Molecular dynamics modeling and simulation of water desalination through a double-walled carbon nanotube with moiré pattern

Freshwater scarcity has emerged as a major challenge of our time. Under this context, the importance of an efficient and energy-saving water desalination method is highlighted. In recent years, carbon nanotube (CNT) membrane characterizing with high permeability has attracted much attention in research, and it is regarded as a promising alternative to the conventional reverse osmosis technology. This work aims at numerically investigating the water desalination ability of a novel type of CNT membrane structure, namely the double-walled carbon nanotube (DWCNT) with Moiré pattern. After establishing the physical CNT models and running the molecular dynamics (MD) simulation of the water desalination system, it is found that both the single-walled carbon nanotube (SWCNT) and DWCNT can desalinate the seawater successfully while the water permeability of DWCNT is at least 18.9% higher than that of SWCNT within the same time. As far as the Moiŕe pattern adopted in this study is concerned, the water permeability of DWCNT without Moiŕe pattern is 18.6% higher than that with Moiré pattern.

Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber

A procedure has been developed for the refinement of crystallographic protein structures based on the biomolecular simulation program Amber. The procedure constructs a model representing a crystal unit cell, which generally contains multiple protein molecules and is fully hydrated with TIP3P water. Periodic boundary conditions are applied to the cell in order to emulate the crystal lattice. The refinement is conducted in the form of a specially designed short molecular-dynamics run controlled by the Amber ff14SB force field and the maximum-likelihood potential that encodes the structure-factor-based restraints. The new Amber-based refinement procedure has been tested on a set of 84 protein structures. In most cases, the new procedure led to appreciably lower R free values compared with those reported in the original PDB depositions or obtained by means of the industry-standard phenix.refine program. In particular, the new method has the edge in refining low-accuracy scrambled models. It has also been successful in refining a number of molecular-replacement models, including one with an r.m.s.d. of 2.15 Å. In addition, Amber-refined structures consistently show superior MolProbity scores. The new approach offers a highly realistic representation of protein–protein interactions in the crystal, as well as of protein–water interactions. It also offers a realistic representation of protein crystal dynamics (akin to ensemble-refinement schemes). Importantly, the method fully utilizes the information from the available diffraction data, while relying on state-of-the-art molecular-dynamics modeling to assist with those elements of the structure that do not diffract well (for example mobile loops or side chains). Finally, it should be noted that the protocol employs no tunable parameters, and the calculations can be conducted in a matter of several hours on desktop computers equipped with graphical processing units or using a designated web service.

Computer simulation of the interaction of the surface of an aluminosilicate filler and an organoelement modifier

Geometry optimization and molecular dynamics modeling are performed in the quantum-classical approximation for a phosphorus-boron-containing oligomer and aluminosilicate microspheres. By modeling the phosphorusboron-containing oligomer with the numbers of units of 3—5, the possibility of the appearance of internal cycles in oligomers with the number of chain units more than 3 as a result of the formation of bonds of boron atoms with the oxygen of the phosphorus atom was established. The interaction of the surface of the aluminosilicate filler and the phosphorus-boron-containing oligomer modifier is due to hydrogen bonds between the hydroxyl groups of the silicon atoms of the aluminosilicate filler and the oxygen and hydrogen atoms of the oligomer. Keywords: phosphorus-boron-containing oligomer, aluminosilicate microspheres, computer simulation. [email protected]

Molecular dynamics modeling of the Vibrio cholera Na+-translocating NADH:quinone oxidoreductase NqrB–NqrD subunit interface

The Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) is the major Na+ pump in aerobic pathogens such as Vibrio cholerae. The interface between two of the NQR subunits, NqrB and NqrD, has been proposed to harbor a binding site for inhibitors of Na+-NQR. While the mechanisms underlying Na+-NQR function and inhibition remain underinvestigated, their clarification would facilitate the design of compounds suitable for clinical use against pathogens containing Na+-NQR. An in silico model of the NqrB–D interface suitable for use in molecular dynamics simulations was successfully constructed. A combination of algorithmic and manual methods was used to reconstruct portions of the two subunits unresolved in the published crystal structure and validate the resulting structure. Hardware and software optimizations that improved the efficiency of the simulation were considered and tested. The geometry of the reconstructed complex compared favorably to the published V. cholerae Na+-NQR crystal structure. Results from one 1 µs, three 150 ns and two 50 ns molecular dynamics simulations illustrated the stability of the system and defined the limitations of this model. When placed in a lipid bilayer under periodic boundary conditions, the reconstructed complex was completely stable for at least 1 µs. However, the NqrB–D interface underwent a non-physiological transition after 350 ns.

Proteomic and molecular dynamic investigations of PTM-induced structural fluctuations in breast and ovarian cancer

Post-translational processing leads to conformational changes in protein structure that modulate molecular functions and change the signature of metabolic transformations and immune responses. Some post-translational modifications (PTMs), such as phosphorylation and acetylation, are strongly related to oncogenic processes and malignancy. This study investigated a PTM pattern in patients with gender-specific ovarian or breast cancer. Proteomic profiling and analysis of cancer-specific PTM patterns were performed using high-resolution UPLC-MS/MS. Structural analysis, topology, and stability of PTMs associated with sex-specific cancers were analyzed using molecular dynamics modeling. We identified highly specific PTMs, of which 12 modified peptides from eight distinct proteins derived from patients with ovarian cancer and 6 peptides of three proteins favored patients from the group with breast cancer. We found that all defined PTMs were localized in the compact and stable structural motifs exposed outside the solvent environment. PTMs increase the solvent-accessible surface area of the modified moiety and its active environment. The observed conformational fluctuations are still inadequate to activate the structural degradation and enhance protein elimination/clearance; however, it is sufficient for the significant modulation of protein activity.