Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture
(A) The logo plots show the frequencies of amino acids in the group-M alignment or the amino-acid preferences from our experiments at a subset of potential N-linked glycosylation sites (see S7 Fig for all 30 sites). The glycosylation sites are conserved in nature, but tolerant of mutations in our experiment. The scatter plot shows that there is a poor correlation between the preferences and natural amino-acid frequencies at all 22 alignable glycosylation sites: red triangles represent the first position in each glycosylation site, whereas gray circles represent all other sites. (B) There is much better concordance between the preferences and natural amino-acid frequencies for Env’s disulfide-bonded cysteines. The logo plots show each pair of cysteines for a subset of disulfides (see S7 Fig for all 10 disulfides). The scatter plot shows that there is a strong correlation between the preferences and natural amino-acid frequencies at all disulfide-bonded cysteines.