The coat protein of tobacco mosaic virus as an anti-tobacco mosaic virus: a molecular dynamics simulation.

The Coat Protein (CP) of the Tobacco Mosaic Virus (TMV) executes an important duty in the protection of virus RNA. The interaction between the virus CP and host plant proteins induces infection in the host and creates dark and light green mosaics on crops, which disturb the growth and function of the plant. The interaction between the virus CP and the modified CP, expressed in transgenic plants, causes Coat Protein-Mediated Resistance (CP-MR), which reduces virus infection in transgenic plants. In this study, a model is suggested for resistance as "stop assembly of CP" in the virus. It is based on the fact that the CP, when mutated, acts as a dead-end in virus assembly. For evaluation of the model, we investigated the effect of four mutants including CBT28I, ABT42W, ABD77R, and ABT89W complexes on plant resistance against TMV infection by molecular dynamics simulation. Previous studies had shown the influence of such mutations on the CP-MR. The MD results of in the present study further confirmed the mentioned effect and demonstrated how the mutations could be the cause of CP-MR. The results are calculated by the RMSD, Rg, H-bond, and g-MMPBSA scripts. The change in binding energy between two chains is consistent with CP-MR such that with increase in binding energy, the affinity between two chains was reduced and the CP-MR increased. Based on this model, it is possible to design mutants with a high level of efficiency.Communicated by Ramaswamy H. Sarma.

Energy effects on the structure and thermodynamic properties of nanoconfined fluids (a density functional theory study).

The structure and properties of fluids confined in nanopores may show a dramatic departure from macroscopic bulk fluids. The main reason for this difference lies in the influence of system walls. In addition to the entropic wall effect, system walls can significantly change the energy of the confined fluid compared to macroscopic bulk fluids. The energy effect of the walls on a nanoconfined fluid appears in two forms. The first effect is the cutting off of the intermolecular interactions by the walls, which appears for example in the integrals for calculation of the thermodynamic properties. The second wall effect involves the wall-molecule interactions. In such confined fluids, the introduction of wall forces and the competition between fluid-wall and fluid-fluid forces could lead to interesting thermodynamic properties, including new kinds of phase transitions not observed in the macroscopic fluid systems. In this article, we use the perturbative fundamental measure density functional theory to study energy effects on the structure and properties of a hard core two-Yukawa fluid confined in a nanoslit. Our results show the changes undergone by the structure and phase transition of the nanoconfined fluids as a result of energy effects.