Paper Citing NAMD - Abstract
Sharma, Gaurav; Rege, Kaushal; Budil, David E.; Yarmush, Martin; Mavroidis, Constantinos
Biological Force Measurement in a Protein-Based Nanoactuator
IEEE TRANSACTIONS ON NANOTECHNOLOGY, 8:684-691, NOV 2009
The mechanical force exerted by a nanoactuator due to pH actuation is discussed from a statistical mechanics and free energy of conformational change viewpoint. We use molecular dynamics to show that the nanoactuator, based on the coiled-coil leucine zipper portion of a yeast transcriptional activator protein, can generate mechanical forces of the order of 20-40 pN upon pH modulation. The forces are generated due to the electrostatic repulsions at low pH between His-tag handles and other charged residues engineered into the protein sequence. The biological force output of the nanoactuator is comparable to that generated by adenosine triphosphate (ATP)-based molecular motors such as myosin and kinesin even though the nanoactuator is smaller in size to these molecular motors. The force calculation technique can readily be applied to other biomolecular systems and has implications in the area of bionanotechnology and in particular to study and characterize the properties of novel protein and DNA-based nanodevices.
