However, 2-bromopalmitate has been shown to occupy the same binding sites within albumin and fatty acid binding proteins, with a similar binding affinity, as unmodified palmitate [ 24].
WDR5-0103 occupies the binding pocket with a similar geometry to that of WDR5-0102, buthehe methoxy substituent induces a 2.5 Å shift of the benzamide ring in the upper shallow region of the pocket, which is accompanied by a motion of the amide linker and flipping of the Ser side chain.
In the presence of CREB1, we observed increased GABPα-GST binding, with a qualitatively similar overall pattern to the binding of GABPα-GST alone.
Epothilones are a novel alternative class of tubule-binding compounds with a similar mode of action to that of taxanes (Bollag et al, 1995; Altaha et al, 2002).
Docking studies show that dialkyation at C-2 and C-3 favors a binding with an orientation similar to that of the known selective inhibitor SC-558.
Thus selecting for mutants that prevented substrate transport but which still allowed substrate binding with an affinity similar to the wild type transporter would result in a transporter with properties more suitable for structural studies i.e. biased towards a single conformation.
As expected for an Hsp70 chaperone (Marcinowski et al., 2011), we found that CH1 bound only to the substrate binding domain of BiP with a similar binding affinity to that of full-length BiP, suggesting that BiP's substrate binding domain was solely responsible for binding to CH1 unfolded protein.
Alternative mutagenic studies using Sec1 have also pointed to domain 3a in SNARE complex binding [33] in accordance with a similar binding interface between Munc18-1 and either closed-conformation syntaxin or the assembled SNARE complex.
We show that the p73 and p63 binding profiles are indistinguishable, with a similar p73∶p63 binding ratio at essentially all genomic loci.
The analysis of the free energy values of the molecular interaction between the terpenes on SCP-2 enzyme showed that all the compounds bind strongly inside the active site with a similar binding mode; binding energies (ΔG) for each molecule are shown in Table 8.
