The recent observation that Ca2+ channels may be highly diffusible in the presynaptic membrane (Schneider et al., 2015) provides another potential mechanism by which interactions with active zone proteins such as Munc13 could modulate effective Ca2+ influx.
A molecular docking simulation and a kinetic assay show that RA controls the activity of caspase-1 by interaction with the active site of caspase-1.
A molecular docking simulation showed that hesperidin, a major component of KMP6, controls the SCF and c-kit binding by interaction with the active site of the c-kit.
Distinct flavonoids and other natural compounds like vitamin C (at high doses such as 8 mmol/L, achievable in patients by i.v. administration) [ 66] are known to act as DNMTi either directly by interaction with the active site of these enzymes or by indirect mechanisms.
It is possible that activators recruit Gcn5 to promoters, as has been demonstrated in vitro [ 25, 26], but that the residence time of Gcn5 on promoters is controlled by interactions with histones, either via active-site interactions with substrates during acetylation or more likely via interactions between the Gcn5 bromodomain and acetylated lysines.
It is thought that, in cellulo, vinculin exists in an equilibrium between active and inactive states and it can be stabilised in the active form by interactions with a subset of binding partners.
The transition state structure of MnmE [23] showed that the hexa-coordinated potassium ion is held in the active site by interactions with K-loop (a part of the switch-I region), α and β phosphates of GDP, the side chain carbonyl oxygen of Asn-226 from P-loop and the fluoride ion from AlFx (that mimics γ-phosphate).
The imine is important because in the following sections we will show how its stability is increased further in SHV-1 β-lactamase's active site by interactions with the 6-hydroxymethyl.
Finally, in the crystal structure, fragment 44 binds to the distal pocket of the active site, defined by interactions with Ser212, Tyr221, and Gly320, not in the oxyanion hole as anticipated by docking.
At the entrance to the active site, KA is stabilized by interactions with Phe197, Pro201, Asn205, and Arg209 (Fig. 3b 22.
