(133c) Characterizing the Structure of Biomineralization Proteins Using Replica-Exchange Molecular Dynamics Simulations
Small biomineralization proteins like Mms6 found in Magnetospirillum magneticumstrain AMB-1, exhibit iron-binding activity and are known to be responsible for the formation of highly ordered magnetite nanoparticles. It is crucial to determine the structure of the Mms6 protein to understand the function and mechanism involved in the biomineralization process. A multidisciplinary study is underway to characterize the structure and function of the Mms6 protein, using NMR and molecular simulation. The focus of this presentation is on the computational aspect of the project. All-atom replica exchange molecular dynamics simulations of Mms6 in explicit water are used to generate well-sampled conformations of the protein. A detailed conformational analysis of the protein is performed that includes dihedral distributions of the protein residues and principal component analysis. A comparison between the protein secondary structural regions identified from the replica exchange simulations and the solution phase NMR experiments is discussed. The data obtained shows that the positions of the helical regions predicted by the simulations are largely consistent with the NMR structure.
This work was supported by the U. S. Department of Energy, Office of Basic Energy Science, Division of Materials Sciences and Engineering. The research was performed at the Ames Laboratory. Ames Laboratory is operated for the U.S. Department of Energy by Iowa State University under Contract No. DE-AC02-07CH11358.