Paper Citing NAMD - Abstract
Balog, Erika; Perahia, David; Smith, Jeremy C.; Merzel, Franci
Vibrational Softening of a Protein on Ligand Binding
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6811-6817, JUN 2 2011
Neutron scattering experiments have demonstrated that binding of the cancer drug methotrexate softens the low-frequency vibrations of its target protein, dihydrofolate reductase (DHFR). Here, this softening is fully reproduced using atomic detail normal-mode analysis. Decomposition of the vibrational density of states demonstrates that the largest contributions arise from structural elements of DHFR critical to stability and function. Mode-projection analysis reveals an increase of the breathing-like character of the affected vibrational modes consistent with the experimentally observed increased adiabatic compressibility of the protein on complexation.
