Absolute Free Energy of Binding and Entropy of the FKBP12-FK506 Complex: Effects of the Force Field

Investigation on drug entrapment location in liposomes and transfersomes based on molecular dynamics simulation

In this study, liposome and transfersome were successfully constructed using molecular dynamics simulation. Three drugs with different polarity, including 5-fluorouracil, ligustrazine, and osthole, were selected as model drugs to study the distribution of drugs in lipid vesicles by calculating the radial distribution function and the potential of mean force. The solubility parameters between drugs and different regions in lipid vesicles were calculated to characterize the compatibility of drugs in different regions in lipid vesicles, which provided the basis for the conclusion of this paper. It showed that the radial distribution function and the potential of mean force were consistent in the characterization of drug distribution in vesicles, and the drug distribution in vesicles was closely related to the compatibility between drugs and vesicles. Therefore, the radial distribution function and the potential of mean force can be used to characterize the distribution of drugs in vesicles, and molecular simulation technology has a great potential in studying the characteristics of vesicles. Graphical abstract.

Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter

Computational evaluation of the energetics of substrate binding, transport, and release events of neurotransmitter transporters at the molecular level is a challenge, as the structural transitions of these membrane proteins involve coupled global and local changes that span time scales of several orders of magnitude, from nanoseconds to seconds. Here, we provide a quantitative assessment of the energetics of dopamine (DA) translocation through the human DA transporter (hDAT), using a combination of molecular modeling, simulation, and analysis tools. DA-binding and -unbinding events, which generally involve local configurational changes, are evaluated using free-energy perturbation or adaptive biasing force methods. The global transitions between the outward-facing state and the inward-facing state, on the other hand, require a dual-boost accelerated molecular dynamics simulation. We present results on DA-binding/unbinding energetics under different conditions, as well as the conformational energy landscape of hDAT in both DA-bound and -unbound states. The study provides a tractable method of approach for quantitative evaluation of substrate-binding energetics and efficient estimation of conformational energy landscape, in general.