Protein Modelling and Surface Folding by Limiting the Degrees of Freedom - Computational Modeling in Tissue Engineering - page 28

CLUSTAL W multiple sequence alignment for 1AQ5
1AQ5_model_1_chain_A
GSHMEEDPCECKSIVKFQTKVEELINTLQQKLEAVAKRIEALENKII
1AQ5_model_1_chain_C
GSHMEEDPCECKSIVKFQTKVEELINTLQQKLEAVAKRIEALENKII
PDBB-AQ5_model_default_chain_A
GSHMEEDPCECKSIVKFQTKVEELINTLQQKLEAVAKRIEALENKII
PDBB-AQ5_model_default_chain_B
GSHMEEDPCECKSIVKFQTKVEELINTLQQKLEAVAKRIEALENKII
PDBB-AQ5_model_default_chain_C
GSHMEEDPCECKSIVKFQTKVEELINTLQQKLEAVAKRIEALENKII
1AQ5_model_1_chain_B
GSHMEEDPCECKSIVKFQTKVEELINTLQQKLEAVAKRIEALENKII
Fig. 7 The Clustal-W for the alignment between the original sequence of 1AQ5 and the
minimized structure labeled as PDBB-1AQ5; colors identify each chain and matching of the files
Fig. 8 The RMSD calculations resulting from the superposition of the 1AQ5 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
4.3 Globular Proteins
1CQD, a globular protein, is a hydrolase from Zingiber officinale (ginger). Choi
et al. [ 19 ] studied the structure via X-ray diffraction. Figure 10 a shows the
superposition of the original known file (green) with the minimized file (purple).
Figure 11 shows the Clustal-W superposition of the sequence of the two files with
1,294 total number of amino acids. The colors identify the individual chains and
the similar strands that are shown together. The superimposed structures of the
PDB and the minimize file match. Figure 12 shows the local and global RMSD of
the a-carbon and back bone. The local gives the RMSD per amino acid per carbon
bone and global gives the RMSD of the sequence. The RMSD compare atom and
the total number back bones of the PDBs. Figure 13 shows the graph of RMSD per
residue and number of residues.