Figure 3
From: A novel framework for engineering protein loops exploring length and compositional variation
InDel assembly coverage of sequence space neighbouring RYYGE and impact of selection. (a) The available sequence space is split into fixed-length landscapes and each analysed separately using the most frequent variant of the desired length as the origin for Hamming distances—a simple count of the number of mutations away from the reference sequence. (b) The biased synthesis used in the InDel assembly of this first library ensured the sequence neighbourhood of the target RYYGE sequence was efficiently explored with lower Hamming distances more effectively sampled. (c) The library remains diverse with only minimal bias for arginine incorporation in the first position, as predicted. The height of each residue in the logo is a measure of their frequency at that position. (d) Selection clearly enriches for an RXY motif particularly in n-1 and n landscapes. (e) Hamming distances to other unique sequences obtained in each landscape after selection, highlighting the presence of a local peak around RYYGE.
