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Fig. 3 | BMC Genomics

Fig. 3

From: Exploiting the recognition code for elucidating the mechanism of zinc finger protein-DNA interactions

Fig. 3

Amino acid propensity with respect to key residue positions of the ZFP helix for each finger. The propensities of all possible amino acids at position −1, +3, +6 of the top predicted ZFPs (considering all 64 codons) of a particular finger are reported. The colour coding for different amino acids are shown on the side panel. I) Amino acid propensity plots obtained by prediction Approach 1: (Ia) Finger 1 α-helix prefers histidine residue at 3 and arginine at −1 & 6 key residue positions. (Ib) Finger 2 α-helix is dominated by arginine at all positions. Aspartic acid has the same frequency as arginine at the key residue position 3. (Ic) Finger 3 α-helix prefers valine residue at position 3 and arginine at positions −1 & 6. II) Amino acid propensity plots obtained by prediction Approach 2: (IIa) Finger 1 α-helix prefers asparagine at −1, valine at 3 and arginine at 6 (IIb) Finger 2 α-helix is dominated by glutamine at −1, threonine at 3 and again arginine at 6 (IIc) Finger 3 α-helix prefers arginine at −1 & 6 and valine at 3. A high preference for arginine is seen at crucial positions like −1 and 6 of the helix, as it is a polar residue bolstering the interactions and the affinity at the interface

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