Paper Citing NAMD - Abstract
Sharma, Gaurav; Rege, Kaushal; Budil, David; Yarmush, Martin; Mavroidis, Constantinos
Design and Modeling of a Protein Based NanoGripper
2008 IEEE/RSJ INTERNATIONAL CONFERENCE ON ROBOTS AND INTELLIGENT SYSTEMS, VOLS 1-3, CONFERENCE PROCEEDINGS, 476-481, 2008
The design hypothesis, architectures, and computational modeling of a novel peptide based nanoGripper are presented in this paper. We engineered the a-helical coiled coil portion of the yeast transcriptional activator peptide called GCN4 to obtain an environmentally-responsive nanoGripper. The dimeric coiled-coil peptide consists of two identical similar to 4.5 nm long and similar to 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 a gripper. 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 nanoGripper. We also investigated the forces generated by the nanoGripper upon pH actuation. Using a new method based on a modified steered molecular dynamics technique we were able to show that the force output of the nanoGripper is comparable to that generated by ATP-based molecular motors such as myosin and kinesin even though our molecular tweezer is smaller in size to these molecular motors.
