This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This research project is aimed at developing novel nanoassemblies using the mammalian iron-regulatory protein, ferritin, as a molecular machine. The idea is to use the ability of ferritin to sequester ions and complexes at its core following transport from the outside through the protein structure. In collaboration with the Watt group at BYU, we are currently using a combined synthetic and molecular simulation approach to understand how novel ions are incorporated into ferritins. The discovery that anions and metal complex ions can be co-deposited in ferritin by the Watt group has opened new synthetic possibilities for preparing nanomaterials in ferritin. This synthetic approach has confirmed that entirely novel nanostructures can be synthesized at the ferritin core, and our major goal is to use molecular dynamics simulations and theory to determine the basic mechanistic questions associated with these processes, and to use the information to guide new synthetic strategies and directions. In order to answer a number of the basic scientific questions, molecular scale simulations will be needed to complement the synthetic and structural studies. In particular, the focus of the theoretical effort will be to perform atomistic molecular dynamics simulations on Ferritin, a multi-subunit 21 kDa protein. The 24 subunits of ferritin form a hollow sphere with channels. Small organic molecules and transition metal complex ions are presumed to pass through the channels and participate in redox reactions within the sphere. For this to happen, the channels or pores would have to widen or open considerably. The timescale of pore opening in proteins is thought to range from tens of nanoseconds to microseconds. In order to simulate these events using atomistic molecular dynamics trajectories, our research group will be required to run molecular dynamics simulations to at least 40 nanoseconds (ns) and carry out subsequent Principal Component Analysis (PCA) and Guided Essential Dynamics runs along the principal components. Preliminary results obtained from a 2ns simulation already show Principal Components with fairly large variances, implying large scale motions. In order to get more accurate representations of the large scale motion, we need to run longer simulations as well as carry out frequent sampling. The required simulations can be effectively carried out only on very fast, multi-processor machines with adequate disk space to ensure that the trajectories can be run to long enough times and the data stored and processed efficiently. In addition, PCA analysis involves solving large eigensystems to include a sufficient number of atoms in the protein in the calculation. For a large protein like ferritin, the memory requirements are considerable, and exceed the resources which we are currently able to access. Our preliminary results have all been generated using the molecular dynamics simulations package GROMACS simulation. Our plan is to continue to use this package since it is already available on both BIGBEN and RACHEL. We will likely use <10 processors for each trajectory as that provides the best scaling in general for molecular dynamics simulations.
Showing the most recent 10 out of 292 publications
