Quantum biochemistry study of the T3-785 tropocollagen triple-helical structure

• Published in: Chemical physics letters Vol. 559; pp. 88 - 93
• Main Authors: Rodrigues, C.R.F., Oliveira, J.I.N., Fulco, U.L., Albuquerque, E.L., Moura, R.M., Caetano, E.W.S., Freire, V.N.
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 20-02-2013
• ISSN: 0009-2614; 1873-4448
• DOI: 10.1016/j.cplett.2012.12.061

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► Quantum mechanics computation methods to survey the structure of the collagen-like peptide T3-785. ► Density functional theory within the local density approximation (LDA). ► Energy profile for each amino acid residue–monomer interaction in the collagen-like peptide T3-785. ► Binding site, interaction energy and residues domain (BIRD) spectra for the collagen-like peptide T3-785.
We estimate the residue–monomer and residue–residue interaction energies of the collagen-like peptide T3-785, whose triple helix structure is the sequence X–Y-glycine (X, Y are often the imino acids proline and hydroxyproline), considering its full X-ray diffraction crystal structure, including a hydratation layer of 111 water molecules. The computations are performed within the density functional theory (DFT) scope together with a Molecular Fractionation with Conjugate Caps (MFCC) approach. We found that the hydroxyproline and proline residues play a very important role in the stabilization of the T3-785 structure, with the arginine residue in a given peptide chain exhibiting the strongest residue–strand interaction.