Публикации за 2006

Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria.
Rodionov, D. A.; Gelfand, M. S.; Todd, J. D.; Curson, A. R.; Johnston, A. W.
PLoS Comput Biol. 2006 Dec 15;2(12):e163. Epub 2006 Oct 18.
PubMed; doi 10.1371/journal.pcbi.0020163

Uncoupling effect of lauryl sulfate on mitochondria can be mediated by release of bound endogenous fatty acids.
Simonian, R. A.; Pustovidko, A. V.; Vyssokikh, M. I. u.; Skulachev, V. P.
Biochemistry (Mosc). 2006 Dec;71(12):1365-9.
PubMed

Theoretical model of interactions between ligand-binding sites in a dimeric protein and its application for the analysis of thiamine diphosphate binding to yeast transketolase.
Ospanov, R.; Kochetov, G.; Kurganov, B.
Biophys Chem. 2006 Nov 20;124(2):106-14. Epub 2006 Jun 15.
PubMed; doi 10.1016/j.bpc.2006.06.001

Identification of Escherichia coli m2G methyltransferases: II. The ygjO gene encodes a methyltransferase specific for G1835 of the 23 S rRNA.
Sergiev, P. V.; Lesnyak, D. V.; Bogdanov, A. A.; Dontsova, O. A.
J Mol Biol. 2006 Nov 17;364(1):26-31. Epub 2006 Sep 8.
PubMed; doi 10.1016/j.jmb.2006.09.008

Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA.
Lesnyak, D. V.; Sergiev, P. V.; Bogdanov, A. A.; Dontsova, O. A.
J Mol Biol. 2006 Nov 17;364(1):20-5. Epub 2006 Sep 8.
PubMed; doi 10.1016/j.jmb.2006.09.009

Human hair growth deficiency is linked to a genetic defect in the phospholipase gene LIPH.
Kazantseva, A.; Goltsov, A.; Zinchenko, R.; Grigorenko, A. P.; Abrukova, A. V.; Moliaka, Y. K.; Kirillov, A. G.; Guo, Z.; Lyle, S.; Ginter, E. K.; Rogaev, E. I.
Science. 2006 Nov 10;314(5801):982-5.
PubMed; doi 10.1126/science.1133276

Mechanism of thermal aggregation of rabbit muscle glyceraldehyde-3-phosphate dehydrogenase.
Markossian, K. A.; Khanova, H. A.; Kleimenov, S. Y.; Levitsky, D. I.; Chebotareva, N. A.; Asryants, R. A.; Muronetz, V. I.; Saso, L.; Yudin, I. K.; Kurganov, B. I.
Biochemistry. 2006 Nov 7;45(44):13375-84.
PubMed; doi 10.1021/bi0610707

Use of the flux model of amino acid metabolism of Escherichia coli.
Lyubetskaya, A. V.; Rubanov, L. I.; Gelfand, M. S.
Biochemistry (Mosc). 2006 Nov;71(11):1256-60.
PubMed

Kinetic mechanism of the bifunctional enzyme prostaglandin-H-synthase. Effect of electron donors on the cyclooxygenase reaction.
Tsaplina, L. A.; Karatasso, Y. O.; Filimonov, I. S.; Vrzheshch, P. V.
Biochemistry (Mosc). 2006 Nov;71(11):1247-55.
PubMed

Morphology and nrITS phylogeny of the genus Pinguicula L. (Lentibulariaceae), with special attention to embryo evolution.
Degtjareva, G. V.; Casper, S. J.; Hellwig, F. H.; Schmidt, A. R.; Steiger, J.; Sokoloff, D. D.
Plant Biol (Stuttg). 2006 Nov;8(6):778-90.
PubMed; doi 10.1055/s-2006-924560

Mapping contacts of the S12-S7 intercistronic region of str operon mRNA with ribosomal protein S7 of E. coli.
Golovin, A.; Spiridonova, V.; Kopylov, A.
FEBS Lett. 2006 Oct 30;580(25):5858-62. Epub 2006 Oct 2.
PubMed; doi 10.1016/j.febslet.2006.09.050

Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis.
Yang, C.; Rodionov, D. A.; Li, X.; Laikova, O. N.; Gelfand, M. S.; Zagnitko, O. P.; Romine, M. F.; Obraztsova, A. Y.; Nealson, K. H.; Osterman, A. L.
J Biol Chem. 2006 Oct 6;281(40):29872-85. Epub 2006 Jul 20.
PubMed; doi 10.1074/jbc.M605052200

