| Studying biological processes at the scale of the individual biomolecules involved presents some interesting challenges. Not only is it difficult to resolve the molecular structure and dynamics at the atomistic level of detail required, but also the physics that describe systems over the time- and length-scales relevant to single-molecule processes is not very well understood. In this work, molecular dynamics simulations were used to examine various properties of spectrin. Spectrin is a protein involved in providing mechanical stability and elasticity to the red blood cell and is constantly subjected to stresses and force. Molecular dynamics is particularly well-suited to studying systems at the scale of individual spectrin molecules, as it allows for tracking the dynamics of all of the constituent atoms. The basic material properties and unfolding behavior of spectrin was examined using molecular dynamics methods. It was found that spectrin acts as an elastic spring until it is stretched far enough that critical alpha-helical hydrogen bonds rupture. The rupture event was examined in further detail by developing a new molecular dynamics simulation technique, called synthetic AFM (atomic force microscopy). Synthetic AFM allowed for investigation of the rupture event in the context of the Fluctuation Theorem, a recent development in the field of statistical mechanics that describes small systems under the influence of external forces. The results provide new and exciting insights into the behavior of biological systems at the single-molecule level. |
