First-principles structures for the close-packed and the 7/2 motif of collagen

Abstract

The recently proposed close-packed motif for collagen is investigated using first principles semi-empirical wave function theory and Kohn-Sham density functional theory. Under these refinements the close-packed motif is shown to be stable. For the case of the 7/2 motif a similar stability exists. The electronic circular dichroism of the close-packed model has a significant negative bias and a large signal. 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

Computational Study of a Heterostructural Model of Type I Collagen and Implementation of an Amino Acid Potential Method Applicable to Large Proteins

“…This study, using a parameterized form for the LDA potential [45][46][47], concentrates on the low energy configurations of dihedral angles of the triplets. Jalkanen et al [48] used a semi-empirical wave function method to calculate a close-packed structural motif for the triple helix [49]. To the best of our knowledge, no detailed electronic structure calculation on collagen models has been attempted.…”

Quantum binding energy features of the T3-785 collagen-like triple-helical peptide

“…16 Suitable ab initio models to explore the stability of the implicit 17 and explicit 18 hydration network of collagen at B3LYP/ 6-31G(d) level of the theory were developed, whose collagen and b-sheet forming sequences GGG and AAG (PPG and POG) triplets destabilize (stabilize) the collagen triple helix. The semiempirical PM6 (Parameterization Method 6) model and the CAM-B3LYP functional were carried out to optimize the geometry of close-packed motif (CP) for collagen and the more established 7/2 structure, 19 suggesting a possible biological function for molecular hydrogen localized in the cavity of the CP structure. Employing ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) and AM1 (Austin Model 1) calculations, Tsai et al evaluated the effect of mutations in collagen-like triple helices, demonstrating the importance of the glycine residue in the repeating triad X-Y-Gly.…”