Protein Modelling and Surface Folding by Limiting the Degrees of Freedom - Computational Modeling in Tissue Engineering - page 27

Fig. 5 The Clustal-W
sequence alignment denoted
in colour show identical
matched regions of alignment
between the original known
1BBF collagen file and the
''PDBB'' minimized file

CLUSTAL W Multiple Sequence Alignment

1BBF model chain A -PPGPPGPPGPPG

PDBB model chain A -PPGPPGPPGPPG

1BBF model chain C PGPPGPPGPPGP—

PDBB model chain C PGPPGPPGPPGP—

1BBF model chain B --GPPGPPGPPGPP-

PDBB model chain B --GPPGPPGPPGPP-

Fig. 6 Root Mean Square Difference (RMSD) resulting from the superposition of the 1BBF
collagen and the minimized model. The RMSD considers local and global solutions for the C a ,
the back bone and the heavy portion of the atoms (i.e. every atom in the molecule, with exception
of the hydrogen). The distances are in Angstroms

4.2 a-Coil Protein

1AQ5 is a coil-coil cartilage matrix protein of Gallus gallus (chicken). Based on
NMR [ 84 ], Fig. 4 b and c show frontal and side superposition of the known original
file and the minimized file with excellent alignment. Figure 7 shows Clustal-W
superposition of sequence of the two files with complete alignment. The adjoining
coils are the sequence matched in the superposition and the others unmatched by
Clustal-W. Figure 8 shows the local and global RMSD of the a-carbon and the
back bone. The local minimization gives the RMSD per amino acid per carbon
bone and global minimization gives the RMSD of the sequence. The RMSD
compares atoms and the total number back bones of the PDBs. Figure 9 shows a
graph of RMSD per amino acid.