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The role of polar and hydrophobic interactions for the molecular packing of type I collagen: A three-dimensional evaluation of the amino acid sequence

Journal of Molecular Biology
Publication Date
DOI: 10.1016/0022-2836(78)90342-x
  • Mathematics


Abstract Using the α1 and α2 chain sequences of type I collagen intermolecular interactions between neighbouring collagen molecules were calculated as a function of various geometrical parameters and their implications for molecular packing were discussed. Interaction scores for polar and hydrophobic interactions were based on a co-ordinate model of the collagen triple helix, and individual lengths were assigned to the polar and hydrophobic side-chains. All calculations were first made for ( α1) 3 molecules, then the α2 chain was inserted in each of the three possible positions: (α2 α1 α1), (α1 α2 α1) and (α1 α1 α2). The axial stagger between the molecules, their azimuthal orientations and the pitch of the triple helix were varied. Variation of the axial stagger showed that staggers of multiples of D are distinguished by interaction maxima at all azimuthal orientations. Higher interaction scores were found for 1 D than for 2 D, especially after insertion of the α2 chain in the combination of (α1 α2 α1). The best interaction edges with the highest interaction scores were found at a triple-helical pitch of 30 residues. The azimuthal angle of 90 ° to 108 ° between these edges suggested a five-stranded left-handed microfibril as the lowest packing unit. Subsequent calculations of the interactions between all combinations of “hole” and “overlap” sections of the collagen molecules led to a modification in which the regular Smith model had to be distorted to improve the interaction between the molecules.

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