Molecular Dynamic Studies of Viral-Protein Based Nano-Actuators

Abstract

In this paper, we perform molecular simulations on novel viral protein linear nanoactuators. The main challenge in the design and performance analysis of nanodevices such as this, which are based on large conformational changes, is the limitation on computational time. A modified molecular dynamic approach known as Targeted Molecular Dynamics (TMD)is adopted to capture conformational changes within a smaller time frame (of the order of picoseconds). We study protonation and mutation of various amino acids. Our results show that when the wild type is protonated, the open state is unfavorable, unless the protonation comes along with a mutation of GLY to ALA. These findings confirm that the protein does not form a helical coil in its natural sequence. These results are in agreement with experimental observations recently made by our group at the Shriners Hospital. Furthermore, we use conventional molecular dynamics to study the effects of temperature on the conformational structure of the peptide at elevated temperatures. High temperatures are used to accelerate the process and to enable torsional barrier crossings. Approaches to quantify the observed behavior of the device, change in the secondary structure of the peptide, energy, and stability characteristics are also studied. One important observation is that classical MD simulations of the order of nanoseconds fail to capture the device motion fully and there is a need to step up into the micro- and millisecond scale.