A Kinematic Observation and Conjecture for Creating Stable Constructs of a Peptide Nanoparticle

Abstract

Abstract. The integration of traditional mechanism theory with biology and medicine at the molecular level enables the use of polypeptide chains to design, manipulate and fabricate biomimetic artificial nano-machines. In this paper we establish a procedure to analyze the mobility of protein molecules based on predicting the formation of hydrogen bonds, which, in turn, is the primary cause for mobility reduction in proteins.We employ our established graph-based approach to evaluate the internal mobility and identify the rigid and flexible segments of the protein molecules. This computational procedure has been used to assess the stability and mobility of three specific candidate proteins to build a nanobiodevice. Our simulations show that only one of these structures is capable of producing a stable nanoparticle, which is in agreement with the experimental results.