In particular, the hydrophobic isoleucine (I44) region, which forms the main binding surface of Ub, is exposed in one model and buried in the other.
Mutation of the charged residues in the vicinity of Asp1023, including E862K (Supplementary information, Figure S5C, Scp1-M7) anD916K/E919K9K (Supplementary information, Figure S5C, Scp1-M8) had no detectable impact on Sre1 binding, suggesting that Asp1023 may demarcate the Sre1-binding surface of Scp1 on one side (Supplementary information, Figure S5A).
Expression of class 1 genes is sensitive to mutations in binding surface of TBP, and their promoters often contain one of the eight variants of the 8 nucleotide-long TATA box consensus sequence [ 18].
Whereas most DNA-binding proteins seem to use a charged surface rich in lysine and arginine residues to bind backbone phosphates, the DNA binding surface of OGG1 is nearly charge neutral.
One way to test this hypothesis is to identify the DNMT3A binding surface of the G9a ANK domain and make point mutations that eliminate DNMT3A binding.
Kobayashi, K. et al. Identification and characterization of the RNA binding surface of the pentatricopeptide repeat protein.
The substrate binding surface lies on one face of the Kelch domain, where a shallow pocket is created by the long loops that connect β-strands D and A (DA loop) as well as β-strands B and C (BC loop).
However, recent studies on the structure of expansins have identified two potential polysaccharide binding surfaces, one of which corresponds to the buried D2 face contacting D1 [ 44].
A triple mutation on a predicted PTEN-binding surface of the BH domain suggests that a least one of the mutated residues is located in the interface.
To quantify the binding we first immobilized sonicated fibrils on the surface of one flow cell of a CM5 biosensor chip and added monomeric α-Syn protein (Supplementary Fig. S9a).
