Protein Modelling and Surface Folding by Limiting the Degrees of Freedom - Computational Modeling in Tissue Engineering - page 25

atoms stay in relative position inside of a bead [ 44 ]. The energy minimization is
determined by the downhill simplex method, which is a heuristic search method and
which converges to a non-stationary point. The objective function technique is
implemented in multiple-space. The method uses a simplex which is a generalization
of a triangle or tetrahedron and can be used for line segments or triangles [ 55 ].
Output The output consists of a molecular coordinate system data file that is
exported to RasMol (Molecular Visualization, Freeware) molecular graphics
visualization tool for export to a GIF three-dimensional image. Five amino acid
sequences for five proteins, including collagen, were tested using the minimizer
and compared to their published three-dimensional structures for confirmation.
The deviation between the ProteoRubix TM model and the known model was

determined.

4 Results

We considered the following examples of available Protein Data Base (PDB) files
in three categories of proteins for the minimization process: 3 10 coil (i.e. collagen
consists of 3 coils and the coil turns every 10 amino acids); a-coil; and, globular
structure protein. The minimization program was used to create three-dimensional
structures of five proteins and was compared with data from the original protein
crystallized structures. A correlation was achieved for each of the proteins as
described below. For illustration purposes, dumps (i.e. the folding process export
as data files for visualization) were added between the stages such that twisted
regions unfold. The data from the original crystallized protein structures were
compared to the data obtained after minimization. Different structural protein
types were minimized by using the objective function and compared to known
structures using a sequencer alignment.

4.1 3 10 Coil Protein

For 1BBF glycoprotein, the source of the original reference structure was a the-
oretical model [ 56 ]. Figure 4 a shows the matching superposition of the original file
given by the green strand and the minimized construct shown by the purple
backbone line along the green strand 1BBF-1. Figure 5 shows the sequence
alignment given by Clustal-W. The sequences of the three coils are superimposed
and differentiated by Coil (chain) A, Coil B and Coil C; note that the superposition
shows the alignment between the minimized file and the original file. Figure 6
shows the local and global root mean square difference (RMSD) of the a-carbon
and the back bone with distances in Angstroms in the structural alignment of the