Question

Consider an important protein like beta-galactosidase, which breaks down lactose. Many bacterial species have beta-galactosidase. But that doesn't mean that the amino acid sequence of beta- galactosidase in all those bacterial species is exactly the same. Far from it. As bacteria diversified into different species over evolutionary time, beta-galactosidase encoded in the genomes of the bacteria also diversified. However, we can assume that even though beta-galactosidase diversified, it was under pressure to maintain structure and function, because the reaction it catalyzes is necessary for bacteria to thrive. The existence of diversity leads under constraint of function leads to an interesting way of analyzing proteins. We can often take a protein sequence and align it with variants of the same protein found across different species, generating a multiple sequence alignment (MSA). The sequence similarities and differences may tell us something interesting about the protein because we have some confidence that all of the variants of the protein still have to fold and function the same way. Let me give you an example of this type of analysis. Consider a protein called protein A. Below is an MSA of a particular region in protein A where each row is that same region of protein A but from a different organism. ... A EIYI E C... - ADA Y VEC ... I EI Y V N G .. ... A E I Y IN M ... ... VEIYI EG .. ... AGI YIO C... Notice that all of the sequences have Yat position 4 (4th column), whereas there is variation at the other positions. So we might conclude that Y at position 4 is really important for the activity of protein A. If we also knew that protein A was an enzyme and that this region corresponds to the active site of the enzyme, perhaps we might hypothesize that is one of the catalytic amino acids in the active site for the reaction. See how we might generate hypotheses based on the patterns in an MSA? Now your turn. Consider a protein called protein B. Here is an MSA of a particular region in protein B where each row is that same region of protein B but from a different organism. VCDFGSMA. VCDFGSMA. V CLF GS F A.. - ICDEASMA - VKDFGDMA. VCDSGS MY... Based on this MSA, do you think the region shown here is more likely to be in an alpha-helix or a beta- sheet? Why? (max 3 sentences)

Answer 1

Considering the case of protein A, "Y" is playing the role of the active site in the sequence but if we consider the other sequence of amino acid residues it can be clear that those amino acid residues are aiding to form the outer part of the enzyme which is important for folding of the structure and form the cavity for the active site. As the E amino acid that is glutamic acid is present in the more amount it will aid to form the hydrophilic outer surface which will lead to providing the stability to protein while other amino acids will form the inner structure of the enzyme to make the whole structure as a functional enzyme. Thus here two amino acid residues play a crucial role which is Y and E

Based on the multiple sequence alignment provided for protein B, it can acquire the structure of the alpha-helix as a secondary structure. The alignment of the peptide provided contains the cysteine amino acid residues in it and it needs to form the disulfide bond which comes under the structure of alpha-helix to increase the structural stability which decides the function of the protein. In this peptide alignment that particular sequence has been conserved.

While the F which is phenylalanine will play a role of forming the active site of a protein B and the G that is glycine molecule to keep the flexibility of the structure as to maintain the integrity.