Paper Citing NAMD - Abstract
Eren, Dilek; Alakent, Burak
Frequency Response of a Protein to Local Conformational Perturbations
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003238, SEP 2013
Signals created by local perturbations are known to propagate long distances through proteins via backbone connectivity and nonbonded interactions. In the current study, signal propagation from the flexible ligand binding loop to the rest of Protein Tyrosine Phosphatase 1B (PTP1B) was investigated using frequency response techniques. Using restrained Targeted Molecular Dynamics (TMD) potential on WPD and R loops, PTP1B was driven between its crystal structure conformations at different frequencies. Propagation of the local perturbation signal was manifested via peaks at the fundamental frequency and upper harmonics of 1/f distributed spectral density of atomic variables, such as C-alpha atoms, dihedral angles, or polar interaction distances. Frequency of perturbation was adjusted high enough (simulation length >similar to 10xperiod of a perturbation cycle) not to be clouded by random diffusional fluctuations, and low enough (
