“… Figure 1 Simulated density ( ρ , a ) and viscosity ( η , b ) of PEG-4 solutions as a function of concentrations at 298.15 and 370 K using Amber14SB and a99SB- disp force fields. Black solid lines are experimental observations [ 78 ]. …”
Section: Resultsmentioning
confidence: 99%
“…For highly concentrated PEG-4 solutions, both water models dramatically overestimated the viscosities of PEG-4 solutions. The viscosity of a pure PEG-4 liquid was estimated to be 4057.45 ± 279.95 mPa·s, two orders of magnitude larger than the experiment of 44.63 mPa·s at 298.15 K [ 78 ]. As the temperature increased, as expected, the density and viscosity of PEG-4 solutions decreased ( Figure 1 ).…”
The behavior of biomolecules in crowded environments remains largely unknown due to the accuracy of simulation models and the limited experimental data for comparison. Here we chose a small crowder of tetraethylene glycol (PEG-4) to investigate the self-crowding of PEG-4 solutions and molecular crowding effects on the structure and diffusion of lysozyme at varied concentrations from dilute water to pure PEG-4 liquid. Two Amber-like force fields of Amber14SB and a99SB-disp were examined with TIP3P (fast diffusivity and low viscosity) and a99SB-disp (slow diffusivity and high viscosity) water models, respectively. Compared to the Amber14SB protein simulations, the a99SB-disp model yields more coordinated water and less PEG-4 molecules, less intramolecular hydrogen bonds (HBs), more protein–water HBs, and less protein–PEG HBs as well as stronger interactions and more hydrophilic and less hydrophobic contacts with solvent molecules. The a99SB-disp model offers comparable protein–solvent interactions in concentrated PEG-4 solutions to that in pure water. The PEG-4 crowding leads to a slow-down in the diffusivity of water, PEG-4, and protein, and the decline in the diffusion from atomistic simulations is close to or faster than the hard sphere model that neglects attractive interactions. Despite these differences, the overall structure of lysozyme appears to be maintained well at different PEG-4 concentrations for both force fields, except a slightly large deviation at 370 K at low concentrations with the a99SB-disp model. This is mainly attributed to the strong intramolecular interactions of the protein in the Amber14SB force field and to the large viscosity of the a99SB-disp water model. The results indicate that the protein force fields and the viscosity of crowder solutions affect the simulation of biomolecules under crowding conditions.
“… Figure 1 Simulated density ( ρ , a ) and viscosity ( η , b ) of PEG-4 solutions as a function of concentrations at 298.15 and 370 K using Amber14SB and a99SB- disp force fields. Black solid lines are experimental observations [ 78 ]. …”
Section: Resultsmentioning
confidence: 99%
“…For highly concentrated PEG-4 solutions, both water models dramatically overestimated the viscosities of PEG-4 solutions. The viscosity of a pure PEG-4 liquid was estimated to be 4057.45 ± 279.95 mPa·s, two orders of magnitude larger than the experiment of 44.63 mPa·s at 298.15 K [ 78 ]. As the temperature increased, as expected, the density and viscosity of PEG-4 solutions decreased ( Figure 1 ).…”
The behavior of biomolecules in crowded environments remains largely unknown due to the accuracy of simulation models and the limited experimental data for comparison. Here we chose a small crowder of tetraethylene glycol (PEG-4) to investigate the self-crowding of PEG-4 solutions and molecular crowding effects on the structure and diffusion of lysozyme at varied concentrations from dilute water to pure PEG-4 liquid. Two Amber-like force fields of Amber14SB and a99SB-disp were examined with TIP3P (fast diffusivity and low viscosity) and a99SB-disp (slow diffusivity and high viscosity) water models, respectively. Compared to the Amber14SB protein simulations, the a99SB-disp model yields more coordinated water and less PEG-4 molecules, less intramolecular hydrogen bonds (HBs), more protein–water HBs, and less protein–PEG HBs as well as stronger interactions and more hydrophilic and less hydrophobic contacts with solvent molecules. The a99SB-disp model offers comparable protein–solvent interactions in concentrated PEG-4 solutions to that in pure water. The PEG-4 crowding leads to a slow-down in the diffusivity of water, PEG-4, and protein, and the decline in the diffusion from atomistic simulations is close to or faster than the hard sphere model that neglects attractive interactions. Despite these differences, the overall structure of lysozyme appears to be maintained well at different PEG-4 concentrations for both force fields, except a slightly large deviation at 370 K at low concentrations with the a99SB-disp model. This is mainly attributed to the strong intramolecular interactions of the protein in the Amber14SB force field and to the large viscosity of the a99SB-disp water model. The results indicate that the protein force fields and the viscosity of crowder solutions affect the simulation of biomolecules under crowding conditions.
A binary liquid system that consists of chlorpheniramine and 1-propanol is prepared at various concentrations by the mole fraction method. The density (ρ), viscosity (η), and ultrasonic velocity (U) of the system are observed at 303 K, 308 K, and 313 K. From the experimental observations, various thermophysical parameters such as adiabatic compressibility (β), free length (Lf), free volume (
V
f
), viscous relaxation time (τ), and Gibbs free energy (
Δ
G
) are determined. The deviations of the excess parameters (βE,
L
f
E
,
V
f
E
, τE, and
Δ
G
E
) from their ideal values are calculated. The excess values are fitted with the Redlich–Kister polynomial function, and the corresponding coefficients are derived. Moreover, the standard deviations of the excess parameters are evaluated. The experimental and theoretical data confirmed the existence of hydrogen bonding interactions among the functional groups of the liquid mixture. The strength of intermolecular interactions decreased with increasing the temperature of the mixture. The strength of intermolecular interaction is noticed as 303 K > 308 K > 313 K.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
