Molecular dynamics simulation of polystyrene copolymer with octyl short-chain branches in toluene

In this study, dimensional, conformational and dynamic behaviors of a short-chain branched styrene/1-octene copolymer chain with different 1-octene percentages, i.e., 0, 2, 4 and 6%, in toluene are investigated at the temperature of 298.15 K via molecular dynamics simulation. The chain dimensions and flexibility in the solvent are evaluated by calculating the radius of gyration (R_g), end-to-end distance (<r₀>), surface area (A_ch), and volume (V_ch) of the copolymer chain. The mean square displacement (MSD) and diffusivity coefficient for each copolymer chain are measured to determine its dynamic behavior and mobility in aromatic media. To consider the effect of increasing the 1-octene co-monomer percentage on the copolymer chain affinity to the solvent molecules, the interaction energy (E_int) and Flory-Huggins (FH) interaction parameter are calculated for each equilibrated solution model. The simulation results indicate that the co-monomer level increment in the copolymer structure reduces the chain R_g amount and its interaction with the solvent. The <r₀> of the chain increases up to 4% co-monomer content, while further co-monomer content decreases the <r₀> value. Additionally, the viscosity of the equilibrated dilute solutions is calculated via non-equilibrium molecular dynamics simulation (NEMD). Moreover, the steric hindrance of the copolymers and the solvent molecules capturing in the dilute solution is determined via radial distribution function (RDF) analysis. Helmholtz free energy and the system entropy changes are calculated to evaluate the tendency of the copolymer to the solvent molecules and its dilute solution irregularity, respectively. Graphical abstract The figure shows the variations trend of the poly(styrene-co-1-octene) chain dimensions in toluene aromatic solvent by increasing the 1-octene content (x), after the equilibration state. Red and blue colors represent the carbon atoms of the copolymer chain backbone and 1-octene side chains, respectively. The styrene rings and the hydrogen atoms of the chains were removed for better view.

Mechanisms of whey protein isolate interaction with basil seed gum: Influence of pH and protein-polysaccharide ratio

In the present work, we determined the structure-function relationships of basil seed gum (BSG) and whey protein isolate (WPI) mixtures at the start of soluble complex formation, maximum soluble complex formation and predominant thermodynamic incompatibility to understand BSG:WPI blends interaction behavior. Accordingly, turbidity and zeta potential were analyzed in the pH range of 2.0-7.0 and BSG:WPI ratios of 1:4, 1:6.6 and 1:9. Dynamic rheometry was used to evaluate samples at three different pHs. Additionally, dilute solution properties of BSG, WPI and their blends were studied at pH = 7.0. Independent of mixture ratio, all dispersions showed maximum interaction at pH = 5.0, the start of soluble complex formation around pH = 6.0 and thermodynamic incompatibility interaction behavior at pH = 7.0. Cole-Cole plots based on dynamic rheometry supported the Gibbs free energy change of mixtures based on intrinsic viscosity data. These results are important to create new structures from mixtures of proteins and polysaccharides.

Catalytic studies of glutathione transferase from Clarias gariepinus (Burchell) in dilute and crowded solutions

Kinetic properties of purified Clarias gariepinus glutathione transferase (CgGST) was studied in the presence of Ficoll 70, Polyethylene glycol (PEG) 6000, bovine serum albumin (BSA) and in dilute solution. This was done to mimic the cytosol thereby unraveling the actual mechanism of detoxication involving glutathione transferase (GST) in the crowded intracellular milieu. CgGST from the liver of Clarias gariepinus was purified to homogeneity by affinity chromatography on glutathione (GSH) - agarose. Initial-velocity study was performed by varying the concentrations of GSH at various fixed concentrations of 1-chloro-2,4-dinitrobenzene (CDNB) and vice-versa. Data obtained were fitted to the three equations representing random-ordered, compulsory-ordered and ping-pong mechanisms to obtain kinetic parameters. Product inhibition studies using sodium chloride (NaCl) was done by varying the concentrations of NaCl and CDNB at a fixed concentration of GSH and vice-versa. Data obtained were fitted to three equations representing competitive, non-competitive and uncompetitive inhibitions to obtain the inhibition constants (K_i^GSH and K_i^CDNB). Optimal temperature of CgGST activity was 20 °C both in dilute and crowded solutions. Maximum velocity (V_max) in dilute solution was decreased, while K_m^GSH and K_m^CDNB were increased in the presence of the crowding agents. Turnover number (k_cat), catalytic efficiency - k_cat/K_m^GSH_,k_cat/K_m^CDNB and inhibition constants - (K_i^GSH and K_i^CDNB) were reduced in crowded solutions. Mechanism of catalysis was steady - state random sequential in both dilute and crowded solutions. The study concluded that although the catalytic efficiency of the enzyme was reduced in crowded solution, mechanism of catalysis remains the same in both crowded and dilute solutions.

Protein-protein interactions in a crowded environment

Protein-protein interactions are important in many essential biological functions, such as transcription, translation, and signal transduction. Much progress has been made in understanding protein-protein association in dilute solution via experimentation and simulation. Cells, however, contain various macromolecules, such as DNA, RNA, proteins, among many others, and a myriad of non-specific interactions (usually weak) are present between these cellular constituents. In this review article, we describe the important developments in recent years that have furthered our understanding and even allowed prediction of the consequences of macromolecular crowding on protein-protein interactions. We outline the development of our crowding theory that can predict the change in binding free energy due to crowding quantitatively for both repulsive and attractive protein-crowder interactions. One of the most important findings from our recent work is that weak attractive interactions between crowders and proteins can actually destabilize protein complex formation as opposed to the commonly assumed stabilizing effect predicted based on traditional crowding theories that only account for the entropic-excluded volume effects. We also discuss the implications of macromolecular crowding on the population of encounter versus specific native complex.