Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation.

Regulation of the mechanical properties of proteins plays an important role in many biological processes, and sheds light on the design of biomaterials comprised of protein. At present, strategies to regulate protein mechanical stability focus mainly on direct modulation of the force-bearing region of the protein. Interestingly, the mechanical stability of GB1 can be significantly enhanced by the binding of Fc fragments of human IgG antibody, where the binding site is distant from the force-bearing region of the protein. The mechanism of this long-range allosteric control of protein mechanics is still elusive. In this work, the impact of ligand binding on the mechanical stability of GB1 was investigated using steered molecular dynamics simulation, and a mechanism underlying the enhanced protein mechanical stability is proposed. We found that the external force causes deformation of both force-bearing region and ligand binding site. In other words, there is a long-range coupling between these two regions. The binding of ligand restricts the distortion of the binding site and reduces the deformation of the force-bearing region through a long-range allosteric communication, which thus improves the overall mechanical stability of the protein. The simulation results are very consistent with previous experimental observations. Our studies thus provide atomic-level insights into the mechanical unfolding process of GB1, and explain the impact of ligand binding on the mechanical properties of the protein through long-range allosteric regulation, which should facilitate effective modulation of protein mechanical properties.

Impacts of the charged residues mutation S48E/N62H on the thermostability and unfolding behavior of cold shock protein: insights from molecular dynamics simulation with Go model.

The cold shock protein from the hyperthermophile Thermotoga maritima (Tm-Csp) exhibits significantly higher thermostability than its homologue from the thermophile Bacillus caldolyticus (Bc-Csp). Experimental studies have shown that the electrostatic interactions unique to Tm-Csp are responsible for improving its thermostability. In the present work, the favorable charged residues in Tm-Csp were grafted into Bc-Csp by a double point mutation of S48E/N62H, and the impacts of the mutation on the thermostability and unfolding/folding behavior of Bc-Csp were then investigated by using a modified Go model, in which the electrostatic interactions between charged residues were considered in the model. Our simulation results show that this Tm-Csp-like charged residue mutation can effectively improve the thermostability of Bc-Csp without changing its two-state folding mechanism. Besides that, we also studied the unfolding kinetics and unfolding/folding pathway of the wild-type Bc-Csp and its mutant. It is found that this charged residue mutation obviously enhanced the stability of the C-terminal region of Bc-Csp, which decreases the unfolding rate and changes the unfolding/folding pathway of the protein. Our studies indicate that the thermostability, unfolding kinetics and unfolding/folding pathway of Bc-Csp can be artificially changed by introducing Tm-Csp-like favorable electrostatic interactions into Bc-Csp.

The Intrinsic Dynamics and Unfolding Process of an Antibody Fab Fragment Revealed by Elastic Network Model.

Antibodies have been increasingly used as pharmaceuticals in clinical treatment. Thermal stability and unfolding process are important properties that must be considered in antibody design. In this paper, the structure-encoded dynamical properties and the unfolding process of the Fab fragment of the phosphocholine-binding antibody McPC603 are investigated by use of the normal mode analysis of Gaussian network model (GNM). Firstly, the temperature factors for the residues of the protein were calculated with GNM and then compared with the experimental measurements. A good result was obtained, which provides the validity for the use of GNM to study the dynamical properties of the protein. Then, with this approach, the mean-square fluctuation (MSF) of the residues, as well as the MSF in the internal distance (MSFID) between all pairwise residues, was calculated to investigate the mobility and flexibility of the protein, respectively. It is found that the mobility and flexibility of the constant regions are higher than those of the variable regions, and the six complementarity-determining regions (CDRs) in the variable regions also exhibit relative large mobility and flexibility. The large amplitude motions of the CDRs are considered to be associated with the immune function of the antibody. In addition, the unfolding process of the protein was simulated by iterative use of the GNM. In our method, only the topology of protein native structure is taken into account, and the protein unfolding process is simulated through breaking the native contacts one by one according to the MSFID values between the residues. It is found that the flexible regions tend to unfold earlier. The sequence of the unfolding events obtained by our method is consistent with the hydrogen-deuterium exchange experimental results. Our studies imply that the unfolding behavior of the Fab fragment of antibody McPc603 is largely determined by the intrinsic dynamics of the protein.

Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD-BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate.

BtuCD-BtuF from Escherichia coli is a binding protein-dependent adenosine triphosphate (ATP)-binding cassette (ABC) transporter system that uses the energy of ATP hydrolysis to transmit vitamin B12 across cellular membranes. Experimental studies have showed that during the transport cycle, the transporter undergoes conformational transitions between the "inward-facing" and "outward-facing" states, which results in the open-closed motions of the cytoplasmic gate of the transport channel. The opening-closing of the channel gate play critical roles for the function of the transporter, which enables the substrate vitamin B12 to be translocated into the cell. In the present work, the extent of opening of the cytoplasmic gate was chosen as a function-related internal coordinate. Then the mean-square fluctuation of the internal coordinate, as well as the cross-correlation between the displacement of the internal coordinate and the movement of each residue in the protein, were calculated based on the normal mode analysis of the elastic network model to analyze the function-related motions encoded in the structure of the system. In addition, the key residues important for the functional motions of the transporter were predicted by using a perturbation method. In order to facilitate the calculations, the internal coordinate was introduced as one of the axes of the coordinate space and the conventional Cartesian coordinate space was transformed into the internal/Cartesian space with linear approximation. All the calculations were carried out in this internal/Cartesian space. Our method can successfully identify the functional motions and key residues for the transporter BtuCD-BtuF, which are well consistent with the experimental observations.

