Highlights of our Work
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ABCG2 is a membrane transporter regulating the absorption and distribution of over 200 chemical toxins and drugs in the human body. Being able to recognize and transport a wide range of molecules, including a diverse array of chemotherapeutic agents, ABCG2 is one of the main contributors to multidrug resistance in cancer cells. In collaboration with Schuetz lab at St. Jude Children's Research Hospital, and using molecular simulations with NAMD and analyzed by VMD, we showed how a single-point mutation in ABCG2 found in tumor cells cannot complete its transport activity. Our simulations show that formation of a salt-bridge at a critical region due to the mutation may lock the transporter in one structure, thereby preventing it from undergoing conformational changes that are needed for transport. Read more in Drug Resistance Updates.
The latest NAMD 3.0 releases
provide GPU-resident molecular dynamics simulation
support for external forces,
now including Colvars and Tcl Forces.
This support allows users to take advantage of a great variety
of additional forces in their GPU-accelerated simulations
and free energy calculations.
The Colvars (collective variables) module and
Tcl Forces scripting both provide mechanisms
to define external forces between groups of atoms,
allowing control over specific structural features during a simulation
to enable the study of complex biomolecular processes and interactions.
These valuable capabilities are now available
from within NAMD's fastest simulation mode.
BmrCD, a multidrug transporter, plays a critical role in drug efflux in bacteria closely related to Staphylococcus aureus. The transporter harvests the energy of ATP to pump drugs out of the cell, thus creating resistance against drugs such as antibiotics. The mechanism of this pumping effect strongly relies on interactions with the lipids in the membrane. To elucidate these underlying protein-lipid interactions, we used VMD to model partially resolved cryo-EM lipids in BmrCD structures solved by the Mchaourab lab at Vanderbilt and simulated their behavior in a bulk membrane using GPU-accelerated NAMD 3.0 at the Center. Simulations revealed that BmrCD engages in an extensive network of interactions with lipids in multiple conformations, elucidating the stabilization of the solved structure. For more details, see our recent publication in Nature Communications.