Red fluorescent protein DsRed: parametrization of its chromophore as an amino acid residue for computer modeling in the OPLS-AA force field.
Dmitrienko, D. V.; Vrzheshch, E. P.; Drutsa, V. L.; Vrzheshch, P. V.
Biochemistry (Mosc). 2006 Oct;71(10):1133-52.
PubMed

Recognition of transmembrane segments in proteins: review and consistency-based benchmarking of internet servers.
Sadovskaya, N. S.; Sutormin, R. A.; Gelfand, M. S.
J Bioinform Comput Biol. 2006 Oct;4(5):1033-56.
PubMed

Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter.
Kovaleva, G. Y.; Bazykin, G. A.; Brudno, M.; Gelfand, M. S.
J Bioinform Comput Biol. 2006 Oct;4(5):981-98.
PubMed

Participation of ATP/ADP antiporter in oleate- and oleate hydroperoxide-induced uncoupling suppressed by GDP and carboxyatractylate.
Khailova, L. S.; Prikhodko, E. A.; Dedukhova, V. I.; Mokhova, E. N.; Popov, V. N.; Skulachev, V. P.
Biochim Biophys Acta. 2006 Sep-Oct;1757(9-10):1324-9. Epub 2006 May 9.
PubMed; doi 10.1016/j.bbabio.2006.04.024

Amino acid residues that determine functional specificity of NADP- and NAD-dependent isocitrate and isopropylmalate dehydrogenases.
Kalinina, O. V.; Gelfand, M. S.
Proteins. 2006 Sep 1;64(4):1001-9.
PubMed; doi 10.1002/prot.21027

If cancer is a special case of phenoptosis, how can we conquer it?
Skulachev, V. P.
Biochemistry (Mosc). 2006 Aug;71(8):930-1.
PubMed

Optimal spectral coordination of subantennae in natural antennae as an efficient strategy for light harvesting in photosynthesis.
Novikov, A. A.; Taisova, A. S.; Fetisova, Z. G.
J Bioinform Comput Biol. 2006 Aug;4(4):887-909.
PubMed

[EDAS, databases of alternatively spliced human genes].
Nurtdinov, R. N.; Neverov, A. D.; Mal'ko, D. B.; Kosmodem'ianskii, I. A.; Ermakova, E. O.; Ramenskii, V. E.; Mironov, A. A.; Gel'fand, M. S.
Biofizika. 2006 Jul-Aug;51(4):589-92.
PubMed

PHOG: a database of supergenomes built from proteome complements.
Merkeev, I. V.; Novichkov, P. S.; Mironov, A. A.
BMC Evol Biol. 2006 Jun 22;6:52.
PubMed; doi 10.1186/1471-2148-6-52

PHOG-BLAST--a new generation tool for fast similarity search of protein families.
Merkeev, I. V.; Mironov, A. A.
BMC Evol Biol. 2006 Jun 22;6:51.
PubMed; doi 10.1186/1471-2148-6-51

Brain pyruvate and 2-oxoglutarate dehydrogenase complexes are mitochondrial targets of the CoA ester of the Refsum disease marker phytanic acid.
Bunik, V. I.; Raddatz, G.; Wanders, R. J.; Reiser, G.
FEBS Lett. 2006 Jun 12;580(14):3551-7. Epub 2006 May 24.
PubMed; doi 10.1016/j.febslet.2006.05.040

A metabolic network in the evolutionary context: multiscale structure and modularity.
Spirin, V.; Gelfand, M. S.; Mironov, A. A.; Mirny, L. A.
Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8774-9. Epub 2006 May 26.
PubMed; doi 10.1073/pnas.0510258103

Comparative genomics of regulation of heavy metal resistance in Eubacteria.
Permina, E. A.; Kazakov, A. E.; Kalinina, O. V.; Gelfand, M. S.
BMC Microbiol. 2006 Jun 5;6:49.
PubMed; doi 10.1186/1471-2180-6-49

Antibodies to inactive conformations of glyceraldehyde-3-phosphate dehydrogenase inactivate the apo- and holoforms of the enzyme.
Arutiunova, E. I.; Pleten, A. P.; Nagradova, N. K.; Muronetz, V. I.
Biochemistry (Mosc). 2006 Jun;71(6):685-91.
PubMed

