The eIF4E complex crystal structures with Bn7GMP and FBn7GMP show that additional favourable contacts of the benzyl groups with eIF4E contribute binding energy that compensates for loss of the β and γ-phosphates.
In a major conformational cluster, GO-Y030 occupied both the pTyr705 and Leu706 binding sites in the STAT3 SH2 domian, which contributed a binding energy of −8.2 kcal mol−1.
Such "dissection" of binding into contributions from different groups suggested that the adenine moiety contributed to binding of nucleotide independently of Mg2+ ions.
We show, using the MCMC method, that, for large sites, such as those of the AcrB bacterial drug transporter, multiple states or binding poses contribute to binding efficiency.
contributed Brachyury binding data from human embryonic stem cell derivatives.
The structures reveal a shared binding element, Phe76, that contributes to binding as part of both PAM2-N and PAM-C.
Importantly, we discovered that valine 337 in the site 2 binding loop is critical for signaling without contributing to binding.
Mutagenesis shows that dimerisation is essential for filamentous actin (F-actin) binding and indicates that the dimerisation helix itself contributes to binding.
Since fragment 151 269 still showed residual binding, residues before aa 270 are also likely to contribute to binding.
We performed docking calculations and the results showed that binding modes of these four inhibitors to their respective host enzymes, including the interacting residues and forces contributing to binding, were consistent with previous docking studies30,31,32.
