Temperature dependent molecular dynamics simulation study to understand the stabilizing effect of NADES on the protein ß-Lactoglobulin.

The thermal stability of a protein is an important concern for its practical application in food processing industries. In this study, we have carried out classical molecular dynamics simulations to systematically investigate the effect of NADES (natural deep eutectic solvent) on the stabilization of the protein ß-Lactoglobulin (BLG) at different temperatures. This study sheds light on the very aspects of NADES composed of betaine and sorbitol on the stability of the protein. NADES provides better stability to the protein up to a temperature of 400 K than in water. It is observed that the protein starts to unfold above temperature 400 K in spite of the presence of NADES which is quiet evident from the root mean square deviation (RMSD) and radius of gyration (Rg) plots. The decreasing average solvent accessible surface area (SASA) values and increasing intra-protein hydrogen bonds indicate better stability of the protein in NADES medium than in water at temperatures 300 K and 400 K. At high temperatures viz. 450 K and 500 K the number and distribution of solvent species (betaine and sorbitol) around the protein surface show an increment that are evident from the calculations of solvation shell, radial and spatial distribution functions. Increased number of betaine molecules that interact with the protein through electrostatic interaction may lead to destabilization of the protein at these temperatures. This study suggests that NADES could be used as an ideal medium for thermal stability of the protein BLG up to a temperature of 400 K. Beyond this temperature, NADES used for this study fails to exert stabilization effect on the protein.

Alpha glucosidase inhibitory properties of a few bioactive compounds isolated from black rice bran: combined in vitro and in silico evidence supporting the antidiabetic effect of black rice.

In view of the recent reports of the antidiabetic effect of the black rice bran extract, an attempt has been made in the present work to evaluate the potential α-glucosidase inhibitory activity of a few selected bioactive compounds present in the pericarp of the black rice. Out of the six bioactive compounds from black rice bran selected for the study, two compounds viz. cyanidin-3-glucoside and 6'-O-feruloylsucrose were identified as novel and highly potent α-glucosidase inhibitors via their in vitro and in silico screenings. The enzyme inhibition assay was corroborated by molecular docking and molecular dynamics simulation studies. Molecular docking studies suggested high binding energies and good binding interactions of these compounds with the active site residues of the receptor protein. A good agreement was found between the results of both modes of evaluation. The experimental results proved that the black rice bran extract can show 62% of alpha glucosidase inhibiting enzyme activity as compared to that of the popular drug Acarbose. While both the docking scores and binding affinity values indicate the formation of a ligand-enzyme complex by the major components of the extract, the molecular dynamics study further indicates the stability of the complex. The pharmacokinetic (ADMET properties) studies of these active compounds also support their use as safe oral anti-diabetic drugs. Thus, the results obtained from these studies of alpha glucosidase inhibition by bioactive compounds present in black rice bran indicate that these bioactive compounds can produce significant antidiabetic activity by inhibiting the active site of the target enzyme and hence these compounds can be used as leads for the synthesis of new antidiabetic drugs.

Insights into the Interaction between Polyphenols and ß-Lactoglobulin through Molecular Docking, MD Simulation, and QM/MM Approaches.

In this work, we have explored the interaction of three different polyphenols with the food protein ß-lactoglobulin. Antioxidant activities of polyphenols are influenced by complexation with the protein. However, studies have shown that polyphenols after complexation with the protein can be more beneficial due to enhanced antioxidant activities. We have carried out molecular docking, molecular dynamics (MD) simulation, and quantum mechanics/molecular mechanics (QM/MM) studies on the three different protein-polyphenol complexes. We have found from molecular docking studies that apigenin binds in the internal cavity, luteolin binds at the mouth of the cavity, and eriodictyol binds outside the cavity of the protein. Docking studies have also provided binding free energy and inhibition constant values that showed that eriodictyol and apigenin exhibit better binding interactions with the protein than luteolin. For eriodictyol and luteolin, van der Waals, hydrophobic, and hydrogen bonding interactions are the main interacting forces, whereas for apigenin, hydrophobic and van der Waals interactions play major roles. We have calculated the root mean square deviation (RMSD), root mean square fluctuations (RMSF), solvent-accessible surface area (SASA), interaction energies, and hydrogen bonds of the protein-polyphenol complexes. Results show that the protein-eriodictyol complex is more stable than the other complexes. We have performed ONIOM calculations to study the antioxidant properties of the polyphenols. We have found that apigenin and luteolin act as better antioxidants than eriodictyol does on complexation with the protein, which is consistent with the results obtained from MD simulations.

