A Kinematic Observation and Conjecture for Creating Stable Constructs of a Peptide Nanoparticle
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 improved our graph-based approach by including side chain and mixed chain hydrogen bond prediction capabilities as well as an energy analysis of these interactions. This method has been emploied 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.
Key wordsProtein molecule hydrogen bond kinematics mobility peptide nanoparticle
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