http://publicationslist.org/data/denis.kainov/atom.xml denis kainovhttp://publicationslist.org/denis.kainov$basepathfavicon.icoRecent additions to denis kainov's PublicationsList.org pagehttp://publicationslist.org/publications.png2009-06-11T13:48:45Z http://publicationslist.org/denis.kainov/refid1 2009-06-11T13:47:15Z

Patients with the rare neurodevelopmental repair syndrome known as group A trichothiodystrophy (TTD-A) carry mutations in the gene encoding the p8 subunit of the transcription and DNA repair factor TFIIH. Here we describe the crystal structure of a minimal complex between Tfb5, the yeast ortholog of p8, and the C-terminal domain of Tfb2, the yeast p52 subunit of TFIIH. The structure revealed that ...<br/><br/>Denis E Kainov, Marc Vitorino, Jean Cavarelli, Arnaud Poterszman, Jean-Marc Egly (2008) <i>Nat Struct Mol Biol</i> <i></i> <i></i> 15: 9 980-984<br/>

http://publicationslist.org/denis.kainov/refid2 2009-06-11T13:47:15Z

The P4 protein of bacteriophage phi12 is a hexameric molecular motor closely related to superfamily 4 helicases. P4 converts chemical energy from ATP hydrolysis into mechanical work, to translocate single-stranded RNA into a viral capsid. The molecular basis of mechanochemical coupling, i.e. how small approximately 1 A changes in the ATP-binding site are amplified into nanometer scale motion along...<br/><br/>Denis E Kainov, Erika J Mancini, Jelena Telenius, Jirí Lísal, Jonathan M Grimes, Dennis H Bamford, David I Stuart, Roman Tuma (2008) <i>J Biol Chem</i> <i></i> <i></i> 283: 6 3607-3617<br/>

http://publicationslist.org/denis.kainov/refid3 2009-06-11T13:47:15Z

A label- and immobilization-free approach to detecting the reversible formation of complexes between nucleic acids and proteins at the single-molecule level is described. The voltage-driven translocation of individual oligoribonucleotides through a nanoscale protein pore is observed by single-channel current recordings. The oligoribonucleotide 5'-C25A(25)-3' gives rise to current blockades with an...<br/><br/>Yann Astier, Denis E Kainov, Hagan Bayley, Roman Tuma, Stefan Howorka (2007) <i>Chemphyschem</i> <i></i> <i></i> 8: 15 2189-2194<br/>

http://publicationslist.org/denis.kainov/refid5 2009-06-11T13:47:15Z

Genome packaging into an empty capsid is an essential step in the assembly of many complex viruses. In double-stranded RNA (dsRNA) bacteriophages of the Cystoviridae family this step is performed by a hexameric helicase P4 which is one of the simplest packaging motors found in nature. Biochemical and structural studies of P4 proteins have led to a surprising finding that these proteins bear mechan...<br/><br/>D E Kainov, R Tuma, E J Mancini (2006) <i>Cell Mol Life Sci</i> <i></i> <i></i> 63: 10 1095-1105<br/>

http://publicationslist.org/denis.kainov/refid4 2009-06-11T13:47:15Z

Many viruses employ molecular motors to package their genomes into preformed empty capsids (procapsids). In dsRNA bacteriophages the packaging motor is a hexameric ATPase P4, which is an integral part of the multisubunit procapsid. Structural and biochemical studies revealed a plausible RNA-translocation mechanism for the isolated hexamer. However, little is known about the structure and regulatio...<br/><br/>Jirí Lísal, Denis E Kainov, TuKiet T Lam, Mark R Emmett, Hui Wei, Paul Gottlieb, Alan G Marshall, Roman Tuma (2006) <i>Virology</i> <i></i> <i></i> 351: 1 73-79<br/>

http://publicationslist.org/denis.kainov/refid6 2009-06-11T13:47:15Z

Molecular motors undergo cyclical conformational changes and convert chemical energy into mechanical work. The conformational dynamics of a viral packaging motor, the hexameric helicase P4 of dsRNA bacteriophage phi8, was visualized by hydrogen-deuterium exchange and high-resolution mass spectrometry. Concerted changes of exchange kinetics revealed a cooperative unit that dynamically links ATP-bin...<br/><br/>Jirí Lísal, Tukiet T Lam, Denis E Kainov, Mark R Emmett, Alan G Marshall, Roman Tuma (2005) <i>Nat Struct Mol Biol</i> <i></i> <i></i> 12: 5 460-466<br/>

http://publicationslist.org/denis.kainov/refid7 2009-06-11T13:47:15Z

Bacteriophage varphi12 protein P7 is a structural component of the polymerase complex and ensures stable packaging of the genomic RNA. varphi12 P7 has been cloned, purified and crystallized. Crystals belong to space group P3(2)21, with unit-cell parameters a = 75.7, b = 75.7, c = 45.2 A, alpha = 90, beta = 90, gamma = 120 degrees , and diffract beyond 2.0 A. Multiple anomalous dispersion data have...<br/><br/>Denis E Kainov, Vladimir Simonov, Dennis H Bamford, Roman Tuma, Paul Gottlieb, Hui Wei, Martin A Walsh, Hassan Belrhali, Michael C Merckel (2004) <i>Acta Crystallogr D Biol Crystallogr</i> <i></i> <i></i> 60: Pt 12 Pt 2 2368-2370<br/>

