Walker, Brandon published the artcileMolecular dynamics free energy simulations of ATP:Mg2+ and ADP:Mg2+ using the polarisable force field AMOEBA, Formula: C9H21NO3, the publication is Molecular Simulation (2021), 47(5), 439-448, database is CAplus and MEDLINE.
ATPases and GTPases are two important classes of protein that play critical roles in energy transduction, cellular signalling, gene regulation and catalysis. These proteins use cofactors such as nucleoside di and tri-phosphates (NTP, NDP) and can detect the difference between NDP and NTP which then induce different protein conformations. Mechanisms that drive proteins into the NTP or NDP conformation may depend on factors such as ligand structure and how Mg2+ coordinates with the ligand, amino acids in the pocket and water mols. Here, we have used the advanced electrostatic and polarisable force field AMOEBA and mol. dynamics free energy simulations (MDFE) to examine the various binding mechanisms of ATP:Mg2+ and ADP:Mg2+. We compared the ATP:Mg2+ binding with previous studies using non-polarisable force fields and exptl. data on the binding affinity. It was found that the total free energy of binding for ATP:Mg2+ (-7.00 2.13 kcal/mol) is in good agreement with exptl. values (-8.6 .2 kcal/mol) [1]. In addition, parameters for relevant protonation states of ATP, ADP, GTP and GDP have been derived. These parameters will allow for researchers to investigate biochem. phenomena involving NTP’s and NDP’s with greater accuracy than previous studies involving non-polarisable force fields.
Molecular Simulation published new progress about 122-20-3. 122-20-3 belongs to alcohols-buliding-blocks, auxiliary class Organic Pigment, name is Triisopropanolamine, and the molecular formula is C8H6ClN, Formula: C9H21NO3.
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