Finally, to minimize the effect of probe bound noncovalently to target DNA, we synthesized a peptide (14) in which the highly positively charged DNA binding domain was separated from biotin (used to capture tagged DNA) and the tagging domain by a cleavable disulfide linkage.
The DNA-binding domain is separated by a short hinge region from the ligand-binding domain, which is the largest domain and contains a dimerization domain and a transcription repression domain.
Crystal structure and EM reconstruction data indicate that the dimeric CRL3 complex would assemble such that the two substrate-binding Kelch domains are separated by 80 95 Å (1 Å=0.1 nm), an appropriate distance to engage both degrons either side of the central helix [ 31, 34].
Moreover, the IBR and RING2 domains are separated by an extended linker that occludes the canonical E2-binding site in RING1.
The two domains are separated by a hinge region of variable length, which has been related to DNA and RNA binding [ 42, 53].
The two domains were separated using RLATT.
The paired domain and the homeodomain are DNA binding domains, and are separated by a linker segment (LNK) and followed by a C-terminal region rich in proline, serine and threonine (PST).
Notably, motifs 5b,c were separated by an extended stretch of 130 aa, and the PDZ binding domain was missing.
In both processes, the extracellular ligand-binding domain of Met is separated from the intracellular kinase domain, preventing survival.
Sla2 is composed of the N-terminal lipid-binding ANTH domain and a C-terminal actin-binding domain, which are separated by a long coiled-coil region.
Here domain I (NADH binding domain) was used as ankerpoint.
