Consistent with HSF 3 prediction, subsequent analysis with SplicePort tool showed that XRCC7 -6721G>T is presented in an acceptor site and it is not only decrease score of the mutation and near acceptor sites, but also able to influence on another acceptor or even donor sites (data not shown).
The prediction of the consequence of XRCC7 -6721G>T mutation via HSF 3 tool showed that this SNP occurred in an acceptor splicing site and the transversion of allele G to allele T causes the increase of HSF score of the mutation and also increased slightly the upstream acceptor splicing site's HSF score, but not created new cryptic splice acceptor site (Table 4(a)).
With the application of POCKET module of Ligbuilder, the key interaction sites inside the binding pocket could be visualized, where nitrogen atoms represent hydrogen-bond donor sites (Blue); oxygen atoms represent hydrogen-bond acceptor sites (Red); and carbon atoms (Green) represent hydrophobic sites (13).
One acceptor site A2 having score -0.22 has also been shown.
Botulinum toxin type A is known to block neuromuscular transmission by binding to acceptor sites
on motor or sympathetic nerve terminals, entering the nerve terminals and inhibiting the release of acetylcholine.
Knowing that the optimal donor and acceptor sites are denoted by the sequences AG/gtRagt and (Y)ncag/GT, respectively, we observed that none (except KLK5) of the classical forms had optimal splice sites in either the donor or acceptor sites (Fig.
In conclusion, it seems that a suboptimal 5' splice site (donor site) and 3' splice site (branch point, pY tract, and acceptor site) play a major role in intron III retention of these genes.
To sample the range of thermodynamically achievable distances between putative H-bond acceptor sites, limited conformational space was explored by constraining the two putative H-bond acceptor atoms to be a fixed distance apart, allowing the remainder of the molecule to relax to the lowest energy configuration, followed by release of the original constraint allowing full relaxation in the extended conformation.
These compounds did not, however, provide a good candidate feature for D-ring H-bond interaction according to the "near-10 [Angstrom] polar interactions rule" (the thiol was computed to be a 7.5 [Angstrom] separation from the A-ring H-bond acceptor site), which is consistent with lack of reported agonist properties.
Dalfopristin is an olefinic macrolactone that binds to the 50S subunit of the prokaryotic ribosome and interferes with the function of peptidyl transferase, thereby inactivating the donor and acceptor sites
of the ribosome.