva, B.A. (1996) Search for the most stable folds of protein chains: I. Application of a self-consistent molecular field theory to a problem of protein three-dimensional structure prediction. Protein Engineering 9, 387-397.
Reva, B.A. and Finkelstein, A.V. (1996) Search for the most stable folds of protein chains: II. Computation of stable architectures of ß-proteins using a self-consistent molecular field theory. Protein Engineering 9, 399-411.

14 June 1996.

Shortle, D., Wang, Y., Gillespie, J.R. and Wrabl, J.O. (1996) Protein folding for realists: A timeless phenomenon. Protein Science 5, 991-1000.

7 June 1996.

Nakamura, H. (1996) Roles of electrostatic interactions in proteins. Q. Rev. Biophys. 29, 1-90.

31 May 1996.

Schreiber, I., Hung, Y.-F. and Ross, J. (1996) Categorization of some oscillatory enzymatic reactions. J. Phys. Chem. 100, 8556-8566.

24 May 1996.

Kisker, C., Schindelin, H., Alber, B.E., Ferry, J.G. and Rees, D.C. (1996) A left-handed ß-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila. EMBO J. 15, 2323-2330.

17 May 1996.

Mattos, C. and Ringe, D. (1996) Locating and characterizing binding sites on proteins. Nature Biotechnol. 14, 595-599.

10 May 1996.

Wittinghofer, A. (1996) Deciphering the alphabet of G proteins: the structure of the , ß, heterotrimer. Structure 4, 357-361.

3 May 1996.

Chen, C.W. (1996) Complications and implications of linear bacterial chromosomes. Trends Genet. 12, 192-196.

26 April 1996.

Panchenko, A.R., Luthey-Schulten, Z. and Wolynes, P.G. (1996) Foldons, protein structural modules, and exons. Proc. Natl. Acad. Sci. USA 93, 2008-2013.

19 April 1996.

Westley, A.M. and Westley, J. (1996) Enzyme inhibition in open systems. Superiority of uncompetitive agents. J. Biol. Chem. 271, 5347-5352.

12 April 1996.

Engelhard, M. and Evans, P.A. (1996) Experimental investigation of sidechain interactions in early folding intermediates. Folding & Design 1, R31-R37.

5 April 1996.

Makhatadze, G.I. and Privalov, P.L. (1996) On the entropy of protein folding. Protein Science 5, 507-510.

29 March 1996.

Rozema, D. and Gellman, S.H. (1996) Artificial chaperone-assisted refolding of carbonic anhydrase B. J. Biol. Chem. 271, 3478-3487.

22 March 1996.

Kleinkauf, H. and von Döhren, H. (1996) A nonribosomal system of peptide biosynthesis. Eur. J. Biochem. 236, 335-351.

15 March 1996.

Naor, D., Fischer, D., Jernigan, R.L., Wolfson, H.J. and Nussinov, R. (1996) Amino acid pair interchanges at spatially conserved locations. J. Mol. Biol. 256, 924-938.

8 March 1996.

Trusov, Yu.A. and Dear, P.H. (1996) A molecular clock based on the expansion of gene families. Nucleic Acids Res. 24, 995-999.

1 March 1996. How to describe enzyme catalytic activity using the time-dependent Schrödinger equation? See

Bala, P., Grochowski, P., Lesyng, B. and McCammon, J.A. (1996) Quantum-classical molecular dynamics simulation of proton transfer processes in molecular complexes and in enzymes. J. Phys. Chem. 100, 2535-2545.

This paper appears in the special issue of The Journal of Physical Chemistry honoring Prof. Martin Karplus on the occasion of his 65th birthday (J. Phys. Chem. vol. 100, no. 7, Feb. 15, 1995).

23 February 1996.

Garner, C.D., Collinson, D. and Pidcock, E. (1996) The nature of the coordination sites of transition metals in proteins. Phil. Trans. R. Soc. Lond. A 354, 325-357.

16 February 1996.

Taubes, G. (1996) Science journals go wired. Science 271, 764-766.
Taubes, G. (1996) Electronic preprints point the way to `author empowerment'. Science 271, 767-768.

9 February 1996.

Tycowski, K.T., Shu, M.-D. and Steitz, J.A. (1996) A mammalian gene with introns instead of exons generating stable RNA products. Nature 379, 464-466.