Paper Citing NAMD - Abstract
McAllister, Karen A.; Zou, Hongling; Cochran, Frank V.; Bender, Gretchen M.; Senes, Alessandro; Fry, H. Christopher; Nanda, Vikas; Keenan, Patricia A.; Lear, James D.; Saven, Jeffery G.; Therien, Michael J.; Blasie, J. Kent; DeGrado, William F.
Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:11921-11927, SEP 10 2008
We have developed a computational design strategy based on the alpha-helical coiled-coil to generate modular peptide motifs capable of assembling into metalloporphyrin arrays of varying lengths. The current study highlights the extension of a two-metalloporphyrin array to a four-metalloporphyrin array through the incorporation of a coiled-coil repeat unit. Molecular dynamics simulations demonstrate that the initial design evolves rapidly to a stable structure with a small rmsd compared to the original model. Biophysical characterization reveals elongated proteins of the desired length, correct cofactor stoichiometry, and cofactor specificity. The successful extension of the two-porphyrin array demonstrates how this methodology serves as a foundation to create linear assemblies of organized electrically and optically responsive cofactors.
