Aquaglyceroporin AQP7's affinity for its substrate glycerol

AQP7 is one of the four human aquaglyceroporins that facilitate glycerol transport across the cell membrane, a biophysical process that is essential in human physiology. Therefore, it is interesting to compute AQP7s affinity for its substrate (glycerol) with reasonable certainty to compare with the experimental data suggesting high affinity in contrast with most computational studies predicting low affinity. In this study aimed at computing the AQP7-glycerol affinity with high confidence, we implemented a direct computation of the affinity from unbiased equilibrium molecular dynamics (MD) simulations of three all-atom systems constituted with 0.16M, 4.32M, and 10.23M atoms, respectively. These three sets of simulations manifested a fundamental physics law that the intrinsic fluctuations of pressure in a system are inversely proportional to the system size (the number of atoms in it). These simulations showed that the computed values of glycerol-AQP7 affinity are dependent upon the system size (the inverse affinity estimations were, respectively, 47.3 mM, 1.6 mM, and 0.92 mM for the three model systems). In this, we obtained a lower bound for the AQP7-glycerol affinity (an upper bound for the dissociation constant). Namely, the AQP7-glycerol affinity is stronger than 1087/M (the dissociation constant is less than 0.92 mM). Additionally, we conducted hyper steered MD (hSMD) simulations to map out the Gibbs free-energy profile. From the free-energy profile, we produced an independent computation of the AQP7-glycerol dissociation constant being approximately 0.18 mM.

Computational Investigation on the MDM2-Idasanutlin Interaction using the Potential of Mean Force method

Background: The Murine Double Minute 2 (MDM2) protein is a well-studied primary negative regulator of the tumor suppressor p53 molecule. Therefore, nowadays, many research studies have focused on the inhibition of MDM2 with potent inhibitors. Idasanutlin (RG7388) is a well-studied small molecule, the antagonist of MDM2 with potential antineoplastic activity. Nevertheless, the highly significant information about the free energy profile, intermediates, and the association of receptor and ligand components in the MDM2-idasanutlin complex remains unclear. Objective: To study the free energy profile of the MDM2-idasanutlin complex in terms of the Potential of Mean Force (PMF) method. Method: We have used the PMF method coupled with umbrella sampling simulations to generate the free energy profile for the association of N-Terminal Domain (NTD) of MDM2 and idasanutlin and a specific reaction coordinate for identifying transition states, intermediates as well as the relative stabilities of the endpoints. We have also determined the binding characteristics and interacting residues at the interface of the MDM2-idasanutlin complex from the Binding Free Energy (BFE) and Per Residue Energy Decomposition (PRED) analyses. Results: The PMF minima for the MDM2-idasanutlin complex was observed at a center of mass (CoM) distance of separation of 11 Å with dissociation energy of 17.5 kcal mol-1. As a function of the distance of separation of MDM2 from idasanutlin. We also studied the conformational dynamics and stability of the NTD of MDM2. We found a high binding affinity between MDM2 and idasanutlin (∆Grinding = -3.19 kcal mol-1). We found that in MDM2, the residues MET54, VAL67, and LEU58 provide the highest energy input for the interaction between MDM2 and idasanutlin. Conclusion: Our results in this study illustrate the significant structural and binding features of the MDM2-idasanutlin complex that may be useful in developing potent inhibitors of MDM2.

Temperature Dependent Entropy Driven Water Uptake in Phase Separated Aerosol from Steered Molecular Dynamics and Intrinsic Surface Analysis

<p>Dynamic water uptake by aerosol is a major driver of cloud droplet activation and growth. Interfacial mass transfer— that governs water uptake if the mean free path of molecules in the vapour phase is comparable to particle size — is represented in models by the mass accommodation coefficient. Although widely used, this approach neglects <em>i</em>) other internal interfaces (e.g., liquid-liquid that may be important for water uptake), and, <em>ii</em>) fluctuations of the liquid surface from capillary waves that modulate the surface and induce ambiguity in the estimation of mass accommodation coefficients. These issues can be addressed if the full path of the water molecule – from vapour to the bulk aqueous phase - is considered.<span> </span></p><p>We demonstrate, using steered molecular simulations, that a full treatment of the water uptake process reveals important details of the mechanism. The simulations are used to reconstruct the free energy profile of water transport across a vapour/hydroxy cis-pinonic acid/water double interface at 300 K and 200 K. In steered molecular dynamics the transferred molecule is pulled with a finite velocity along an aptly chosen reaction coordinate and the work exerted is used to reconstruct the free energy profile. Due to the finite velocity pulling, this method takes the effect of friction on the transport mechanism into account, which is important for phases of considerably different friction coefficients and is neglected by<span>  </span>quasi equilibrium free energy methods. Free energy profiles are used to estimate surface and bulk uptake coefficients and are decomposed into entropic and enthalpic contributions.<span> </span></p><p>Surface accommodation coefficients are unity at both temperatures, while bulk uptake at 300 K from the internal interface is strongly hindered (k<sub>b</sub>=0.05) by the increased density and molecular order in the first layer of the aqueous phase, which results in decreased orientational entropy. The difference between bulk and surface uptake coefficients also implies that water accumulates in the organic shell, which cannot be predicted using a single uptake coefficient for the whole particle. The minimum of the free energy profile at the organic/water interface, rationalised by increased conformational entropy due to local mixing and the depleted system density, results in a concentration gradient which helps maintain low surface tension and phase separation. Low surface tensions may explain increased CCN activity. These entropic features of the free energy profiles diminish at low temperature, which invokes a completely different mechanism of water uptake. Our results point out the need to describe water uptake in aerosol growth models using a temperature dependent parametrisation.</p>

Free energy profile analysis to identify factors activating the aggregation-induced emission of a cyanostilbene derivative

The contributing factors that cause the aggregation-induced emission (AIE) are determined by identifying characteristic differences in the free energy profiles of the AIE processes of the AIE-active E-form of CN-MBE and the inactive Z-form.

Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation

Entecavir, triphosphorylated in liver cells, is an antiviral reagent against Hepatitis B virus (HBV). The reagent inhibits reverse transcription of RNA inside the virus capsid. In the present study, free energy profile of an Entecavir triphosphate (ETVTP) molecule has been calculated when it passes through pores of the capsid along two- and three-fold rotational symmetry axes in order to investigate permeation pathway of the reagent to the inside of the capsid. The calculations have been done based on thermodynamic integration (TI) method combined with all-atomistic molecular dynamic (MD) calculations. A free energy minimum of −19 kJ/mol was found at the entrance of the pore from the outside along the three-fold symmetry axis. This stabilization is from the interaction of negatively charged ETVTP with positively charged capsid methionine residues. This excess free energy concentrates of the reagent at the entrance of the pore by a factor of about 2000. A free energy barrier of approximately 13 kJ/mol was also found near the exit of the pore to the inside of the capsid due to narrow space of the pore surrounded by hydrophobic wall made by proline residues and negatively charged wall by aspartic acid residues. There, ETVTP is partially dehydrated in order to pass through the narrow space, which causes the great free energy loss. Further, the negatively charged residues produce repulsive forces on the ETVTP molecule. In contrast, in the case of the pore along the two-fold symmetry axis, the calculated free energy profile showed shallower free energy minimum, −4 kJ/mol at the entrance in spite of the similarly high barrier, 7 kJ/mol, near the exit of the pore.