Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Session VIII Abstracts

Integrative Modeling of Proteins Ken Dill , Justin MacCallum, Alberto Perez. Stony Brook University, Stony Brook, NY, USA.

We are developing methods for combining physical forcefield-based MD simulations of proteins with external information, such as from experiments, heuristics, or database inferences. The method (MELD) is based on a statistical mechanical approach to applying spring-forces in a forgiving and adaptive way throughout an REMD simulation. We are finding it useful for refining protein structures based on NMR data, for finding peptide binding poses to receptor proteins, and for using heuristics to guide protein-structure prediction.

Protein-Protein Interactions that Inhibit the Activity of the p53 Tumor Suppressor Batu Erman . Sabanci University, Turkey. Through homology modeling, in silico docking and functional studies we identified that a BTB- Zinc Finger transcription factor, PATZ1 interacts with the tumor suppressor protein p53. PATZ1 is a ubiquitously expressed protein with known transcriptional suppressor functions. PATZ1 interacts with p53 and suppresses its transcriptional activity by competing with DNA binding by p53. Genome wide analysis of genes that are controlled by PATZ1 by RNA Sequencing revealed that PATZ1 can not only inhibit p53 activity but in some cases can activate the expression of p53 target genes. Thus we identified PATZ1 as a context dependent regulator of p53.

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