The research in our group focuses on the application and development of theoretical and computational methods with the intent of gaining an in-depth understanding of biomolecular switches. Many interactions in cell signaling pathways are mediated by intricate networks of interacting proteins and RNAs. Deregulation of these pathways could trigger cellular transformation, oncogenesis, and a host of other diseases. The research in our lab seeks to decipher the underlying principles governing cell signaling mechanisms and biomolecular interactions involving proteins and RNAs. In these endeavors, we use simulation based approaches, and related statistical mechanics, classical and quantum mechanical methods, as a complementary tool to experiments.
Velazquez H. A., Hamelberg D., (2013). Conformation-Directed Catalysis and Coupled Enzyme–Substrate Dynamics in Pin1 Phosphorylation-Dependent Cis–Trans Isomerase Journal of Physical Chemistry B, 117, 11509–11517
Nagaraju M., McGowan L. C., Hamelberg D., (2013). Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug Design. Journal of Chemical Information and Modeling, 53, 403–410
McGowan L. C., Hamelberg D., (2013). Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover Biophysical Journal, 104, 216-226
Doshi U., Hamelberg D., (2012). Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions. Journal of Chemical Theory and Computation, 8, 4004–4012
Tork-Ladani S., Hamelberg D., (2012). Entropic and Surprisingly Small Intramolecular Polarization Effects in the Mechanism of Cyclophilin A. Journal of Physical Chemistry B, 116, 10771–10778
Doshi U., McGowan L. C., Tork-Ladani S., Hamelberg D., (2012). Resolving the complex role of enzyme conformational dynamics in catalytic function. Proceedings of the National Academy of Sciences of the United States of America, 109, 5699-5704