No abstract

In the present work the binding of inhibitor TMC114 (darunavir) to wild type (WT), single (I50V) as well as double (I50L/A71V) mutant HIV-proteases (HIV-pr) was investigated with all-atom molecular dynamics (MD) simulations as well as molecular mechanic-Poisson Boltzmann surface area (MM-PBSA) calculation. For both the apo and complexed HIV-pr, many intriguing effects due to double mutant, I50L/A71V, are observed. For example, the flap-flap distance and the distance from the active site to the flap residues in the apo I50L/A71V-HIV-pr are smaller than those of WT- and I50V-HIV-pr, probably making the active site smaller in volume and closer movement of flaps. For the complexed HIV-pr with TMC114, the double mutant I50L/A71V shows a less curling of the flap tips and less flexibility than WT and the single mutant I50V. As for the other previous studies, the present results also show that the single mutant I50V decreases the binding affinity of I50V-HIV-pr to TMC, resulting in a drug resistance; whereas the double mutant I50L/A71V increases the binding affinity, and as a result of the stronger binding the I50L/A71V may be well adapted by the TMC114. The energy decomposition analysis suggests that the increase of the binding for the double mutant I50L/A71V-HIV-pr can be mainly attributed to the increase in electrostatic energy by −5.52 kacl/mol and van der Waals by −0.42 kcal/mol, which are cancelled out in part by the increase of polar solvation energy of 1.99 kcal/mol. The I50L/A71V mutant directly increases the binding affinity by approximately −0.88 (Ile50 to Leu50) and −0.90 (Ile50’ to Leu50’) kcal/mol, accounting 45% for the total gain of the binding affinity. Besides the direct effects from the residues Leu50 and Leu50’, the residue Gly49’ increases the binding affinity of I50L/A71V-HIV-pr to the inhibitor by −0.74 kcal/mol, to which the electrostatic interaction of Leu50’s backbone contributes by −1.23kcal/mol. Another two residues Ile84 and Ile47’ also increase the binding affinity by −0.22 and −0.29kcal/mol, respectively, which can be mainly attributed to van der waals terms (ΔTvdw: −0.21 and −0.39 kcal/mol).

No abstract

No abstract

No abstract

Abrus agglutinin (AGG), a type II ribosome-inactivating protein has been found to induce mitochondrial apoptosis. In the present study, we documented that AGG-mediated Akt dephosphorylation led to ER stress resulting the induction of autophagy-dependent cell death through the canonical pathway in cervical cancer cells. Inhibition of autophagic death with 3-methyladenine (3-MA) and siRNA of Beclin-1 and ATG5 increased AGG-induced apoptosis. Further, inhibiting apoptosis by Z-DEVD-FMK and N-acetyl cysteine (NAC) increased autophagic cell death after AGG treatment, suggesting that AGG simultaneously induced autophagic and apoptotic death in HeLa cells. Additionally, it observed that AGG-induced autophagic cell death in Bax knock down (Bax-KD) and 5-FU resistant HeLa cells, confirming as an alternate cell killing pathway to apoptosis. At the molecular level, AGG-induced ER stress in PERK dependent pathway and inhibition of ER stress by salubrinal, eIF2α phosphatase inhibitor as well as siPERK reduced autophagic death in the presence of AGG. Further, our in silico and colocalization study showed that AGG interacted with pleckstrin homology (PH) domain of Akt to suppress its phosphorylation and consequent downstream mTOR dephosphorylation in HeLa cells. We showed that Akt overexpression could not augment GRP78 expression and reduced autophagic cell death by AGG as compared to pcDNA control, indicating Akt modulation was the upstream signal during AGG's ER stress mediated autophagic cell death. In conclusion, we established that AGG stimulated cell death by autophagy might be used as an alternative tumor suppressor mechanism in human cervical cancer. © 2016 Wiley Periodicals, Inc.

Although some metal clusters and molecules were found to more significantly bind to defective graphenes than to pristine graphenes, exhibiting chemisorptions on defective graphenes, the present investigation shows that the adsorption of DNA bases on mono- and di-vacant defective graphenes does not show much difference from that on pristine graphene, and is still dominantly driven by noncovalent interactions. In the present study the adsorptions of the nucleobases, adenine (A), cytosine (C), guanine, (G), and thymine (T) on pristine and defective graphenes, are fully optimized using a hybrid-meta GGA density functional theory (DFT), M06-2X/6-31G*, and the adsorption energies are then refined with both M06-2X and B97-D/6-311++G**. Graphene is modeled as nano-clusters of C72H24, C71H24, and C70H24 for pristine, mono- and divacant defective graphenes, respectively, supplemented by a few larger ones. The result shows that guanine has the maximum adsorption energy in all of the three adsorption systems; and the sequence of the adsorption strength is G>A>T>C on the pristine and di-vacant graphene and G>T>A>C on the mono-vacant graphene. In addition, the binding energies of the DNA bases with the pristine graphene are less than the corresponding ones with di-vacant defective graphene; however, they are greater than those of mono-vacant graphene with guanine and adenine, while it is dramatic that the binding energies of mono-vacant graphene with thymine and cytosine appear larger than those of pristine graphene.

The gonadotropin known as follicle-stimulating hormone (FSH) plays a key role in regulating reproductive processes. Physiologically active FSH is a glycoprotein that can accommodate glycans on up to four asparagine residues, including two sites in the FSHα subunit that are critical for biochemical function, plus two sites in the β subunit, whose differential glycosylation states appear to correspond to physiologically distinct functions. Some degree of FSHβ hypo-glycosylation seems to confer advantages toward reproductive fertility of child-bearing females. In order to identify possible mechanistic underpinnings for this physiological difference we have pursued computationally intensive molecular dynamics simulations on complexes between the high affinity site of the gonadal FSH receptor (FSHR) and several FSH glycoforms including fully-glycosylated (FSH24), hypo-glycosylated (e.g., FSH15), and completely deglycosylated FSH (dgFSH). These simulations suggest that deviations in FSH/FSHR binding profile as a function of glycosylation state are modest when FSH is adorned with only small glycans, such as single N-acetylglucosamine residues. However, substantial qualitative differences emerge between FSH15 and FSH24 when FSH is decorated with a much larger, tetra-antennary glycan. Specifically, the FSHR complex with hypo-glycosylated FSH15 is observed to undergo a significant conformational shift after 5–10 ns of simulation, indicating that FSH15 has greater conformational flexibility than FSH24 which may explain the more favorable FSH15 kinetic profile. FSH15 also exhibits a stronger binding free energy, due in large part to formation of closer and more persistent salt-bridges with FSHR.