Furthermore, an inter-domain motion during ligand binding as well as a ligand binding pocket located at the dimeric interface of form-II AckA has been reported 74 that is very hard to address through in silico docking software.
From this analysis, it is clear that the potential second binding site does not allow as tight a binding as the crystallographically determined docking site due to sub-optimal shape complementarity of 0.72 for the crystallographic interface vs 0.31 for the modeled, second binding site).
As described in the Supplementary Material, we considered the various different types of binding sites as a single united binding region important for protein function and we also considered each binding site type separately.
It is also possible that in many instances MYCN is not binding directly to DNA sequences, but instead is interacting with another DNA binding partner, such as a methyl binding protein.
The most abundant reads included those encoding lipid or fatty acid-binding proteins, such as a phosphatidylethanolamine binding protein (PEBP -homolog, acyl-CoA-binding PEBP -homologacyl-CoA-bindingtein.
DNA binding was dependent on the size of the DNA fragments used in the assay, suggesting there were multiple sites for binding, as would be expected of a protein binding to DNA in a sequence-independent manner.
A LooCI binding is realised as an outgoing binding entry on the sending node and an incoming binding entry on the receiving node, which is established by issuing bindTo and bindFrom calls to the sender and receiver, respectively.
Hog1 phosphorylates Sko1 in response to stress (Proft and Struhl 2002), but we find that this phosphorylation is not required for stress-induced Sko1 binding, suggesting that Hog1 regulates Sko1 binding as well as Hot1 binding through a sustained physical interaction rather than via phosphorylation.
As shown in Figure 3E and Supplementary Figure S5A, we identified significant enrichment of GATA transcription factor family binding sites, namely GATA1 and GATA2 binding sites, as well as a common binding site assigned to all GATA proteins (P-values for enrichment ranged from 2.38 × 10−15 to 3.28 × 10−13; Supplementary Figure S5).
GO annotation revealed that most of these specific transcripts are involved in binding, such as ATP binding, receptor binding, RNA binding, and nucleotide binding, as well as transporter- and translation-related biological processes.
We identified pattern 2 DMRs as sites of EZH2 and REST binding, as well as CTCF/RAD21 binding, in H1ESC (summarized in Figure 8B).
