A Benzene-Mapping Approach for Uncovering Cryptic Pockets in Membrane-Bound Proteins was written by Zuzic, Lorena;Marzinek, Jan K.;Warwicker, Jim;Bond, Peter J.. And the article was included in Journal of Chemical Theory and Computation in 2020.SDS of cas: 26662-94-2 The following contents are mentioned in the article:
Mol. dynamics (MD) simulations in combination with small organic probes present in the solvent have previously been used as a method to reveal cryptic pockets that may not have been identified in exptl. structures. The authors report such a method implemented within the CHARMM force field using the GROMACS simulation package to effectively explore cryptic pockets on the surfaces of membrane-embedded proteins using benzene as a probe mol. This method, for which the authors have made implementation files freely available, relies on modified nonbonded parameters in addition to repulsive potentials between membrane lipids and benzene mols. The method was tested on part of the outer shell of the dengue virus (DENV), for which research into a safe and effective neutralizing antibody or drug mol. is still ongoing. In particular, the envelope (E) protein, associated with the membrane (M) protein, is a lipid membrane-embedded complex which forms a dimer in the mature viral envelope. Solvent mapping was performed for the full, membrane-embedded EM protein complex and compared with similar calculations performed for the isolated, soluble E protein ectodomain dimer in the solvent. Ectodomain-only simulations with benzene exhibited unfolding effects not observed in the more physiol. relevant membrane-associated systems. A cryptic pocket which has been exptl. shown to bind n-octyl-尾-
(2R,9Z)-1-(((2-Aminoethoxy)(hydroxy)phosphoryl)oxy)-3-(palmitoyloxy)propan-2-yl oleate (cas: 26662-94-2) belongs to esters. Carboxylic acid esters of low molecular weight are colourless, volatile liquids with pleasant odours, slightly soluble in water. Esters are more polar than ethers but less polar than alcohols. They participate in hydrogen bonds as hydrogen-bond acceptors, but cannot act as hydrogen-bond donors, unlike their parent alcohols. This ability to participate in hydrogen bonding confers some water-solubility.SDS of cas: 26662-94-2
Referemce:
Ester – Wikipedia,
Ester – an overview | ScienceDirect Topics