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Gram-negative bacteria are often resistant to antibiotics, posing a major threat to human health. A key defense is their outer membrane, which acts as a protective barrier to keep many antibiotics out. To maintain this barrier, they use specialized proteins to transport lipids, the main membrane building blocks, from the inner membrane across the watery space to the outer membrane. How these proteins carry out this task remains poorly understood. In collaboration with the Bhabha/Ekiert lab at Hopkins, Resource researchers used molecular dynamics simulations with NAMD 3.0 to study LetAB, one of the protein systems involved in this process. They found that this process involves lifting lipids out of the inner membrane by LetA and transferring them to the tunnel protein LetB, aided by a positively charged amino acid. These findings help explain how bacteria move membrane building blocks to maintain their protective barrier and could guide new strategies to weaken this defense against antibiotics. More details are available in Nature.
The Future of Biomolecular Modeling
A 2015 TCBG Symposium brought together scientists from across the Midwest to brainstorm about what's on the horizon for computational modeling. See a summary of what these experts foresee.
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NAMD History: The Drama
In the 1980s Klaus Schulten let two students build him a supercomputer. This
risky project, and a 1990s student revolt, led to NAMD. Now with 50,000 users
worldwide, this article charts the colorful history of NAMD. By Lisa Pollack.
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Recent Publications All Publications
- Probing Solution Dynamics of Tissue Factor Using Molecular Dynamics Simulations Guided by NMR Chemical Shifts. J. Phys. Chem. B, 2026.
- Elucidating the binding and metabolic interactions of sunitinib and sorafenib with cytochrome P450s CYP2U1 and CYP2D6. Mol. Pharmacol., 108(4):100114. 2026.
- LetA defines a structurally distinct transporter family. Nature, 651(8107): 1097–1106. 2026.
- Single-Molecule Electron Transport in Peptoids. J. Phys. Chem. B, 130(11):3054–3064. 2026.
- Cholesterol efflux protein, ABCA1, supports anticancer functions of myeloid immune cells. Sci. Adv., 12(1):eadx5490. 2026.
- Thermodynamic and Kinetic Analysis of Molecular Conformational Dynamics in a Riemannian Framework. J. Phys. Chem. A, 130(5):1220–1232. 2026.
- Simulating Gas Permeation Through the Central Pore of AQP5. Adv Exp Med Biol., 1498:105–113. 2026.
Highly Cited
Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal-phases. Journal of Physical Chemistry, 97:8343-8360, 1993.
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