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Molecular Dynamics Simulation & Structural Studies of a Designed Macromolecular Wire

img013a
Two views of the 4-helix bundle peptide showing the evolution from the design (red) to the fully equilibrated structure (green). The cofactors are positioned along the length of the bundle within its core via axial bis-histidyl ligation of the porphyrin metal (Fe) atom.

PIs: J.K. Blasie, J. Saven, W. DeGrado & M.J. Therien

Biological electron transfer occurs over large distances through cofactors whose spatial positions are controlled by the 3-D structure of the protein. Saven & DeGrado have designed an a-helical bundle incorporating a non-biological cofactor (Therien) at selected positions along the length of the bundle as a prototypical “macromolecular wire”. The chemistry and positioning of the cofactors can be used to tailor the electronic properties of the “wire”. Residues at the ends of the peptide bundle can be used to tailor its interaction with the environment allowing its positioning within nano-electronic devices. Molecular dynamics simulations (Blasie) incorporating explicit solvent have demonstrated the stability of the designed peptide “wire” in aqueous solution. Non-resonance small-angle X-ray scattering (SAXS) will will be used to characterize the overall structure of peptide “wire” in solution while resonance SAXS will determine the positions of the cofactors along the length of the bundle.

img013b
Calculated non-resonance SAXS (left) from the designed (dotted) and fully equilibrated structure (green) resulting from the MD simulation. The autocorrelation of the equilibrated structure’s electron density distribution (right) contains the distance statistics characterizing the overall bundle structure.
 

 

 

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