Molecular insights on poly(N-isopropylacrylamide) coil-to-globule transition induced by pressure.
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ABSTRACT:
SUBMITTER: Tavagnacco L
PROVIDER: S-EPMC8247264 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:By means of atomistic molecular dynamics simulations we investigate the behaviour of poly(N-isopropylacrylamide), PNIPAM, in water at temperatures below and above the lower critical solution temperature (LCST), including the undercooled regime. The transition between water soluble and insoluble states at the LCST is described as a cooperative process involving an intramolecular coil-to-globule transition preceding the aggregation of chains and the polymer precipitation. In this work we investigate the molecular origin of such cooperativity and the evolution of the hydration pattern in the undercooled polymer solution. The solution behaviour of an atactic 30-mer at high dilution is studied in the temperature interval from 243 to 323 K with a favourable comparison to available experimental data. In the water soluble states of PNIPAM we detect a correlation between polymer segmental dynamics and diffusion motion of bound water, occurring with the same activation energy. Simulation results show that below the coil-to-globule transition temperature PNIPAM is surrounded by a network of hydrogen bonded water molecules and that the cooperativity arises from the structuring of water clusters in proximity to hydrophobic groups. Differently, the perturbation of the hydrogen bond pattern involving water and amide groups occurs above the transition temperature. Altogether these findings reveal that even above the LCST PNIPAM remains largely hydrated and that the coil-to-globule transition is related with a significant rearrangement of the solvent in the proximity of the surface of the polymer. The comparison between the hydrogen bonding of water in the surrounding of PNIPAM isopropyl groups and in the bulk displays a decreased structuring of solvent at the hydrophobic polymer-water interface across the transition temperature, as expected because of the topological extension along the chain of such interface. No evidence of an upper critical solution temperature behaviour, postulated in theoretical and thermodynamics studies of PNIPAM aqueous solution, is observed in the low temperature domain.
| S-EPMC5932979 | biostudies-literature
Project description:The coil-to-globule transition of poly(N-isopropylacrylamide) (PNIPAM) microgel particles suspended in water has been investigated in situ as a function of heating and cooling rate with four optical process analytical technologies (PAT), sensitive to structural changes of the polymer. Photon Density Wave (PDW) spectroscopy, Focused Beam Reflectance Measurements (FBRM), turbidity measurements, and Particle Vision Microscope (PVM) measurements are found to be powerful tools for the monitoring of the temperature-dependent transition of such thermo-responsive polymers. These in-line technologies allow for monitoring of either the reduced scattering coefficient and the absorption coefficient, the chord length distribution, the reflected intensities, or the relative backscatter index via in-process imaging, respectively. Varying heating and cooling rates result in rate-dependent lower critical solution temperatures (LCST), with different impact of cooling and heating. Particularly, the data obtained by PDW spectroscopy can be used to estimate the thermodynamic transition temperature of PNIPAM for infinitesimal heating or cooling rates. In addition, an inverse hysteresis and a reversible building of micrometer-sized agglomerates are observed for the PNIPAM transition process.
| S-EPMC5233752 | biostudies-literature
Project description:Upon transfer from strongly denaturing to native conditions, proteins undergo a collapse that either precedes folding or occurs simultaneously with it. This collapse is similar to the well known coil-globule transition of polymers. Here we employ single-molecule fluorescence methods to fully characterize the equilibrium coil-globule transition in the denatured state of the IgG-binding domain of protein L. By using FRET measurements on freely diffusing individual molecules, we determine the radius of gyration of the protein, which shows a gradual expansion as the concentration of the denaturant, guanidinium hydrochloride, is increased all the way up to 7 M. This expansion is observed also in fluorescence correlation spectroscopy measurements of the hydrodynamic radius of the protein. We analyze the radius of gyration measurements using the theory of the coil-globule transition of Sanchez [Sanchez, I. C. (1979) Macromolecules 12, 980-988], which balances the excluded volume entropy of the chain with the average interresidue interaction energy. In particular, we calculate the solvation energy of the denatured protein, a property that is not readily accessible in other experiments. The dependence of this energy on denaturant concentration is nonlinear, contrasting with the common linear extrapolation method used to describe denaturation energy. Interestingly, a fit to the binding model of chemical denaturation suggests a single denaturant binding site per protein residue. The size of the denatured protein under native conditions can be extrapolated from the data as well, showing that the fully collapsed state of protein is only approximately 10% larger than the folded state.
| S-EPMC1544205 | biostudies-literature
Project description:Single polymer chains undergo a phase transition from coiled conformations to globular conformations as the effective attraction between monomers becomes strong enough. In this work, we investigated the coil-globule transition of a semiflexible chain confined between two parallel plates, i.e. a slit, using the lattice model and Pruned-enriched Rosenbluth method (PERM) algorithm. We find that as the slit height decreases, the critical attraction for the coil-globule transition changes non-monotonically due to the competition of the confinement free energies of the coiled and globular states. In wide (narrow) slits, the coiled state experiences more (less) confinement free energy, and hence the transition becomes easier (more difficult). In addition, we find that the transition becomes less sharp with the decreasing slit height. Here, the sharpness refers to the sensitivity of thermodynamic quantities when varying the attraction around the critical value. The relevant experiments can be performed for DNA condensation in microfluidic devices.
