Three-Dimensional Structure and Dynamics of a de Novo Designed, Amphiphilic, Metallo-Porphyrin-Binding Protein Maquette at Soft Interfaces by Molecular Dynamics Simulations

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Hongling Zou, Joseph Strzalka, Ting Xu, Andrey Tronin, J. Kent Blasie

Abstract:
The three-dimensional structure and dynamics of de novo designed, amphiphilic four-helix bundle peptides (or "maquettes"), capable of binding metallo-porphyrin cofactors at selected locations along the length of the core of the bundle, are investigated via molecular dynamics simulations. The rapid evolution of the initial design to stable three-dimensional structures in the absence (apo-form) and presence (holo-form) of bound cofactors is described for the maquettes at two different soft interfaces between polar and nonpolar media. This comparison of the apo- versus holo-forms allows the investigation of the effects of cofactor incorporation on the structure of the four-helix bundle. The simulation results are in qualitative agreement with available experimental data describing the structures at lower resolution and limited dimension.