Adsorption of water molecules in slit pores

We report molecular dynamics (MD) simulations on the adsorption of water in attractive and repulsive slit pores, where the slit and a bulk region are in contact with each other. Water structure, surface force and adsorption behavior are investigated as a function of the overall density in the bulk region. The gas–liquid transition in both types of pores occurs at similar densities of the bulk region.     

Influence of hydrophobe content on the solution rheology of hydrophobically modified terpolymer of SO2, N,N-diallyl-N-carboethoxymethylammonium chloride

Rheological properties of hydrophobically modified copolymer of SO₂, N,N-diallyl-N-carboethoxymethylammonium chloride and the hydrophobic monomer N,N-diallyl-N-octadecylammonium chloride were studied. The influence of hydrophobe content (HP) and polymer concentration was investigated. Polymers with HP content in the range 1.5-5% were examined and the concentration was varied in the range 2-5 wt%. Both dynamic and steady-shear experiments were performed in ARES rheometer. Copolymers were observed to exhibit typical viscoelastic behavior even with low HP content. Both the dynamic viscosity, η′ and storage modulus, G′, increase with the increase of both the polymer concentration and the HP content of the system. The viscosity of the high HP content polymer showed a strong shear dependency, while G′ was a weak function of frequency and gel-like behavior was observed. The zero-shear viscosity, η₀, showed a strong concentration dependency (η₀ ∼ ?^α; 1.1 < α < 5.9). The concentration dependency of η₀ suggests that intermolecular association is dominant in the high HP content polymer. Control of the HP content and polymer concentration of this class of polymers can lead to a wide range of interesting rheological properties.     

SDOCK: a global protein-protein docking program using stepwise force-field potentials

Fast Fourier transform (FFT) method limits the forms of scoring functions in global protein-protein docking. On the other hand, force field potentials can effectively describe the energy hyper surface of biological macromolecules. In this study, we developed a new protein-protein docking program, SDOCK, that incorporates van der Waals attractive potential, geometric collision, screened electrostatic potential, and Lazaridis-Karplus desolvation energy into the scoring function in the global searching process. Stepwise potentials were generated from the corresponding continuous forms to treat the structure flexibility. After optimization of the atom solvation parameters and the weights of different potential terms based on a new docking test set that contains 142 cases with small or moderate conformational changes upon binding, SDOCK slightly outperformed the well-known FFT based global docking program ZDOCK3.0. Among the 142 cases tested, 52.8% gave at least one near-native solutions in the top 100 solutions. SDOCK was also tested on six blind testing cases in Critical Assessment of Predicted Interactions rounds 13 to 18. In all six cases, the near-native solutions could be found within the top 350 solutions. Because the SDOCK approach performs global docking based on force-field potentials, one of its advantages is that it provides global binding free energy surface profiles for further analysis. The efficiency of the program is also comparable with that of other FFT based protein-protein docking programs. SDOCK is available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi-bin/down.cgi.     

CHO Cells Adhering to Nitrogen‐Rich Plasma‐Polymerised Ethylene Exhibit High Production of a Specific Recombinant Protein

In many industrial applications, inadequate cell attachment can be a limitation, especially when serum‐free media are used. Nitrogen‐rich plasma‐polymerised ethylene (PPE:N) exhibits high concentrations of polar groups that can help to promote the attachment of weakly adherent cell types. Tissue plasminogen activator‐producing Chinese hamster ovary (CHO) cells, adapted to suspension, were grown in the presence PPE:N flakes and were found to adhere to them. The growth rate was reduced, but cell viability was enhanced and their metabolism was more efficient, with generally higher recombinant protein productivity. Finally, cell adhesion on PPE:N surfaces was found to be independent of integrins, and was probably mediated by certain non‐specific interactions with the PPE:N surface.

     

On the mechanism of solute retention in RP-HPLC systems with B+AB1+AB2 type eluents

Summary Intermolecular interactions between the solute and the moieties constituting the mobile phase significantly contribute to the overall retention pattern of a given solute in a given chromatographic system. In this paper retention of solute is discussed in the case of the B+AB₁+AB₂ type mobile phase, which, in a quasithermodynamic way, can be divided into seven individual moieties. One evaluates the influence of each moiety on solute retention, and refers these regularities to the polarity of the solutes.     

