The Effect of β-Sheet Secondary Structure on All-β Proteins by Molecular Dynamics Simulations.

The effect of β-sheet ratio and chain length on all-β proteins was investigated by MD simulations. Protein samples composed of different repeating units with various β-sheet ratios or a different number of repeating units were simulated under a broad temperature range. The simulation results show that the smaller radius of gyration was achieved by the protein with the higher proportion of β-sheet secondary structure, which had the lower nonbonded energy with more HBs within the protein.

A Study on the Through-Plane Permeability of Anisotropic Fibrous Porous Material by Fractal Stochastic Method.

The through-plane permeability is of great importance for understanding the transport phenomenon in anisotropic fibrous porous material. In this paper, a novel pore-scale model based on the equilateral triangle representative unit cell (RUC) and capillary bundle model is developed for the fluid flow through the anisotropic fibrous porous material according to fractal theory, and the effective through-plane permeability is presented accordingly. The digital structures of the fibrous porous material are generated by a fractal stochastic method (FSM), and the single-phase fluid flow through the 3D-reconstructed model is simulated by using the finite element method (FEM).

Effects of Residual Composition and Distribution on the Structural Characteristics of the Protein.

The effect of ratio and consecutive number of hydrophobic residues in the repeating unit of protein chains was investigated by MD simulation. The modified off-lattice HNP model was applied in this study. The protein chains constituted by different HNP ratios or different numbers of consecutively hydrophobic residues with the same chain length were simulated under a broad temperature range.

Effects of the Temperature and Salt Concentration on the Structural Characteristics of the Protein (PDB Code 1BBL).

The effect of the temperature and salt solution on the structural characteristics of the protein 1BBL was investigated by molecular dynamics simulations. The paper presents simulation results regarding the non-bonded energy and the structural stability of the protein immersed in salt solutions with different concentrations and temperatures. Our work demonstrates that the electrostatic potential energy and van der Waals energy of the system show the opposite changes with the influence of the external environment.

Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies.

The effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuation, the dipole moment distribution, and the secondary structure analysis were used to assess the protein samples' structural characteristics. In the simulation, we found that the higher frequency of the electric field influences the rapid response to the secondary structural transitions.

Effects of an Electric Field on the Conformational Transition of the Protein: A Molecular Dynamics Simulation Study.

The effect of the electric field on the conformational properties of the protein 1BBL was investigated by molecular dynamics simulations. Our simulation results clearly capture the structural transitions of the protein sample from helix to turn or random coil conformation induced by the increasing strength of the electric field. During our analysis, we found that the conformational stability is weakened, and the protein sample is stretched as an unfolded structure when it was exposed in a sufficiently high electric field.

Translocation of a Polymer through a Crowded Channel under Electrical Force.

The translocation of a polymer chain through a crowded cylindrical channel is studied using the Langevin dynamics simulations. The influences of the field strength , the chain length , and the crowding extent ρ on the translocation time are evaluated, respectively. Scaling relation τ ~ is observed.

Liquid crystalline assembly of rod-coil diblock copolymer and homopolymer blends by dissipative particle dynamics simulation.

Liquid crystalline assembly of rod-coil diblock copolymers blended with coil or rod homopolymers is investigated by dissipative particle dynamics simulation, considering systematically the effect of the interactions between rods and coils, the volume fraction and length of the added coil or rod homopolymers. The addition of coil or rod homopolymers induces disorder-order or order-liquid crystalline transition. In rod-coil/coil blends, the solubilization of homopolymers will saturate at a certain amount of homopolymers and then the excess homopolymers will be segregated into the central regions of coil block domains, forming "wet-dry mixture" lamellae.

Self-assembly of cyclic rod-coil diblock copolymers.

The phase behavior of cyclic rod-coil diblock copolymer melts is investigated by the dissipative particle dynamics simulation. In order to understand the effect of chain topological architecture better, we also study the linear rod-coil system. The comparison of the calculated phase diagrams between the two rod-coil copolymers reveals that the order-disorder transition point (χN)ODT for cyclic rod-coil diblock copolymers is always higher than that of equivalent linear rod-coil diblocks.

Predicting protein structure from long-range contacts.

Short-range and long-range contacts are important in forming protein structure. The proteins can be grouped into four different structural classes according to the content and topology of alpha-helices and beta-strands, and there are all-alpha, all-beta, alpha/beta and alpha+beta proteins. However, there is much difference in statistical property for those classes of proteins.