Examining Evolutionary Similarities and Differences in 3D
In the past lab we aligned 4-5 amino acid sequences of related human proteins from one family. We then superimposed these aligned sequences onto the structure of one of the members of the family. This allowed us to study conserved regions of the protein in 3-dimensions.
We can use the same tactics and techniques to study the evolution of proteins in different species. To do this we would select the same protein in several species, align the amino acid sequences and superimpose them onto the 3D structure of the protein from one species.
An easy way to obtain sequences of the same protein from different species is to either use Biology Workbench and select specific databases to search, i.e. one each from mammals, invertebrates, plants/fungi and bacteria. Another method is to perform an Entrez search and then use Blink to identify related sequences. The program colors sequences from different kingdoms in different colors making it easy to identify distantly related species.
Try to obtain 3-4 more amino acid sequences of the protein you were assigned from different species. Perform a Clustal W alignment as before and use Protein Explorer to create a consensus structure of this protein.
Which regions were conserved?
Which were not?
Did there appear to be more conservation over evolutionary time or within the family of proteins in humans?
Explain your observations.
Again you will need to show your model to an instructor, these cannot be saved.