Dr Adele Williamson from The University of Waikato explains how scientists research the function of enzymes1. Her research on extremophilic microorganisms2 is discovering unique enzymes. Finding out the function of these newly discovered enzymes is an important step to exploring if they may be useful in other fields of science.
Find out more about Dr Adele Williamson’s research in these articles:
Transcript
Dr Adele Williamson
First of all, to identify a gene3 that encodes for a protein4, you need to have a look in the DNA5 of the organism6. We do that by sequencing the DNA. So that’s actually reading the As, Ts, Gs and Cs of the DNA.
Then, to find the gene, you have a look for patterns in the nucleotides7 of the DNA which signal start making a protein here and stop making a protein further down, with a long chain of amino acids8 in between. So that’s just finding the gene that encodes for a protein.
To then know what the function of that protein is, we use what we call bioinformatics9, which is a method where we’re using computational and statistical techniques to look at biological information about DNA and protein sequences, and we use computer algorithms10 which look for specific patterns of amino acids11 in these gene and protein sequences.
To identify the function of an enzyme12, we have a look at the conserved bits of an enzyme, which means bits that are really similar. So when you think of an active site13 of an enzyme – where the chemistry is going to happen – the parts of that enzyme tend to be quite similar irrespective of what the rest of the enzyme structure is doing. And that’s because these are the essential bits, so they need to be in a particular position for that chemistry to occur. And by honing in on those conserved parts of an enzyme, we know that that’s the function that the enzyme has.
One way of doing that is to get the gene – or maybe the protein sequence if you’re talking about the amino acid sequence – of a whole lot of different enzymes which we know have the same function. So this could be from several bacteria14, from a human, from several other animals, several other eukaryotes15. And then you line all these up to try and find the parts of that protein sequence that are very similar or the same. Then you would say that that’s the conserved part of the sequence.
You can make a statistical model of how likely it is that one amino acid is going to be in that position and that a different amino acid is going to be in the next position for example. So you can use that pattern recognition and then go to other protein sequences that we don’t know what they do, use a computer algorithm16 to have a look for those patterns in the unknown protein sequences. And if we find that pattern in this particular place in the enzyme – even though the rest of the enzyme might be different – you have a very good clue that that might be what that enzyme is doing.
Acknowledgements
Dr Adele Williamson, The University of Waikato
Animated footage source, PDB-101. PDB-101 is the educational portal of RCSB Protein Data17 Bank
