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	Kirill Degtyarenko, home page of
last modified: 1 April 2008

CV

Projects

June 20. 1967: born in Perhushkovo, Moscow region, Russia.

1989: M.D.; M.Sc. in Biochemistry, Medico-Biological Faculty, N.I.Pirogov 2nd Moscow Medical Institute.

Secondary structure and membrane topology of P450

1992: Ph.D. in Biological Sciences, Institute of Biomedical Chemistry, Moscow.

Molecular evolution of P450 superfamily
CPD (Cytochrome P450 Database) (until 1993)

February 1994 - January 1995: postdoctoral fellow, Protein Structure and Function Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy

SBASE (until 1995)
Directory of P450-containing Systems

January 1995 - April 1998: research fellow at Department of Biochemistry and Molecular Biology, the University of Leeds, UK

PRINTS (until 1998)
PROMISE (until 1999)

From June 1998: staff member, European Bioinformatics Institute, Hinxton, UK

PFBP aka aMAZE (until 2000)
ChEBI: Chemical Entities of Biological Interest
IntEnz: Integrated Enzyme database
UniProt/Swiss-Prot
Physico-chemical ontologies for biology
- Physico-Chemical Properties and Methods (FIX)
- Physico-Chemical Processes (REX)
- See also @ OBO site
Bio, M. et al.

Papers on P450

Posting this information here, the author does not intend to convince anybody that his papers somehow changed the (P450) world or at least influenced the P450 community.

Tretiakov, V.E., Degtyarenko, K.N., Uvarov, V.Yu. and Archakov, A.I. (1989) Secondary structure and membrane topology of cytochrome P450s. Arch. Biochem. Biophys. 275, 429-439.

This is a translation of a paper written originally in Russian and published the same year in Molekuliarnaya Biologiya:

Tretiakov, V.E., Degtyarenko, K.N., Uvarov, V.Yu., Archakov, A.I., Tretiakova, L.Z. and Varenitsa, A.I. (1989) Structural organization and localization of cytochromes P450 in the membrane. Mol. Biol. (Moscow) 23, 1321-1331 (in Russian).

Now it looks a bit naive... but this was a first work where a model for P450s containing single transmembrane helix has been proposed. In addition, the Rossmann domain was predicted in microsomal P450s close to the N-terminal anchor.

Degtyarenko, K.N. and Archakov, A.I. (1993) Molecular evolution of P450 superfamily and P450-containing monooxygenase systems. FEBS Lett. 332, 1-8.

This minireview contains some original speculations, at least one of which has been proven to be completely wrong :)

Archakov, A.I. and Degtyarenko, K.N. (1993) Structural classification of the P450 superfamily based on consensus sequence comparison. Biochem. Mol. Biol. Int. 31, 1071-1080.

I will be really surprised if somebody will ever use this latter classification!

Degtyarenko, K.N. (1995) Structural domains of P450-containing monooxygenase systems. Protein Engineering 8, 737-747.

The review deals with most of the stuff collected here. Alas, it is not error-free. I'm posting here the corrected version in postscript format.

Couple of papers describing our P450 server:

Degtyarenko, K.N. and Fábián, P. (1996) The directory of P450-containing systems on WorldWide Web. CABIOS 12, 237-240.
Fábián, P. and Degtyarenko, K.N. (1997) The Directory of P450-containing Systems in 1996. Nucleic Acids Res. 25, 274-277.

And finally...

Degtyarenko, K.N. and Kulikova, T.A. (2001) Evolution of bioinorganic motifs in P450-containing systems. Biochem. Soc. Trans. 29, 139-147.

Other papers

Rukavishnikov, I.G., Uvarov, V.Yu., Degtyarenko, K.N., Tretiakov, V.E. and Archakov, A.I. (1990) The role of microenvironment in formation of microsomal epoxide hydrolase catalytically active conformational state. Biol. Membrany (Moscow) 7, 593-599 (in Russian).

In this work, the influence of phospholipid microenvironment on rat microsomal EH catalytic activity has been studied. Activation thermodynamic parameters of phenanthrene 9,10-oxide hydration and those of thermal denaturation of soluble enzyme and enzyme incorporated into phospholipid bilayer were determined. It was shown that enzyme activity is controlled by phase state of lipid bilayer. The CD spectroscopy was employed to estimate the gross secondary structure content.

A short trip in the world of restriction-modification systems:

Karyagina, A.S., Lunin, V.G., Degtyarenko, K.N., Uvarov, V.Yu. and Nikolskaya, I.I. (1993) Analysis of the nucleotide and derived amino acid sequences of the SsoII restriction endonuclease and methyltransferase. Gene 124, 13-19.

My small contribution to SBASE...

Pongor, S., Hátsági, Z., Degtyarenko, K., Fábián, P., Skerl, V., Hegyi, H., Murvai, J. and Bevilacqua, V. (1994) The SBASE protein domain library, release 3.0: a collection of annotated protein sequence segments. Nucleic Acids Res. 22, 3610-3615.
Murvai, J., Gabrielian, A., Fábián, P., Hátsági, Z., Degtyarenko, K., Hegyi, H. and Pongor, S. (1996) The SBASE protein domain library, Release 4.0: a collection of annotated protein sequence segments. Nucleic Acids Res. 24, 210-213.

...and PRINTS:

Attwood, T.K., Beck, M.E., Bleasby, A.J., Degtyarenko, K.N. and Parry-Smith, D.J. (1996) Progress with the PRINTS protein fingerprint database. Nucleic Acids Res. 24, 182-188.
Attwood, T.K., Beck, M.E., Bleasby, A.J., Degtyarenko, K.N., Michie, A.D. and Parry-Smith, D.J. (1997) Novel developments with the PRINTS protein fingerprint database. Nucleic Acids Res. 25, 212-217.
Attwood, T.K., Avison, H., Beck, M.E., Bewley, M., Bleasby, A.J., Brewster, F., Cooper, P., Degtyarenko, K.N., Geddes, A.J., Flower, D.R., Kelly, M.P., Lott, S., Measures, K.M., Parry-Smith, D.J., Perkins, D.N., Scordis, P., Scott, D. and Worledge, C. (1997) The PRINTS database of protein fingerprints: A novel information resource for computational molecular biology. J. Chem. Inf. Comput. Sci. 37, 417-424.

These latest papers describe what I was doing until April 1999:

Degtyarenko, K.N., North, A.C.T. and Findlay, J.B.C. (1997) PROMISE: a new database of information on prosthetic centres and metal ions in protein active sites. Protein Engineering 10, 183-186.
Degtyarenko, K.N., North, A.C.T., Perkins, D.N. and Findlay, J.B.C. (1998) PROMISE: a database of information on prosthetic centres and metal ions in protein active sites. Nucleic Acids Res. 26, 376-381.
Degtyarenko, K.N., North, A.C.T. and Findlay, J.B.C. (1999) PROMISE: a database of bioinorganic motifs. Nucleic Acids Res. 27, 233-236.

The first review on "BIM and BOM" bioinformatics:

Kirill Degtyarenko, home page of

CV

Projects

Papers on P450

Other papers