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.
From our understanding drawn from experience with the THIQ systems these compounds could well act as chimeras addressing both the steroidal A-ring binding area and the trimethoxyaryl binding area of the colchicine binding site on tubulin.
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).
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].
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.
These binding densities yield an estimated ∼220 bound streptavidin molecules to the available nanorod binding area of 8000 nm.
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 empirical energy function [ 3], such as the score function, is usually used to evaluate the results of ligand molecular docking conformation which is suitable or not for binding area of receptor.
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.
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.
