Multiple Sequence Alignments

Multiple Sequence Alignments

Figure 1 is a comparison of Arp2 sequences across several different species. Figure 2 is a comparison of Arp3 sequences, similarly across several different species. Figure 3 compares multiple isoforms of the same subunits, i.e. this is a comparison of sequences within the human species. The first sequence is that of the Arp2 isozyme A and the second is that of the Arp2 isozyme B. The last sequence corresponds to Arp3.

Figure 1. Comparison of Arp2 Sequences Across Species

Figure 1. Comparison of Arp2 Sequences Across Species

Figure 2. Comparison of Arp3 Sequences Across Species

Figure 2. Comparison of Arp3 Sequences Across Species

Figure 3. Comparison of Isozyme Sequences

Figure 3. Comparison of Isozyme Sequences

Observations

The first multiple sequence analysis shows very similar sequences in all organisms with only a few amino acids difference in fruit flies with ARP 2. The sequences between organisms for ARP 3 are identical. The comparison of sequences in different organisms shows how important a protein is; this particular protein must be very important for life as it is identical across a wide range of species with a very similar sequence being found invertebrate too; it has been maintained throughout evolution and therefore must play a significant role in life.

The second multiple sequence analysis shows that isozyme A and B are the same. However, A has an additional 5 amino acids (NNKKM) at position 55 (click here to read more). What is the significance of this?

A BLAST of these two isozymes shows that both isozyme A and B contain a Nucleotide-Binding Domain (NBD) of the sugar kinase/HSP70/actin superfamily. However, in isozyme A the domain is a lot shorter. This could be due to the extra 5 amino acids-NNKKM- interrupting a motif in the sequence. This could mean that isozyme A can bind a different molecule than the other isoforms giving it a gain of function perhaps.

Other notable features (REF: http://www.uniprot.org/uniprot/P61160):

3 ATP Binding Sites:

Positions: 160-162, 214-218, 305-310

Protein Modifications:

At positions 299 and 311 there are protein modifications. The lysine has been acetylated to become N6-acetyllysine. What is the significance of this?

REF: http://www.sciencemag.org/content/325/5942/834.full.pdf

The acetylation of lysine is a reversible post translational modification. It neutralises the positive charge that lysine normally carries. This can affect the other molecules that the protein can bind with as well as interactions within the protein itself. Study has shown that three proteins which interact with ARP2, cortactin, coffilin, and coronin, also contain acetylated lysine’s indicating this could be the way these proteins interact with each other. Acetylation of lysine’s can also play a part in cell signalling in the case of some proteins, perhaps this could be a route for further research.

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