| Beta-solenoids are helical proteins stabilized by beta sheets that run perpendicular to the helical axis. These proteins can be found in nature, with lengths on the order of nanometers and symmetric cross-sections resembling rectangles and triangles. Due to their layers of beta sheets, which associate via hydrogen bonds, beta-solenoids are symmetric, rigid proteins that are stable even in relatively extreme environments. The prevalence of beta sheet secondary structures also allows beta-solenoid monomers to self-assemble into larger, more complex oligomers. The robustness, size, shape, and propensity for self-assembly of beta-solenoids make them promising candidates for bottom-up, self-assembly applications, such as templates for the growth of other structures and self-healing materials. The work of this dissertation attempts to quantify the mechanical properties of individual beta-solenoid monomers as well as study their self-assembly behavior, to better understand the potential role of beta-solenoids as structural building blocks. To do this, we use molecular dynamics to simulate the stress-strain behavior of individual monomers and the cooperative behavior of many interacting monomers.;In chapter 1, biological background on beta-solenoids and self-assembly, as well as theoretical background for molecular dynamics, analysis methods such as umbrella sampling and construction of potentials of mean force, and the model used to define strength quantities for the beta-solenoids, are presented. In chapter 2, a study of the mechanical properties of a set of beta-solenoid proteins is presented. In chapter 3, another strength study is shown, with a more detailed focus on two particular beta-solenoids and a comparison to experiment. The contents of chapters 2 and 3 have each been published elsewhere, and are simply reformatted for presentation in this dissertation. Chapter 4 covers work on simulating the self-assembly of beta-solenoid proteins, including a review of methods of simulating large systems. Finally, chapter 5 briefly summarizes the work and comments on possible next steps. |