Disruption of androgen receptor signaling by chlorpyrifos (CPF) and its environmental degradation products: a structural insight.

Androgen-disruptors are chemicals that interfere with the biosynthesis, metabolism or function of endogenous androgens affecting normal male reproductive development and health. Several epidemiological studies have indicated a link between exposure to androgen disrupting chemicals with reduced sperm counts and increased infertility. The actions of androgens within target cells are transduced by the androgen receptors (ARs). Chlorpyrifos (CPF), a chlorinated organophosphorus pesticide, is known to cause impairment in both male and female reproductive systems. Recent publications have shown molecular interactions of CPF and its environmental degradation products with human progesterone receptor and human estrogen receptor. Exposure to CPF causes a marked reduction in sperm counts with lowering in serum testosterone level, which suggests possible molecular interaction of CPF with AR. The investigation to reveal the possibility and the extent of binding of CPF and some of its degradation products (chlorpyrifos-oxon [CPYO], desethyl chlorpyrifos [DEC], trichloromethoxypyridine [TMP] and trichloropyridinol [TCP]) with AR using molecular docking simulation are reported. The findings of the present docking, binding energy and molecular dynamics studies reveal that CPF and its degradation products may bind to ARs and act as a potent androgen disruptor.Communicated by Ramaswamy H. Sarma.

Binding interaction of a potential statin with ß-lactoglobulin: An in silico approach.

This article reports the interaction between a synthetic statin, fluvastatin with bovine milk protein, ß-lactoglobulin (BLG) through docking, constant pH molecular dynamics simulation (cpHMD) and binding free energy calculations. Docking provides the best fitted binding mode of the ligand with the receptor. We have carried out MD simulations of the protein and protein-ligand complex at two different pH viz. 7.0 and 1.5. We have found that the protein shows more compact behavior at pH 1.5 and this behavior is more prominent on complexation with the ligand. In support of this we have utilized the properties viz. root mean square deviations, root mean square fluctuations, radius of gyration, protein-ligand hydrogen bond and binding free energy calculations. Calculation of radius of gyration shows that the value decreases from 14.51 Å to 14.03 Å on complexation at pH 1.5. Calculations of hydrogen bonds at pH 1.5 confirms that hydrogen bonding interactions of the binding residues of the protein with the ligand provides stability to the complex. We have used molecular mechanics-generalized Born surface area (MMGBSA) method to estimate binding free energies of the protein with the ligand. MMGBSA calculations suggest that there is favorable binding interactions between the protein and the ligand with major contributions from Van der Waals interactions. We have found that the net average binding free energy is -29.394 kcal/mol that reveals a favorable binding interactions of BLG with the ligand. This study suggests that in spite of the acidic environment in the stomach BLG can act as a carrier for the acid-sensitive drug molecules such as fluvastatin because of its highly stable conformational behavior in the acidic pH.

Structural and functional changes of the protein ß-lactoglobulin under thermal and electrical processing conditions.

In the present study we have tried to explore the effect of static external electric field of strength 3.0 V/nm on the conformational changes adopted by the protein ß-lactoglobulin. We have chosen different temperatures viz. 300 K, 400 K and 450 K to evaluate the temperature dependent effect of electric field. We have observed that combined effect of high temperature and static external electric field show significant changes on the structural conformation of the protein which in turn may affect the functional properties of the protein. Calculations of root mean square deviations reveal that both helical and ß-sheet regions of the protein are noticeably affected at high temperature. We have used solvent accessible surface area (SASA) and dipole moment values to explain that there is changes in hydrophobicity of the protein surface due to presence of external electric field. The study reveals that electric field in combination with high temperature can be used to alter the conformation of the protein and the effect of external electric field is more pronounced at high temperature than that of low temperature. The study provides a better understanding of the conformational changes adopted by the protein under the stress of external electric field and high temperature and provide guidance to choose optimum conditions for processing without loss of nutritional properties.

