Lab 2

VIMENTIN ALIGNMENT

Vimentin, one of the main proteins that make up intermediate filaments, is mostly used as an indicator during the development of cells and tissues. Its complete function remains elusive, though this protein is homologous in most vertebrates (Ivaska et al., 2007). For this study, six vimentin homologous sequences (protein and DNA) of the following vertebrates: Danio rerio (NP_571947.1), Heterocephalus glaber (ADP20550.1), Cyprinus carpio (AAB20706.2), Ovis aries (AAF87226.1_AF251147_1), Cricetulus griseus (CAA60679.1), and Gallus gallus (AAW49255.1) were analyzed through CLUSTALW, ALIGN, LALIGN in Biology Workbench. Since this protein can be found in most vertebrates, these six sequences were examined to see if they were analogous at the protein level. The two most similar sequences were analyzed at the protein and DNA level.

When the protein sequences were aligned with CLUSTALW (set with the program parameters), there were seventeen identical amino acids that appeared to be conserved across the six different species. There were other amino acids that appeared to be conserved among five out of the six organisms. The sequences for Cyprinus carpio and Danio rerio were the most similar. When the parameters were changed (the gap open penalty and gap extension penalty), it was expected that these two different parameters would alter the protein alignment. However, the alignment of these six proteins with a gap open penalty of 50 (five times the program’s gap open penalty) did not change. It was the same as the alignment with the program’s parameters. Another alignment was run with a gap open penalty and gap extension penalty of 10, the results were the same as the previous alignments. The lack of change in all of these alignments might seem surprising and skeptic, though this might be due to the fact that protein sequences were used to do all of these alignments rather than DNA sequences. The modification of parameters might actually not cause an enormous change in the protein alignments, thus giving the same results.

The two most closely related sequences were Cyprinus carpio and Danio rerio; since both of these species shared a morphological resemblance (they were both aquatic vertebrates), the protein alignment appeared to capture the similarity between species. However, when a pairwise alignment was run (using ALIGN) with these two amino-acid sequences, they were different from same amino-acid sequences that were aligned with CLUSTALW. This was due to the difference in gap penalties. In CLUSTALW, there were no gaps until the very end of the sequences. These two gaps were inserted in both sequences to probably match the rest of sequences. While for ALIGN, there were also two gaps for the entire alignment though they were inserted in different areas. For Cyprinos carpio, one gap was inserted a couple of amino acids before Danio rerio. Also something to note was that these two proteins were only 89% identical. If this protein was conserved among all vertebrates, then the identity would probably be higher and there would be more conserved regions. The DNA sequence data for these two closely related sequences were also aligned using ALIGN. The results did not match the amino-acid sequence alignment from CLUSTALW nor ALIGN. There were more gaps at begging and end of the DNA alignment; the identity at the DNA level was also much lower. Another pairwise alignment was run (using LALIGN) of these two sequences, the output did not match the protein alignment from ALIGN. At the begging of the DNA alignment from LALIGN, it appeared to have few gaps however further down, there were more gaps that were inserted between the sequences and the identity was also lower (82.5%).

At the protein level, all of these organisms appeared to have some regions that were conserved. However, when looking closely into just two organisms and at the DNA level there were more differences that illustrated the divergenc of vimentin.

REFERENCES

Ivaska et al. 2007. Novel functions of vementin in cell adhesion, migration, and signaling. Experimental Cell Research. 313(10): 2050-2062.

ALIGNMENTS

See FILES Below

vimentin_ALIGN_DNA.rtf
Vimentin_clustaw_protein_programparameters.rtf
vimentin_LALIGN_DNA.rtf
vimentin_protein_ALIGN.rtf
vimentin_protein_clustaw_gap_ext_pen_10.rtf
vimentin_protein_clustw_gap_open_penalty_50.rtf