Ion channel gene expression in the inner ear.

The ion channel genome is still being defined despite numerous publications on the subject. The ion channel transcriptome is even more difficult to assess. Using high-throughput computational tools, w…

Authors: Irene S Gabashvili, Bernd H A Sokolowski, Cynthia C Morton, Anne B S Giersch

Source: Journal of the Association for Research in Otolaryngology : JARO 2007 Sep

Ribosomal dynamics inferred from variations in experimental measurements.

The crystal structures of the ribosome reveal remarkable complexity and provide a starting set of snapshots with which to understand the dynamics of translation. To augment the static crystallographic…

Authors: Irene S Gabashvili, Michelle Whirl-Carrillo, Michael Bada, D Rey Banatao, Russ B Altman

Source: RNA (New York, N.Y.) 2003 Nov

Mining biochemical information: lessons taught by the ribosome.

The publication of the crystal structures of the ribosome offers an opportunity to retrospectively evaluate the information content of hundreds of qualitative biochemical and biophysical studies of th…

Authors: Michelle Whirl-Carrillo, Irene S Gabashvili, Michael Bada, D Rey Banatao, Russ B Altman

Source: RNA (New York, N.Y.) 2002 Mar

The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22.

Variations in the inner ribosomal landscape determining the topology of nascent protein transport have been studied by three-dimensional cryo-electron microscopy of erythromycin-resistant Escherichia …

Authors: I S Gabashvili, S T Gregory, M Valle, R Grassucci, M Worbs, M C Wahl, A E Dahlberg, J Frank

Source: Molecular cell 2001 Jul

Movement of the decoding region of the 16 S ribosomal RNA accompanies tRNA translocation.

The ribosome undergoes pronounced periodic conformational changes during protein synthesis. Of particular importance are those occurring around the decoding site, the region of the 16 S rRNA interacti…

Authors: M S VanLoock, R K Agrawal, I S Gabashvili, L Qi, J Frank, S C Harvey

Source: Journal of molecular biology 2000 Dec 8

Oxygen evolution loss and structural transitions in photosystem II induced by low intensity UV-B radiation of 280 nm wavelength.

UV-B radiation of 280 nm wavelength (UV280) and low intensity (2.0 W/m2) gives rise to an important oxygen evolution (OE) loss in photosystem II (PSII) particles isolated from the thylakoid membrane o…

Authors: J A Ségui, V Maire, I S Gabashvili, M Fragata

Source: Journal of photochemistry and photobiology. B, Biology 2000 Jun

Solution structure of the E. coli 70S ribosome at 11.5 A resolution.

Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map of the complex. This map allows identificati…

Authors: I S Gabashvili, R K Agrawal, C M Spahn, R A Grassucci, D I Svergun, J Frank, P Penczek

Source: Cell 2000 Mar 3

Major rearrangements in the 70S ribosomal 3D structure caused by a conformational switch in 16S ribosomal RNA.

Dynamic changes in secondary structure of the 16S rRNA during the decoding of mRNA are visualized by three-dimensional cryo-electron microscopy of the 70S ribosome. Thermodynamically unstable base pai…

Authors: I S Gabashvili, R K Agrawal, R Grassucci, C L Squires, A E Dahlberg, J Frank

Source: The EMBO journal 1999 Nov 15

Structure and structural variations of the Escherichia coli 30 S ribosomal subunit as revealed by three-dimensional cryo-electron microscopy.

A three-dimensional reconstruction of the 30 S subunit of the Escherichia coli ribosome was obtained at 23 A resolution. Because of the improved resolution, many more structural details are seen as co…

Authors: I S Gabashvili, R K Agrawal, R Grassucci, J Frank

Source: Journal of molecular biology 1999 Mar 12

Dumb" versus "smart" kinetochore models for chromosome congression during mitosis in vertebrate somatic cells.

Authors: A Khodjakov, I S Gabashvili, C L Rieder

Source: Cell motility and the cytoskeleton 1999

Escherichia coli 70 S ribosome at 15 A resolution by cryo-electron microscopy: localization of fMet-tRNAfMet and fitting of L1 protein.

Cryo-electron microscopy of the ribosome in different binding states with mRNA and tRNA helps unravel the different steps of protein synthesis. Using over 29,000 projections of a ribosome complex in s…

Authors: A Malhotra, P Penczek, R K Agrawal, I S Gabashvili, R A Grassucci, R Jünemann, N Burkhardt, K H Nierhaus, J Frank

Source: Journal of molecular biology 1998 Jul 3

Polymorphism of bacteriophage T7.

For viruses made of nucleic acid and protein, the structure of the protein outer shell has, in the past, been found to be uniquely determined by the viral genome. However, here, non-denaturing agarose…

Authors: I S Gabashvili, S A Khan, S J Hayes, P Serwer

Source: Journal of molecular biology 1997 Oct 31

Dynamics of double stranded DNA reptation from bacteriophage.

The dynamics of dsDNA release process from a phage head has been analyzed theoretically. The process was considered as dsDNA reptation through the phage tail. The driving force is assumed to be the de…

Authors: I S Gabashvili, Grosberg AYu

Source: Journal of biomolecular structure & dynamics 1992 Apr

A theoretical model of DNA packaging in the phage head

Statistical model of dsDNA packaging to icosahedral bacteriophage capsid is presented. The model describes intraphage DNA as a globule, i.e. intramolecular liquid crystal. We analyse the free energy o…

Authors: I S Gabashvili, A Iu Grosberg, D V Kuznetsov, G M Mrevlishvili

Source: Biofizika 1991 Sep-Oct