Molecular dynamics approach to understand the denaturing effect of a millimolar concentration of dodine on a λ-repressor and counteraction by trehalose.

Commonly used denaturants for protein denaturation are conventionally required in high concentrations in order to produce their effects. In this study, a molecular dynamics simulation of a mutated version of the N-terminal domain of a λ-repressor is carried out in the presence of a 10 millimolar (mM) concentration of dodine. Such a small concentration is found to be effective for denaturation of the protein. Both electrostatic and van der Waals interactions (between protein and dodine) play a role in the denaturation process and we observe more denaturation at the terminal helices. Three different molar concentrations of trehalose are used in order to check the counteraction against the action of dodine. This study shows that 0.5 and 1.0 M trehalose are sufficient to counteract the action of dodine. The study also sheds light on the fact that some protein sites are more responsive to unfolding, which is evident from the helical fractions of the terminal helices for different systems. The counteraction of trehalose on dodine-induced protein denaturation is found to be due to the replacement of some of the dodine molecules by trehalose molecules in the solvation shell of the protein. Preferential solvation of dodine molecules by trehalose molecules through hydrogen bonding interactions also plays a vital role in stabilizing the native conformation of the protein in a high trehalose concentration. Replacement of protein-dodine and protein-water hydrogen bonds by protein-trehalose hydrogen bonds is also observed.

Use of molecular dynamics simulation to explore structural facets of human prion protein with pathogenic mutations.

Prion diseases are caused by mutations at different positions of the prion protein. A large number of pathogenic mutations are reported in the literature. Two of such point mutations T193I and R148H located at two different helical strands (H2 and H1) of the prion protein associated with fCJD (familial Creutzfeld-Jacob disease) are studied. We have used classical molecular dynamics (MD) simulation technique to understand the conformational changes and dynamics of the protein under the effect of mutation and compared with the native prion protein. The results indicate that: both mutated forms are conformationally steadier than the native prion protein; although there are no major conformational transitions, R148H leads to decreased native ß-sheet content, H1 helix becomes less fluctuating, two new turn regions appear and conversion of a 310 region to coil form takes place. Mutation T193I leads to a steady H1 helix, a decreased native ß-sheet content and a new 310 region appears in H2 helix. Moreover, mutation R148H results in decreased conformational space with a highly compact and nonfluctuating form.

Model Dependency of TMAO's Counteracting Effect Against Action of Urea: Kast Model versus Osmotic Model of TMAO.

Classical molecular dynamics simulation of GB1 peptide (a 16-residue ß-hairpin) in different osmotic environments is studied. Urea is used for denaturation of the peptide, and trimethylamine-N-oxide (TMAO) is used to offset the effect of urea. Protein-urea electrostatic interactions are found to play a major role in protein-denaturation. To emphasize on protein protecting action of TMAO against urea, two different models of TMAO are used, viz., the Kast model and the Osmotic model. We observe that the Osmotic model of TMAO gives the best protection to counteract urea's action when used in ratio 1:2 of urea:TMAO (i.e., reverse ratio). This is because the presence of TMAO makes urea-protein electrostatic interactions more unfavorable. Preferential solvation of TMAO molecules by urea (and water) molecules is also observed, which causes depletion in the number of urea molecules in the vicinity of the protein. The calculations of intraprotein hydrogen bonds between different residues of protein further reveal the breaking of backbone hydrogen bonds of residues 2 and 15 in the presence of urea, and the same is preserved in the presence of TMAO. Free energy landscapes show that the narrowest distribution is obtained for the osmotic TMAO model when used in reverse ratio.