Protein Modelling and Surface Folding by Limiting the Degrees of Freedom - Computational Modeling in Tissue Engineering - page 24

peptides, such as the collagen triple helix. The model presented in this section
includes the collagen fibril as a three stranded braid.
2.2 Orientation of Protein Structures
Collagen is a 3 10 helix which contains 3.6 residues per turn and has 10 atoms in the
ring which is formed by making the hydrogen bond three residues up the chain [ 32 ].
The distance is determined by H bonds that lie parallel to the helix, and the carbonyl
groups pointing along the axis in the opposite direction [ 66 ]. The opposite direction
of nitrogen and the carbonyl will set the preference distance and define the a-helix.
Since the direction is measured from the carbonyl, the distance between each turn is
3.6 residues [ 3 , 26 , 77 , 86 ].
A protein b-sheet orientation is symmetric. The b-sheet is measured from the
nitrogen terminal to the carbonyl terminal. The residue, carbonyl, and nitrogen are
on the same side [ 5 ]. The inter-strand symmetric amide proton is the donor of the
hydrogen bond to the carbonyl. For an anti-parallel orientation the exchange is
perpendicular. This is not the case for a parallel orientation. The distance between
residues is *0.347 nm for anti-parallel and *0.325 nm for parallel pleated sheet.
Parallel b-sheets tend to be more regular than anti-parallel b-sheets [ 73 ]. The range
of angles U and H angles for the peptide bonds in parallel sheets is much smaller
than that for anti-parallel sheets [ 72 ]. Parallel sheets are typically large structures
and sheets that are composed of less than five strands are rare [ 24 ]. Anti-parallel
sheets however typically consist of only a few strands [ 50 ].
Parallel sheets characteristically distribute hydrophobic side chains on both
sides of the sheet, while anti-parallel sheets are usually arranged with all their
hydrophobic residues on one side of the sheet [ 57 ]. This required an alteration of
hydrophilic and hydrophobic residues in the primary structure of peptides involved
in anti-parallel b-sheets because alternate side chains project to the same side of
the sheet [ 37 ].
In general the N-H and the C=O (each with an individual dipole moment) need
to be in the same plane to create a large net dipole for the structure whether it is an
a, b or 3 10 structure [ 46 ].
3 Computer Program
A computer program was developed to implement area minimization [ 14 , 41 ]. The
program accepts Protein Data Base (PDB) files or just amino acid sequences as
input.
Input Parameters The data from the PDB or the amino acid sequence
are randomized to simulate pre-coiling of the structure. The data are relaxed
[ 23 , 42 , 54 ] and flattened by randomly given the H and U bonds a twist [ 4 ]. All the