Provide a desriptive and thorough answer easy to understand: 3. In the c subunit

Question

Provide a desriptive and thorough answer easy to understand:

3. In the c subunit of ATP synthase, alpha helices pack tightly together to form a ring structure. Shown below is a segment of an amino acid sequence alignment of helix 1 of subunit c from several species Bovine mitochondria Spinach chloroplast Yeast mitochondria E. coli bacterium Bacillus bacterium Clostridium Cyanobacterium VGVAGSGAGIGTVEG IGSIGPGLGQGQAAG IGLLGVGIGIAIVFA LAAIGAAIGIGILGG LGALGAGIGNGLIVS LAGIGAGIGIGIATA IGSIGPGLGQGQAAG a. Based on this alignment, write the sequence motif (e.g. PxxxRxG) that appears to be essential for structure and/or function. Note: there is more than one correct answer depending on the arbitrary threshold you use decide conserved vs. not conserved.

Explanation / Answer

a) Sequence motif is an amino acid pattern that is conserved between species and carries a biological significance.

sequence motif 1: Amino acids that are conserved in more than or equal to 3 species were only considered.

according to this threshold the sequence motif is : I/LGxI/LGAGIGIGIAxG

sequence motif 2: Amino acids that are conserved in more than or equal to 4 species upon alignment were considered.

according to this threshold, the sequence motif comes out to be :xGxIGxGIGIGxxxG

b) amino acids such as leucine, lysine, alanine have high propensity to form alpha helices, whereas Glycine and proline disrupts the helix where it is present. considering this, sequence motif 1 & 2 have less chances to form a alpha helix as both these motifs are rich in Glycine which due to its high conformational flexibility hinders in formation of a rigid alpha helix.

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