Paper Citing NAMD - Abstract
Sharma, Gaurav; Mavroidis, Constantinos; Rege, Kaushal; Yarmush, Martin L.; Budil, David
Computational Studies of a Protein-based Nanoactuator for Nanogripping Applications
INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH, 28:421-435, APR 2009
The design hypothesis, architectures, and computational modeling of a novel peptide-based nanoactuator are presented in this paper. We engineered the alpha-helical coiled-coil portion of the yeast transcriptional activator peptide called GCN4 to obtain an environmentally responsive nanoactuator. The dimeric coiled-coil peptide consists of two identical approximately 4.5 nm long and approximately 3 nm wide polypeptide chains. The actuation mechanism depends on the modification of electrostatic charges along the peptide by varying the pH of the solution resulting in the reversible movement of helices and, therefore, creating the motion of an actuator. Using molecular dynamics simulations we showed that pH changes led to a reversible opening of up to 1.5 nm which is approximately 150% of the initial separation of the nanoactuator. We also investigated the forces generated by the nanoactuator upon pH actuation, using a new method based on a modified steered molecular dynamics technique. Owing to its open and close motion resembling that of tweezers, the new nanoactuator can potentially be used as a nanogripper in various nanomanipulation tasks such as detection and removal of heavy metal ions during nanofabrication processes or as a molecular switch.
