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Recent theoretical studies have demonstrated that the behaviour of molecular knots is a sensitive indicator of polymer structure. Here, we use knots to verify the ability of two state-of-the-art algorithms—configuration assembly and hierarchical backmapping—to equilibrate high-molecular-weight (MW) polymer melts. Specifically, we consider melts with MWs equivalent to several tens of entanglement lengths and various chain flexibilities, generated with both strategies. We compare their unknotting probability, unknotting length, knot spectra, and knot length distributions. The excellent agreement between the two independent methods with respect to knotting properties provides an additional strong validation of their ability to equilibrate dense high-MW polymeric liquids. By demonstrating this consistency of knotting behaviour, our study opens the way for studying topological properties of polymer melts beyond time and length scales accessible to brute-force molecular dynamics simulations.

The mechanical properties of pristine graphene oxide paper and paper-like films of polyvinyl alcohol (PVA)-graphene oxide nanocomposite are investigated in a joint experimental-theoretical and computational study. In combination, these studies reveal a delicate relationship between the stiffness of these papers and the water content in their lamellar structures. ReaxFF-based molecular dynamics (MD) simulations elucidate the role of water molecules in modifying the mechanical properties of both pristine and nanocomposite graphene oxide papers, as bridge-forming water molecules between adjacent layers in the paper structure enhance stress transfer by means of a cooperative hydrogen-bonding network. For graphene oxide paper at an optimal concentration of ~5 wt % water, the degree of cooperative hydrogen bonding within the network comprising adjacent nanosheets and water molecules was found to optimally enhance the modulus of the paper without saturating the gallery space. Introducing PVA chains into the gallery space further enhances the cooperativity of this hydrogen-bonding network, in a manner similar to that found in natural biomaterials, resulting in increased stiffness of the composite. No optimal water concentration could be found for the PVA-graphene oxide nanocomposite papers, as dehydration of these structures continually enhances stiffness until a final water content of ~7 wt % (additional water cannot be removed from the system even after 12 h of annealing).

Assuming dipole–dipole interaction as the dominant relaxation mechanism of protons of water molecules adsorbed onto macromolecule (biopolymer) surfaces we have been able to model the dependences of relaxation rates on temperature and frequency. For adsorbed water molecules the correlation times are of the order of 10 −5 s, for which the dispersion region of spin–lattice relaxation rates in the rotating frame R 1 ρ = 1/ T 1 ρ appears over a range of easily accessible B 1 values. Measurements of T 1 ρ at constant temperature and different B 1 values then give the “dispersion profiles” for biopolymers. Fitting a theoretical relaxation model to these profiles allows for the estimation of correlation times. This way of obtaining the correlation time is easier and faster than approaches involving measurements of the temperature dependence of R 1 = 1/ T 1 . The T 1 ρ dispersion approach, as a tool for molecular dynamics study, has been demonstrated for several hydrated biopolymer systems including crystalline cellulose, starch of different origins (potato, corn, oat, wheat), paper (modern, old) and lyophilized proteins (albumin, lysozyme).

Biological membranes are continuously remodeled in the cell by specific membrane-shaping machineries to form, for example, tubes and vesicles. We examine fundamental mechanisms involved in the vesiculation processes induced by a cluster of envelope (E) and membrane (M) proteins of the dengue virus (DENV) using molecular dynamics simulations and a coarse-grained model. We show that an arrangement of three E-M heterotetramers (EM3) works as a bending unit and an ordered cluster of five such units generates a closed vesicle, reminiscent of the virus budding process. In silico mutagenesis of two charged residues of the anchor helices of the envelope proteins of DENV shows that Arg-471 and Arg-60 are fundamental to produce bending stress on the membrane. The fine-tuning between the size of the EM3 unit and its specific bending action suggests this protein unit is an important factor in determining the viral particle size.

In the preceding paper of this series [Leontidis, E. Aroti, A. Belloni, L. J. Phys. Chem. B 2009, 113, 1447], we considered and modeled the increase of the surface pressure of dipalmitoyl phosphatidylcholine (DPPC) monolayers over electrolyte solutions of various monovalent sodium salts. The experimental results for salts with large, less hydrophilic anions can be successfully described by models treating ionic specificity either as specific partitioning in the interfacial lipid layer or as a result of ion-lipid dispersion interactions. However, the results for salts with more hydrophilic anions, such as chloride and fluoride, cannot be fitted by any of these models, while they clearly demonstrate the existence of a specific sodium-DPPC interaction. In the present paper, we first prove that the experimental results for sodium fluoride (NaF) can be fitted by a model that is based on simultaneous complexation of sodium ions with up to three lipid molecules, as suggested by recent molecular dynamics simulations. We then return to the experimental results of sodium salts with more hydrophobic anions, treated in the preceding paper, and prove that these can be fitted equally well with a complex model, which accounts for both sodium complexation with the lipid head groups and anion partitioning within the lipid monolayers. The partitioning parameters obtained from this more complete model correlate well with several measures of ion specificity, such as ionic volume, von Hippel chromatographic parameters, or viscosity B-coefficients. A model for these partitioning chemical potentials is created based on the competition of cavity and ion hydration terms. The model leads to an excellent correlation of the partitioning chemical potentials with a function of the ionic radius, suggesting that specific anion effects on this lipid model system are mostly a matter of ionic size. Two notable exceptions from this correlation are thiocyanate and acetate ions, the charge distribution of which is not spherically symmetric, so that they are expected to have orientational-dependent interactions with the water-lipid interface. The implications of the present results on ion specificity in general are discussed. © 2009 American Chemical Society. 113 5 1460 1467 Cited By :43

International audience; Mutagenesis experiments suggest that Asp79 in cellulase Cel6A (E2) from Thermobifida fusca has a catalytic role, in spite of the fact that this residue is more than 13 Å from the scissile bond in models of the enzyme–substrate complex built upon the crystal structure of the protein. This suggests that there is a substantial conformational shift in the protein upon substrate binding. Molecular mechanics simulations were used to investigate possible alternate conformations of the protein bound to a tetrasaccharide substrate, primarily involving shifts of the loop containing Asp79, and to model the role of water in the active site complex for both the native conformation and alternative low-energy conformations. Several alternative conformations of reasonable energy have been identified, including one in which the overall energy of the enzyme–substrate complex in solution is lower than that of the conformation in the crystal structure. This conformation was found to be stable in molecular dynamics simulations with a cellotetraose substrate and water. In simulations of the substrate complexed with the native protein conformation, the sugar ring in the –1 binding site was observed to make a spontaneous transition from the 4C1 conformation to a twist-boat conformer, consistent with generally accepted glycosidase mechanisms. Also, from these simulations Tyr73 and Arg78 were found to have important roles in the active site. Based on the results of these various MD simulations, a new catalytic mechanism is proposed. Using this mechanism, predictions about the effects of changes in Arg78 were made which were confirmed by site-directed mutagenesis.

We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described by the structure-based coarse-grained model augmented by electrostatic interactions. Previous studies of the capsid self-assembly involved solid objects of a supramolecular scale, e.g. corresponding to capsomeres, with engineered couplings and stochastic movements. In our approach, a single capsid is dissociated by an application of a high temperature for a variable period and then the system is cooled down to allow for self-assembly. The restoration of the capsid proceeds to various extent, depending on the nature of the dissociated state, but is rarely complete because some proteins depart too far unless the process takes place in a confined space., 13 figures