Design and Modeling of a Peptide Based Nanotweezer

The design hypothesis, architectures, and preliminary computational results of a peptide based nanoTweezer are presented in this paper. We engineered the α-helical coiled coil portion of the yeast transcriptional activator peptide called GCN4 to obtain an environmentally-responsive nanoTweezer. The dimeric coiled coil peptide consists of two identical ~4.5 nm long and ~3 nm wide polypeptide chains. The actuation mechanism depends on the modifying 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 the tweezer. Preliminary molecular dynamics results indicated that pH changes led to a reversible deflection of 1-2 nm with the nanoTweezer. The force profile of the nanoTweezer motion and some potential applications are also discussed. INTRODUCTION Recent advances in the field of nanotechnology have enabled widespread opportunities to investigate and manipulate matter on the nanoscale. This exciting young field is bound to shed new light on the world around us, as well as provide new opportunities for the design and development of devices exhibiting unprecedented capabilities. The assembly of these nano-devices will require a sophisticated toolbox of wellcharacterized nanorobotic elements. Fortunately, nature has already provided us with a head start in the evolution of potential nanorobotic elements, as many organisms already have molecular components that possess these desired functionalities. For example, a large body of work already exists that is focused on the study and characterization of several natural nano-devices, such as the well-known ATPase Motor [1]. The majority of these elements have been chosen for investigation due to their role in either cellular locomotion or cellular membrane transport. These devices are generally protected inside of the cell wall, where there is ample access to high-energy fuel molecules, such as ATP. Although extremely relevant in the context of cellular activities, the requirement for continual supply of high-energy fuel molecules can be a significant limitation in the use of autonomous nanorobotic devices. In this paper we present the design hypothesis, architectures and preliminary computational results of a peptide based nano-tweezer. Proteins are biopolymers that are made up from 20 different amino acids. Each of these amino acids is referred to as a residue. About fifty to hundreds of these residues are connected together via peptide bonds to create a long chain. The chain is known as a polypeptide chain or simply a protein. We used a nanoscale length two-stranded parallel α-helical coiled-coil protein/peptide to create a robust nano-tweezer that can be used for nanoscale manipulation and sensing. The coiled-coil is a ubiquitous protein motif made up of α-helices wrapping around each other forming a supercoil [2]. Coiled coils are ideal candidates for protein design studies, as they represent probably the simplest secondary structure with physical properties that make them ideal for both nanoscale manipulation and measurement. They are found to be very stable in the native state largely due a repeat of hydrophobic core (hydrophobic residues that are spaced every four and then three residues apart) in their primary sequence [34]. The particular coiled-coil model studied here is the one corresponding to the leucine zipper of the yeast transcriptional activator GCN4 [5]. This peptide consists of two identical 31residue polypeptide chains which were engineered to obtain an environmentally responsive nano-tweezer involving the reversible movement of helices towards and away from each other. The actuation mechanism depends on the creation of like electrostatic charges along the peptide chain which forces the two coils to repel each other and move apart thus creating an opening motion of the tweezer. This motion can be reversed by