Evolution of transcriptional regulatory networks in microbial genomes.
Gelfand, M. S.
Curr Opin Struct Biol. 2006 Jun;16(3):420-9. Epub 2006 May 2.
PubMed; doi 10.1016/j.sbi.2006.04.001

[Membrane probability profile construction based on amino acids sequences multiple alignment].
Sutormin, R. A.; Mironov, A. A.
Mol Biol (Mosk). 2006 May-Jun;40(3):541-5.
PubMed

[ClusterTree-RS: the binary tree algorithm for identification of co-regulated genes by clustering regulatory signals].
Stavrovskaia, E. D.; Makeev, V. I. u.; Mironov, A. A.
Mol Biol (Mosk). 2006 May-Jun;40(3):524-32.
PubMed

Fast rate of evolution in alternatively spliced coding regions of mammalian genes.
Ermakova, E. O.; Nurtdinov, R. N.; Gelfand, M. S.
BMC Genomics. 2006 Apr 18;7:84.
PubMed; doi 10.1186/1471-2164-7-84

Bioenergetic aspects of apoptosis, necrosis and mitoptosis.
Skulachev, V. P.
Apoptosis. 2006 Apr;11(4):473-85.
PubMed; doi 10.1007/s10495-006-5881-9

Unfolded, oxidized, and thermoinactivated forms of glyceraldehyde-3-phosphate dehydrogenase interact with the chaperonin GroEL in different ways.
Naletova, I. N.; Muronetz, V. I.; Schmalhausen, E. V.
Biochim Biophys Acta. 2006 Apr;1764(4):831-8. Epub 2006 Mar 6.
PubMed; doi 10.1016/j.bbapap.2006.02.002

Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes.
Malko, D. B.; Makeev, V. J.; Mironov, A. A.; Gelfand, M. S.
Genome Res. 2006 Apr;16(4):505-9. Epub 2006 Mar 6.
PubMed; doi 10.1101/gr.4236606

RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA.
Danilova, L. V.; Pervouchine, D. D.; Favorov, A. V.; Mironov, A. A.
J Bioinform Comput Biol. 2006 Apr;4(2):589-96.
PubMed

Polymorphism in the 5'-promoter region of serine racemase gene in schizophrenia.
Goltsov, A. Y.; Loseva, J. G.; Andreeva, T. V.; Grigorenko, A. P.; Abramova, L. I.; Kaleda, V. G.; Orlova, V. A.; Moliaka, Y. K.; Rogaev, E. I.
Mol Psychiatry. 2006 Apr;11(4):325-6.
PubMed; doi 10.1038/sj.mp.4001801

Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression.
Boeva, V.; Regnier, M.; Papatsenko, D.; Makeev, V.
Bioinformatics. 2006 Mar 15;22(6):676-84. Epub 2006 Jan 10.
PubMed; doi 10.1093/bioinformatics/btk032

A new method for spectrophotometric assay of activity of cross-linked penicillin acylase aggregates.
Pchelintsev, N. A.; Youshko, M. I.; Svedas, V. K.
Biochemistry (Mosc). 2006 Mar;71(3):315-9.
PubMed

Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius.
Rogaev, E. I.; Moliaka, Y. K.; Malyarchuk, B. A.; Kondrashov, F. A.; Derenko, M. V.; Chumakov, I.; Grigorenko, A. P.
PLoS Biol. 2006 Mar;4(3):e73. Epub 2006 Feb 7.
PubMed; doi 10.1371/journal.pbio.0040073

Computational identification of BioR, a transcriptional regulator of biotin metabolism in Alphaproteobacteria, and of its binding signal.
Rodionov, D. A.; Gelfand, M. S.
FEMS Microbiol Lett. 2006 Feb;255(1):102-7.
PubMed; doi 10.1111/j.1574-6968.2005.00070.x

Low cetyltrimethylammonium bromide concentrations induce reversible amorphous aggregation of tobacco mosaic virus and its coat protein at room temperature.
Panyukov, Y. V.; Nemykh, M. A.; Rafikova, E. R.; Kurganov, B. I.; Yaguzhinsky, L. S.; Arutyunyan, A. M.; Drachev, V. A.; Dobrov, E. N.
Int J Biochem Cell Biol. 2006;38(4):533-43. Epub 2005 Nov 14.
PubMed; doi 10.1016/j.biocel.2005.10.014

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