The research in our group focuses on the application and development of theoretical and computational methods to gain an in-depth understanding of subcellular processes. Many interactions in cell signaling pathways are mediated by intricate networks of interacting biomolecules. 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, such as allostery, governing cell signaling mechanisms at the atomic level. 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
Souffrant M. G., Yao X-Q., Hamelberg D., (2023). Evolving Mutational Buildup in HIV-1 Protease Shifts Conformational Dynamics to Gain Drug Resistance. Journal of Chemical Information and Modeling, 12, 3892–3902
Ahmed F., Yao X-Q., Hamelberg D., (2023). Conserved Conformational Dynamics Reveal a Key Dynamic Residue in the Gatekeeper Loop of Human Cyclophilins. Journal of Physical Chemistry B, 127, 3139–3150
Kumutima J., Yao X-Q., Hamelberg D., (2022). Post-translational Modifications of Cyclophilin D Fine-Tune Its Conformational Dynamics and Activity: Implications for Its Mitochondrial Function. Journal of Physical Chemistry B, 51, 10844–10853
Yao X-Q., Hamelberg D., (2022). From Distinct to Differential Conformational Dynamics to Map Allosteric Communication Pathways in Proteins. Journal of Physical Chemistry B, 126, 2612–2620(Cover Issue)
Yao X-Q., Hamelberg D., (2022). Residue–Residue Contact Changes during Functional Processes Define Allosteric Communication Pathways. Journal of Chemical Theory and Computation, 18, 1173–1187
Deng X., Yao X-Q., Berglund K., Dong B., Ouedrago D., Ghane M. A., Zhuo Y., McBean C., Wei Z. Z., Gozem S., Yu S. P., Wei L., Fang N., Mabb A. M., Gadda G., Hamelberg D., Yang J. J., (2021). Tuning Protein Dynamics to Sense Rapid Endoplasmic‐Reticulum Calcium Dynamics. Angewandte Chemie, 60, 23289-23298