Macrophage scavenger receptors from both classes bind modified LDL [12], [13], and mediate its delivery to lysosomes for processing and degradation [14].
In the native TBE gel (Fig. 2A), we can see that M.SssI efficiently binds modified (ds-Z and ds-F) and non modified (ds-C) duplexes as shown by the retarded band.
Chromatin remodelers bind modified histone residues via specific domains.
SR recognize and bind modified low-density lipoprotein (LDL), multiple polyanionic ligands and cell wall components [ 41].
Gene repression and activation are regulated by proteins that interact with DNA, by enzymes that modify the core histones in nucleosomes and by proteins that bind modified residues in histones [ 13].
For example ASXL1 (additional sex comb-like 1) is a member of the Polycomb group of proteins that bind modified histones and is mutated in 11% of myelodysplastic syndromes and 43% of chronic myelomonocytic leukaemias [ 16, 17].
Second, 53BP1 is expected to have a post-DSB-repair presence because it binds modified nucleosomes (Lukas et al., 2011b; Fradet-Turcotte et al., 2013) rather than DNA, which is also compatible with our data.
The initial P6 sequence was subjected to an evolution of over several hundred thousands of rounds of 15-amino acid peptide sequences that, based on binding energies, should recognize and bind modified hASLLys3UUU with a similar or higher affinity than that of P6.
As more proteins were discovered that fit this definition, the SRs came to represent a polyphyletic group of receptors with varying domain architectures and protein structures that appear to have arose independently (for example, although CD36, a class B SR, also binds modified lipids, permutation tests show that it is unrelated to SRAI (data not shown)).
All in vivo validation experiments were performed using a technique that preserves the substrate modification and limits co-purification with non-covalently bound modifiers of modified interacting proteins [35].
