Search results for "dynamics."

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

2013

Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We sho…

Thermodynamically induced shear degradation

1988

The shear degradation of polymers in semiconcentrated solutions is viewed as a function of solvent quality. It is shown that the deterioration of the thermodynamic quality of the solvent leads to a marked flow resistance due to an increasing number of contacts between the chains. This may be probed by viscosimetric measurements as well as by degradation experiments (“thermodynamically induced shear degradation”). For a detailed discussion of this phenomenon the experimental setup for the mechanochemical experiment is outlined first, followed by a survey of the kinetics of chain scission. Finally, experiments mostly obtained on polystyrene in the theta-solvent trans-decalin are discussed. Th…

Temperature and pressure dependence of phase separation of trans-decahydronaphthalene/polystyrene solution

2004

Abstract The cloud-point temperatures (Tcl’s) of trans-decahydronaphthalene (TD)/polystyrene (PS, Mw=270 kg/mol) solutions were determined by light scattering measurements over a range of temperatures (1–16 °C), pressures (100–900 bar), and compositions (4.2–21.6 vol% polymer). The system phase separates upon cooling and the Tcl was found to increase with the rising pressure for the constant composition. In the absence of special effects this finding indicates positive excess volumes. The special attention was paid to the demixing temperatures as a function of the pressure for the different polymer solutions and the plots in the T-volume fraction plane and P-volume fraction plane. The cloud…

Interactions between proteins and poly(ethylene-glycol) investigated using molecular dynamics simulations

2017

Poly(ethylene-glycol) (PEG) is a polymer used to coat therapeutic preparations, like drugs or drug nanocarriers, and improve their efficacy. This effect is probably due to a reduction of the interactions of the coated species with the host organism. Nevertheless, experiments show that PEGylated materials do interact with the surrounding biological milieu, and in particular with blood proteins. Here, we use atomistic molecular dynamics simulations to characterize the interactions between the polymer and several blood proteins. In these simulations, the proteins are immersed in a mixture of PEG and water molecules. We observe how PEG distributes around the protein surface and measure PEG-prot…

The protein dynamical transition does not require the protein polypeptide chain

2011

We give experimental evidence that the main features of protein dynamics revealed by neutron scattering, i.e., the “protein dynamical transition” and the “boson peak”, do not need the protein polypeptide chain. We show that a rapid increase of hydrogen atoms fluctuations at about 220 K, analogous to the one observed in hydrated myoglobin powders, is also observed in a hydrated amino acids mixture with the chemical composition of myoglobin but lacking the polypeptide chain; in agreement with the protein behavior, the transition is abolished in the dry mixture. Further, an excess of low-frequency vibrational modes around 3 meV, typically observed in protein powders, is also observed in our mi…

Interactions Between Blood Proteins and Nanoparticles Investigated Using Molecular Dynamics Simulations

2019

In the development of new therapeutic agents based on nanoparticles it is of fundamental importance understanding how these substances interact with the underlying biological milieu. Our research is focussed on simulating in silico these interactions using accurate atomistic models, and gather from these information general pictures and simplified models of the underlying phenomena. Here we report results about the interactions of blood proteins with promising hydrophilic polymers used for the coating of therapeutic nanoparticles, about the salt dependent behavior of one of these polymers (poly-(ethylene glycol)) and about the interactions of blood proteins with silica, one of the most used…

1979

The kinetics of the anionic polymerization of styrene were investigated under pressure (1≤p/bar < 1800) with Na+ as counter ion in tetrahydropyran (THP) as solvent and with Cs+ as counter ion in 1,2-dimethoxyethane (DME) as solvent. The results yielded the activation volume of the contact ion pair ΔV and the sum (ΔV + ΔVcs) of the activation volume of the solvent separated ion pair ΔV and the volume change upon formation of solvent separated ion pairs from contact ion pairs ΔVcs. The numerical values are negative. The activation volume of the solvent separated ion pairs could be estimated.

Stability of negatively charged platelets in calcium-rich anionic copolymer solutions.

2014

Controlling the stability of anisotropic particles is key to the development of advanced materials. Here, we report an investigation, by means of mesoscale molecular dynamics simulations, of the stability and structural change of calcium-rich dispersions containing negatively charged nanoplatelets, neutralized by calcium counterions, in the presence of either comb copolymers composed of anionic backbones with attached neutral side chains or anionic-neutral linear block copolymers. In agreement with experimental observations, small stacks of platelets (tactoids) are formed, which are greatly stabilized in the presence of copolymers. In the absence of polymers, tactoids will grow and aggregat…

Polymeric scaffolds prepared via Thermally Induced Phase Separation (TIPS): Tuning of structure and morphology

2007

Scaffolds suitable for tissue engineering applications were prepared by Thermally Induced Phase Separation (TIPS) starting from a ternary solution PLLA/dioxane/water. The experimental protocol consisted of three consecutive steps, a first quench from the homogeneous solution to an appropriate demixing temperature (within the metastable region), a holding stage for a given residence time and a final quench from the demixing temperature to a low temperature (within the unstable region). A large variety of morphologies, in terms of average pore size and interconnection, were obtained upon modifying the demixing time and temperature, owing to the interplay of nucleation and growth processes dur…

Thermodynamics and Kinetics of the Interactions Between Proteins and Hydrophilic Polymers

2021

Hydrophilic polymers are being investigated as possible coating agents for therapeutic nanoparticles because of their capacity to reduce immune response and increase circulation life time. The mechanism of action of these coatings is not well understood although it is clear that they unspecifically reduce the amount of proteins adsorbing on the nanoparticle surface coming in contact with biological fluids. Here we have investigated, using state-of-the-art atomistic molecular dynamics simulations, the equilibrium and kinetic properties of the interactions forming between human serum albumin, the most abundant protein in the blood stream, and two different and promising polymers poly(ethylene…