[Effect of magnesium deficiency on photosynthetic physiology and triacylglyceride (TAG) accumulation of Chlorella vulgaris].

As an excellent biological resource, Chlorella has wide applications for production of biofuel, bioactive substances and water environment restoration. Therefore, it is very important to understand the photosynthetic physiology characteristics of Chlorella. Magnesium ions play an important role in the growth of microalgae, not only the central atom of chlorophyll, but also the cofactor of some key enzyme in the metabolic pathway. A laboratory study was conducted to evaluate the effects of magnesium deficiency on several photosynthetic and physiological parameters and the triacylglyceride (TAG) accumulation of the green alga, Chlorella vulgaris, in the photoautotrophic culture process. Chlorella vulgaris biomass, protein, chlorophyll a and chlorophyll b contents decreased by 20%, 43.96%, 27.52% and 28.07% in response to magnesium deficiency, while the total oil content increased by 19.60%. Moreover, magnesium deficiency decreased the maximal photochemical efficiency F(v)/F(m) by 22.54%, but increased the non-photochemical quenching parameters qN. Our results indicated the decline of chlorophyll caused by magnesium, which affected the photosynthesis efficiency, lead to the growth inhibition of Chlorella vulgaris and affected the protein synthesis and increased the triacylglyceride (TAG) accumulation.

Red yeast rice increases excretion of bile acids in hamsters.

OBJECTIVE: To investigate the hypocholesterolemic activity of red yeast rice (RYR) and its underlying mechanism. METHODS: Three groups of hamsters were fed either the control diet or one of the two experimental diets containing by weight 0.1% RYR (0.1RYR) or 0.3% RYR (0.3RYR). Blood (0.5 mL) was collected from the retro-orbital sinus into a heparinized capillary tube at the end of week 0, 3, and 6. Plasma lipoproteins were measured using enzymatic kits, while fecal neutral and acidic sterols were quantified using a gas-liquid chromatography. RESULTS: Plasma total cholesterol was reduced by 12% in 0.1RYR group and by 18% in 0.3RYR group compared with the control value. Similarly, plasma triacylglycerol was decreased by 11% in 0.1RYR group and by 24% in 0.3RYR group. Western blotting analysis demonstrated that RYR had no effect on sterol regulatory element binding protein 2, liver X receptor, 3-hydroxy-3-methylglutary-CoA reductase, LDL receptor, and cholesterol-7alpha-hydroxylase. HPLC analysis confirmed that RYR contained 0.88% monacolin K. It was recently found that RYR supplementation increased excretion of fecal acidic sterols by 3-4 folds compared with the control value. CONCLUSION: Hypocholesterolemic activity of RYR is mediated at least partially by enhancement of acidic sterol excretion.

Self-microemulsifying drug delivery system (SMEDDS) improves anticancer effect of oral 9-nitrocamptothecin on human cancer xenografts in nude mice.

9-Nitrocamptothecin (9-NC) is an orally administered topoisomerase-I inhibitor for the treatment of pancreatic carcinoma, but its oral absorption and bioavailability are poor. The main objective of this study was to develop optimal 9-nitrocamptothecin (9-NC) microemulsion prepared by self-microemulsifying drug delivery system (SMEDDS). Two SMEDDS formulations of 9-NC prepared from a mixture of ethyl oleate, Tween-80 (T-form) or Cremophor EL (C-form), and PEG-400/ethanol were formed as microemulsions under dilution with aqueous phase. The resulting microemulsions were evaluated in vitro and in vivo, including the kinetics and antitumor effects in SKOV-3 human ovarian cancer xenograft in nude mice. Following 1:10 aqueous dilution of optimal 9-NC SMEDDS, the droplet sizes of resulting microemulsions were (30.8+/-4.6)nm and (39.8+/-8.2)nm for SMEDDS T-form and C-form, respectively, and the zeta potential values were -(4.3+/-0.5)mV and -(5.7+/-0.5)mV, respectively. In SKOV-3 cells, the growth inhibition (IC50) of various 9-NC formulations was greatest with SMEDDS T-form (3.5+/-0.7 nM) followed by SMEDDS C-form (4.6+/-0.4 nM), 9-NC solution (6.6+/-1.4 nM) and 9-NC suspension (26.0+/-2.9 nM) (P<0.01). It was indicated that the area under the plasma concentration-time curve (AUC0-->8h) values of various formulations of 9-NC after oral administration ranked as the following sequence: SMEDDS T-form (360.12+/-19.44 ngh/ml) approximately SMEDDS C-form (351.71+/-33.66 ngh/ml) >9-NC solution (241.21+/-24.67 ngh/ml)>9-NC suspension (161.24+/-24.31 ngh/ml). The 9-NC SMEDDS formulations also produced significantly more tumor shrinkage (P<0.01) when compared to 9-NC suspension in nude mice bearing human ovarian cancer xenografts. The results suggest that SMEDDS is a promising drug delivery system to increase the oral bioavailability and antitumor effects of 9-NC and may be applied to other lipophilic drugs. 9-NC SMEDDS represents a novel 9-NC therapy for cancer patients.