As intended, this study is aimed at developing a search technique using suffix trees to find recurring sequence motifs, which are corresponding to concrete binding areas of the aptamers.
Molecular docking simulations demonstrated that scutellarein and luteolin could be well-docked into the catalytic site of EcGUS, while the binding areas of these two natural inhibitors on EcGUS were highly overlapped with that of PNPG on EcGUS.
This interacting surface is equivalent to the known binding area of prosurvival Bcl-2 members from the reported structures of the complexes, suggesting that Diva could function at the structural level similarly to the antiapoptotic proteins of the Bcl-2 family.
The binding area of IgG to FcRn is located between the CH2 and CH3 domain, distinctly different from the FcγR binding domain that is located between the CH1 and CH2 domain (Kim et al., 1994a; Roopenian & Akilesh, 2007).
E311 is highly exposed on the outer surface of the dimer and is only 6 9Å from EDII fusion peptide residues G106 and L107 of the alternate monomer, well within the binding area of a typical Fab footprint (Fig. 1).
The binding surface area of hTFIIEα AC-D and p62 PH-D is calculated as ∼2300 Å, which is much larger than the binding area of p53 TAD2 for Tfb1 calculated as ∼800 Å.
The second peptide involved in cross-linking (fragment 193 205) is part of the linker L12 connecting subdomains VIII and IX and is immediately following the P+1 binding area of ERK2 [2], [2].
The CD dimer plays a dominant role in Bre2DBM binding with a buried area of about 836.2 Å2, while the AB dimer assists in the interaction, forming a binding area of about 292.5 Å2 with Bre2.
These binding densities yield an estimated ∼220 bound streptavidin molecules to the available nanorod binding area of 8000 nm.
According to this binding pose, compounds stretch across most of the binding area occupied by the N-terminus of the cognate AnxA2 ligand (Fig. 2c).
