Biomedical subjects

Nizar N Batada

Publications and source records attributed to Nizar N Batada.

3 recordsLinked to original sources

PubMed2004

Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center.

Nucleoside triphosphates (NTPs) diffuse to the active center of RNA polymerase II through a funnel-shaped opening that narrows to a negatively charged pore. Computer simulation shows that the funnel and pore reduce the rate of diffusion by a factor of approximately 2 x 10(-7). The resulting limitation on the rate of RNA synthesis under conditions of low NTP concentration may be overcome by NTP binding to an entry site adjacent to the active center. Binding to the entry site greatly enhances the lifetime of an NTP in the active center region, and it prevents "backtracking" and the consequent occlusion of the active site.

Binding Sites↗

PubMed2004

Stochastic model of protein-protein interaction: why signaling proteins need to be colocalized.

Colocalization of proteins that are part of the same signal transduction pathway via compartmentalization, scaffold, or anchor proteins is an essential aspect of the signal transduction system in eukaryotic cells. If interaction must occur via free diffusion, then the spatial separation between the sources of the two interacting proteins and their degradation rates become primary determinants of the time required for interaction. To understand the role of such colocalization, we create a mathematical model of the diffusion based protein-protein interaction process. We assume that mRNAs, which serve as the sources of these proteins, are located at different positions in the cytoplasm. For large cells such as Drosophila oocytes we show that if the source mRNAs were at random locations in the cell rather than colocalized, the average rate of interactions would be extremely small, which suggests that localization is needed to facilitate protein interactions and not just to prevent cross-talk between different signaling modules.

Models, Molecular↗

PubMed2004

CNplot: visualizing pre-clustered networks.

SUMMARY: CNplot is a simple technique for the visualization of global connectivity within pre-clustered network data. CNplot is easy to implement and in most cases produces informative and satisfactory summary of the data. AVAILABILITY: A Java implementation is available that allows users to modify graphics parameters and produces a LaTeX output. This software is free and is available at http://csb.stanford.edu/nbatada/VCN.html

Cluster Analysis↗