Paper Citing NAMD - Abstract
Tagami, Katsunori; Tsukada, Masaru
Atomistic simulation of compression of single human serum albumin molecule by AFM tip
PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON NANOSCIENCE AND TECHNOLOGY, 61:1122-1126, 2007
The compression process of a single human serum albumin (HSA) molecule by an atomic force microscope (AFM) tip in ultra high vacuum (UHV) condition is studied by the molecular dynamics (MD) simulations with the all-atom empirical force field model. The temperature is assumed to be 0 and 300 K, and the force curves are calculated assuming that both the tip and surface are rigid. At T = 300 K the thermal motion is found to promote the relaxation inside the protein and reduce the normal force observed. Furthermore, the saw-tooth peaks observed in the force curves are found to originate from abrupt structural changes in the sidechains at the atomic level.
