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Paper of the Month
Principles of Ligand Binding within a Completely Buried Cavity in HIF2α PAS-B
Key J., Scheuermann T.H., Anderson P.C., Daggett V., and Gardner K.H.
JACS, In Press, 2009
Hypoxia-inducible factors (HIFs) are heterodimeric transcription factors responsible for the metazoan hypoxia response and promote tumor growth, metastasis, and resistance to cancer treatment. The C-terminal Per-ARNT-Sim (PAS) domain of HIF2α (HIF2a PAS-B) contains a preformed solvent-inaccessible cavity that binds artificial ligands that allosterically perturb the formation of the HIF heterodimer. More...
Goals: Realistic simulation of protein dynamics, unfolding/folding, and conformational transitions linked to disease.
Latest News
- Congratulations go out to undergraduate Sara Calhoun who was awarded a Washington Research Foundation Fellowship!
- We have recently developed an XML schema for standardizing, cataloging and sharing parameters and molecular definitions for molecular mechanics force fields.
- The Microsoft External Research booklet on Socially Relevant Computing featured an article on the Dynameomics Project and how it pertains to understanding and developing treatments for diseases such as Alzheimers, Parkinson's, and cancer.
- The Daggett Group and other labs are working with Microsoft External Research to create a GrayWulf cluster optimized to analyze their Dynameomics data. Read more about the project in this report from Microsoft and on the msdn eScience blog.
- The Daggett Group was awarded 1.5 million hours on the National Energy Research Scientific Computing Center (NERSC) for 2009! This computer time supports the Dynameomics Project.
- The Dynameomics Project, which began running on the supercomputers at NERSC in 2005 with the goal of simulating the unfolding pathways of all known protein folds, was listed as a major accomplishment in Advanced Scientific Computing Research at Lawrence Berkeley National Lab.
- The group's recent paper, "The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins" published in PNAS, was highlighted by both NewsRX and Pharmacy Choice.
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