Question

How do you know if an MSA is in an alpha helix or beta sheet?? Do either of them have certain patterns?

Answer 1

MSA- multiple sequence alignment is the alignment of proteins in specific sequences according to their occurance in different forms like in secondary and tertiary structures. These sequences can also help in knowing the sequence of even nucleotides or amino acids. Yes, different types of them have certain patterns through which they are easily recognised. In case of Alpha helix in protein sequences, the secondary structure of proteins is twisted into a right handed manner with hydrogen bond formation between N-H group of one amino acid to the C=O group of another amino acid . The another amino acid is 4 residues away. The major difference in the beta sheet in MSA is that they are made up of pleated sheets of amino acids residues of beta strands that are linked together by hydrogen bonds. Both the structures in MSA have hydrogen bonding but they have different structure and bonding is between different amino acids. In Beta sheets ,the bonding is with the adjacent amino acid only. So we can easily recognise the difference despite between some common similarities.

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