First-principles structures for the close-packed and the 7/2 motif of collagen
1 DTU Nanotech, Ørsteds Plads, Technical University of Denmark - DK-2800 Kongens Lyngby, Denmark
2 Division of Functional Genome Analysis, German Cancer Research Center - D-69120 Heidelberg, Germany
Received: 12 July 2012
Accepted: 24 September 2012
The newly proposed close-packed motif for collagen and the more established 7/2 structure are investigated and compared. First-principles semi-empirical wave function theory and Kohn-Sham density functional theory are applied in the study of these relatively large and complex structures. The structures are refined, and comparable stability is displayed using these methods. The electronic circular dichroism of the close-packed model is shown to have a significant negative bias and a large signal. This bias is consistent with existing experimental data, though it is not unambiguously possible from the circular dichroism calculations to select one structure over the other. An interesting feature of the close-packed structure is the existence of a central channel. Simulations show that, if hydrogen atoms are placed in the cavity, a chain of molecular hydrogens is formed suggesting a possible biological function for molecular hydrogen.
PACS: 87.14.em – Fibrils (amyloids, collagen, etc.) / 87.15.ag – Quantum calculations / 87.15.M- – Spectra of biomolecules
© EPLA, 2012