Force field parameters for rotation around chi torsion axis in nucleic acids

To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis. The reliability of molecular dynamics (MD) simulation was significantly increased by improving the torsion parameters at C8--N9--C1'--X (X = H1', C2', O4') in A, G and those at C6--N1--C1'--X in C, T, and U. In this work, we constructed small models representing the chemical structure of A, G, C, T, and U, and estimated energy profile for chi-axis rotation by executing numerous quantum mechanical (QM) calculations. The parameters were derived by discrete Fourier transformation of the calculated QM data. A comparison in energy profile between molecular mechanical (MM) calculation and QM one shows that our presently derived parameters well reproduce the energy surface of QM calculation for all the above torsion terms. Furthermore, our parameters show a good performance in MD simulations of some nucleic acids. Hence, the present refinement of parameters will enable us to perform more accurate simulations for various types of nucleic acids.     

The effect of conjugating RGD into 3D alginate hydrogels on adipogenic differentiation of human adipose-derived stromal cells

The effects of RGD peptide conjugation to alginate hydrogel on the adipogenic differentiation of ASCs was investigated. After 3 d of culture, RGD-modified alginate hydrogels significantly stimulated FAK and integrin α1 gene expressions and vinculin expression in ASCs. In addition, RGD-modified alginate hydrogels significantly enhanced the adipogenic differentiation of human ASCs to exhibit higher expression levels of oil red O staining and adipogenic genes compared to those of the control group (unmodified gels). These results suggest potential applications of RGD-modified alginate gels for adipose tissue regeneration.     

The mechanism of double proton transfer in dimers of uracil and 2-thiouracil--the reaction force perspective

The intermolecular double proton transfer in dimers of uracil and 2-thiouracil is studied through density functional theory calculations. The reaction force framework provides the basis for characterizing the mechanism that in all cases has been associated to a dynamic balance between polarization and charge transfer effects. It has been found that the barriers for proton transfer depend upon the nature of the acceptor atoms and its position within the seminal monomer. Actually, the change in the nature of the hydrogen bonds connecting the two monomers along the reaction coordinate may favor or disfavor the double-proton transfer.     

Origin of intrinsic 3(10)-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field

Current all-atom force fields often fail to recognize the native structure of a protein as the lowest free energy minimum. One possible cause could be the mathematical form of the potential based on the assumption that the conformation of a residue is independent of its neighbors. Here, using quantum mechanical (QM) methods (MP2/6-31g**//HF/6-31g** and MP2/cc-pVDZ//cc-pVDZ//HF/cc-pVDZ), the intrinsic correctness of the gas phase terms (without solvation) of the Amber ff03 and ff99 potentials are examined by testing their ability to reproduce the relative 3(10)-helix versus extended structure stabilities in the gas phase for 1-7-residue alanine, valine, leucine, and isoleucine homopolypeptides. The 3(10)-helix versus extended state stability strongly depends on chain length and less on the amino acid identity. The helical conformation becomes lower in energy than the extended conformation for all tested peptides longer than two residues, and its stability increases with the increase of chain length. The ff03 potential better describes the 3(10)-helix versus extended state energy than ff99 and also reproduces the curvature of the relative helix-extended state energies. Therefore, the mathematical form of the Amber potential is sufficient to describe the local effect of 3(10)-helix versus extended structure stabilization in the gas phase. However, the energy curves are shifted and the backbone geometries differ compared with the QM results. This may cause significant geometric discrepancies between native and predicted structures. Therefore, extant molecular mechanics force fields, such as Amber, need refinement of their parameters to correctly describe helix-extended state energetics and geometry of major conformations.     

Periodic solutions of damped differential systems with repulsive singular forces

We consider the periodic boundary value problem for the singular differential system: where , , and . The singular potential is of repulsive type in the sense that as . Under Habets-Sanchez's strong force condition on at the origin, the existence results, obtained by coincidence degree in this paper, have no restriction on the damping forces . Meanwhile, some quadratic growth of the restoring potentials at infinity is allowed.