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.
Recent Selected Publications
Barman A., Hamelberg D., (2014). Cysteine-Mediated Dynamic Hydrogen-Bonding Network in the Active Site of Pin1. Biochemistry, 53, 3839–3850
Tork-Ladani S., Hamelberg D., (2014). Intricacies of interactions, dynamics and solvent effects in enzyme catalysis: a computational perspective on cyclophilin A. Molecular Simulation, 40, 765-776
Doshi U., Hamelberg D., (2014). Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent. Journal of Physical Chemistry Letters, 5, 1217–1224
Zhang C., Huang Y., Jiang Y., Mulpuri N., Wei L., Hamelberg D., Brown E. M., Yang J. J., (2014). Identification of an L-Phenylalanine Binding Site Enhancing The Cooperative Responses of The Calcium Sensing Receptor to Calcium. Journal of Biological Chemistry, 289, 5296-5309
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