Study of Basic Local Alignment Search Tool (BLAST) and Multiple Sequence Alignment (Clustal- X) of Monoclonal mice/human antibodies

In this work, we have focused on the study of the Basic Local Alignment Search Tool (BLAST) and Multiple Sequence Alignment (Clustal-X) of different monoclonal mice antibodies to understand better the multiple alignments of sequences. Our strategy was to compare the light chains of multiple monoclonal antibodies to each other, calculating their identity percentage and in which amino acid portion. (See below figure 2) Subsequently, the same survey of heavy chains was carried out with the same methodology. (See below figure 3) Finally, sequence alignment between the light chain of one antibody and the heavy chain of another antibody was studied to understand what happens if chains are exchanged between antibodies. (See below figure 4) From our results of BLAST estimation alignment, we have reported that the Light Chains (Ls) of Monoclonal Antibodies in Comparison have a sequence Homology of about 60-80% and they have a part identical in sequence zone in range 100-210 residues amino acids, except ID PDB 4ISV, which it turns out to have a 40% lower homology than the others antibodies. As far as, the heavy chains (Hs) of Monoclonal Antibodies are concerned, however they tend to have a less homology of sequences, compared to lights chains consideration, equal to 60%-70% and they have an identical part in the sequence zone between 150-210 residues amino acids; with the exception of ID PDB 3I9G-3W9D antibodies that have an equal homology at 50%. (See supporting part) Summing up: about 70-80% identity among 2 light chains of 2 antibodies, 60-70% identity between 2 heavy chains of 2 antibodies, 30% identity between the two chains of a antibody and 30% if you compare the light chain of one antibody with the heavy chain of another antibody. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/451785v2_fig2.gif" ALT="Figure 2"> View larger version (61K): org.highwire.dtl.DTLVardef@1a5d6b1org.highwire.dtl.DTLVardef@b214daorg.highwire.dtl.DTLVardef@176fed3org.highwire.dtl.DTLVardef@153eb17_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig 2C_FLOATNO Comparison of two light chains between 5 antibodies C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/451785v2_fig3.gif" ALT="Figure 3"> View larger version (57K): org.highwire.dtl.DTLVardef@6f66f9org.highwire.dtl.DTLVardef@1d19afforg.highwire.dtl.DTLVardef@17119forg.highwire.dtl.DTLVardef@85fe98_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig 3C_FLOATNO Comparison of two heavy chains between 5 antibodies C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/451785v2_fig4.gif" ALT="Figure 4"> View larger version (43K): org.highwire.dtl.DTLVardef@10dc2f7org.highwire.dtl.DTLVardef@7b0885org.highwire.dtl.DTLVardef@16c72c8org.highwire.dtl.DTLVardef@e3c1d1_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig 4C_FLOATNO Comparison of two light chains (ID PDB 1PSK and ID PDB 1F11) of antibodies, estimated on the left side by ClustalX and on the right side by BLAST C_FIG