http://publicationslist.org/denis.kainov/refid8 2009-06-11T13:47:15Z

Many viruses package their genome into preformed capsids using packaging motors powered by the hydrolysis of ATP. The hexameric ATPase P4 of dsRNA bacteriophage phi12, located at the vertices of the icosahedral capsid, is such a packaging motor. We have captured crystallographic structures of P4 for all the key points along the catalytic pathway, including apo, substrate analog bound, and product ...<br/><br/>Erika J Mancini, Denis E Kainov, Jonathan M Grimes, Roman Tuma, Dennis H Bamford, David I Stuart (2004) <i>Cell</i> <i></i> <i></i> 118: 6 743-755<br/>

http://publicationslist.org/denis.kainov/refid12 2009-06-11T13:47:51Z

Many complex viruses acquire their genome by active packaging into a viral precursor particle called a procapsid. Packaging is performed by a viral portal complex, which couples ATP hydrolysis to translocation of nucleic acid into the procapsid. The packaging process has been studied for a variety of viruses, but the mechanism of the associated ATPase remains elusive. In this study, the mechanism ...<br/><br/>Jíri Lísal, Denis E Kainov, Dennis H Bamford, George J Thomas, Roman Tuma (2004) <i>J Biol Chem</i> <i></i> <i></i> 279: 2 1343-1350<br/>

http://publicationslist.org/denis.kainov/refid10 2009-06-11T13:47:15Z

The hexameric ATPase P4 from bacteriophage phi 12 is responsible for packaging single-stranded genomic precursors into the viral procapsid. P4 was overexpressed in Escherichia coli and purified. Crystals of native and selenomethionine-derivatized P4 have been obtained that belong to space group I222, with half a hexamer in the asymmetric unit and unit-cell parameters a = 105.0, b = 130.5, c = 158....<br/><br/>Erika J Mancini, Denis E Kainov, Hui Wei, Paul Gottlieb, Roman Tuma, Dennis H Bamford, David I Stuart, Jonathan M Grimes (2004) <i>Acta Crystallogr D Biol Crystallogr</i> <i></i> <i></i> 60: Pt 3 588-590<br/>

http://publicationslist.org/denis.kainov/refid9 2009-06-11T13:47:15Z

Double-stranded RNA viruses sequester their genomes within a protein shell, called the polymerase complex. Translocation of ssRNA into (packaging) and out (transcription) of the polymerase complex are essential steps in the life cycle of the dsRNA bacteriophages of the Cystoviridae family (phi6-phi14). Both processes require a viral molecular motor P4, an NTPase, which bears structural and functio...<br/><br/>Denis E Kainov, Jirí Lísal, Dennis H Bamford, Roman Tuma (2004) <i>Nucleic Acids Res</i> <i></i> <i></i> 32: 12 3515-3521<br/>

http://publicationslist.org/denis.kainov/refid14 2009-06-11T13:47:51Z

Double-stranded RNA (dsRNA) viruses are complex RNA processing machines that sequentially perform packaging, replication and transcription of their genomes. In order to characterize the assembly intermediates of such a machine we have developed an efficient in vitro assembly system for the procapsid of bacteriophage phi8. The major structural protein P1 is a stable and soluble tetramer. Three tetr...<br/><br/>Denis E Kainov, Sarah J Butcher, Dennis H Bamford, Roman Tuma (2003) <i>J Mol Biol</i> <i></i> <i></i> 328: 4 791-804<br/>

http://publicationslist.org/denis.kainov/refid13 2009-06-11T13:47:51Z

Genomes of complex viruses have been demonstrated, in many cases, to be packaged into preformed empty capsids (procapsids). This reaction is performed by molecular motors translocating nucleic acid against the concentration gradient at the expense of NTP hydrolysis. At present, the molecular mechanisms of packaging remain elusive due to the complex nature of packaging motors. In the case of the do...<br/><br/>Denis E Kainov, Markus Pirttimaa, Roman Tuma, Sarah J Butcher, George J Thomas, Dennis H Bamford, Eugene V Makeyev (2003) <i>J Biol Chem</i> <i></i> <i></i> 278: 48 48084-48091<br/>

http://publicationslist.org/denis.kainov/refid11 2009-06-11T13:47:51Z

The packaging of genomic RNA in members of the Cystoviridae is performed by P4, a hexameric protein with NTPase activity. Across family members such as Phi6, Phi8 and Phi13, the P4 proteins show low levels of sequence identity, but presumably have similar atomic structures. Initial structure-determination efforts for P4 from Phi6 and Phi8 were hampered by difficulties in obtaining crystals that ga...<br/><br/>Erika J Mancini, Jonathan M Grimes, Robyn Malby, Geoffrey C Sutton, Denis E Kainov, Jarmo T Juuti, Eugene V Makeyev, Roman Tuma, Dennis H Bamford, David I Stuart (2003) <i>Acta Crystallogr D Biol Crystallogr</i> <i></i> <i></i> 59: Pt 12 2337-2341<br/>

http://publicationslist.org/denis.kainov/refid15 2009-06-11T13:47:51Z

The C gene product of the modification-restriction system PvuII binds to its own promoter (C box) and stimulates transcription of both the C gene and the endonuclease gene. According to our data the same regulatory mechanism is realized in the EcoRV system. It was found that upstream of the EcoRV endonuclease gene two ATG codons give rise to two open reading frames (ORF1 and ORF2) ending at the sa...<br/><br/>L A Zheleznaya, D E Kainov, A K Yunusova, N I Matvienko (2003) <i>Biochemistry (Mosc)</i> <i></i> <i></i> 68: 1 105-110<br/>