| S-EPMC4683450 | biostudies-literature
Project description:Random walks (RWs) have been important in statistical physics and can describe the statistical properties of various processes in physical, chemical, and biological systems. In this study, we have proposed a self-interacting random walk model in a continuous three-dimensional space, where the walker and its previous visits interact according to a realistic Lennard-Jones (LJ) potential uLJr=εr0/r12-2r0/r6. It is revealed that the model shows a novel globule-to-helix transition in addition to the well-known coil-to-globule collapse in its trajectory when the temperature decreases. The dependence of the structural transitions on the equilibrium distance r0 of the LJ potential and the temperature T were extensively investigated. The system showed many different structural properties, including globule-coil, helix-globule-coil, and line-coil transitions depending on the equilibrium distance r0 when the temperature T increases from low to high. We also obtained a correlation form of kBTc = λε for the relationship between the transition temperature Tc and the well depth ε, which is consistent with our numerical simulations. The implications of the random walk model on protein folding are also discussed. The present model provides a new way towards understanding the mechanism of helix formation in polymers like proteins.
| S-EPMC10537616 | biostudies-literature
Project description:BackgroundLocalized functional domains within chromosomes, known as topologically associating domains (TADs), have been recently highlighted. In Drosophila, TADs are biochemically defined by epigenetic marks, this suggesting that the 3D arrangement may be the "missing link" between epigenetics and gene activity. Recent observations (Boettiger et al. in Nature 529(7586):418-422, 2016) provide access to structural features of these domains with unprecedented resolution thanks to super-resolution experiments. In particular, they give access to the distribution of the radii of gyration for domains of different linear length and associated with different transcriptional activity states: active, inactive or repressed. Intriguingly, the observed scaling laws lack consistent interpretation in polymer physics.ResultsWe develop a new methodology conceived to extract the best information from such super-resolution data by exploiting the whole distribution of gyration radii, and to place these experimental results on a theoretical framework. We show that the experimental data are compatible with the finite-size behavior of a self-attracting polymer. The same generic polymer model leads to quantitative differences between active, inactive and repressed domains. Active domains behave as pure polymer coils, while inactive and repressed domains both lie at the coil-globule crossover. For the first time, the "color-specificity" of both the persistence length and the mean interaction energy are estimated, leading to important differences between epigenetic states.ConclusionThese results point toward a crucial role of criticality to enhance the system responsivity, resulting in both energy transitions and structural rearrangements. We get strong indications that epigenetically induced changes in nucleosome-nucleosome interaction can cause chromatin to shift between different activity states.
| S-EPMC6515630 | biostudies-literature
Project description:This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) covalently grafted as an "on/off"-switch in triggering interactions with the cancer-cell protein around its lower critical solution temperature. The atomic building blocks of the aptamer and the PNIPAM adsorbed onto the GO was investigated at the density functional theory (DFT) level. The presence of the monomer of PNIPAM stabilised the system's ?-? interaction between GO and its nucleobases as confirmed by higher bandgap energy, satisfying the eigenvalues of the single-point energy observed rather than the nucleobase and the GO complex independently. The unaltered geometrical structures of the surface emphasise the physisorption type interaction between the nucleobase and the GO/NIPAM surface. The docking result for the aptamer and the protein, highlighted the behavior of the PNIPAM-graft-GO is exhibiting globular and extended conformations, further supported by molecular dynamics (MD) simulations. These studies enabled a better understanding of the thermal responsive behavior of the polymer-enhanced GO complex for whole-cell protein interactions through computational methods.
| S-EPMC6536548 | biostudies-literature
Project description:An end-grafted hydrophobic-polar (HP) model protein chain with alternating H and P monomers is studied to examine interactions between the critical adsorption transition due to surface attraction and the collapse transition due to pairwise attractive H-H interactions. We find that the critical adsorption phenomenon can always be observed; however, the critical adsorption temperature T(CAP) is influenced by the attractive H-H interactions in some cases. When the collapse temperature T(c) is lower than T(CAP), the critical adsorption of the HP chain is similar to that of a homopolymer without intrachain attractions and T(CAP) remains unchanged, whereas the collapse transition is suppressed by the adsorption. In contrast, for cases where T(c) is close to or higher than T(CAP), T(CAP) of the HP chain is increased, indicating that a collapsed chain is more easily adsorbed on the surface. The strength of the H-H attraction also influences the statistical size and shape of the polymer, with strong H-H attractions resulting in adsorbed and collapsed chains adopting two-dimensional, circular conformations.
| S-EPMC4280116 | biostudies-other
Project description:Polymers with advanced topological architectures are promising materials for wide applications due to their structure-generated unique properties different from that of the linear analogues. The elegant integration of stimuli-responsive polymers with such advanced architectures can create novel materials with virtues from both moieties, are thus a hot subject of research for both fundamental and practical investigations. To fabricate cyclic brush polymer-based intelligent materials for biomedical applications, herein, we designed and synthesized thermo-sensitive cyclic brush polymers with poly(N-isopropylacrylamide) (PNIPAAm) brushes by controlled living radical polymerization using cyclic multimacroinitiator. The thermo-induced phase transition behaviors of the resultant cyclic brush polymers with different compositions were investigated in detail by temperature-dependent optical transmittance measurements, and compared with the properties of bottlebrush and linear counterparts. Interestingly, the cloud point transition temperature (Tcp) of cyclic brush PNIPAAm could be regulated by the chain length of PNIPAAm brush. Although the bottlebrush polymers with the same composition exhibited similarly structurally dependent Tcps behaviors to the cyclic brush polymers, the cyclic brush PNIPAAm did show higher critical aggregation concentration (CAC) and enhanced stability against dilution than the bottlebrush counterpart. The readily tailorable Tcps together with the ability to form highly stable nanoparticles makes thermo-sensitive cyclic brush PNIPAAm a promising candidate for controlled drug delivery.
| S-EPMC6432030 | biostudies-literature
Project description:Thermoresponsive materials are generating significant interest on account of the sharp and tunable temperature deswelling transition of the polymer chain. Such materials have shown promise in drug delivery devices, sensing systems, and self-assembly. Incorporation of nanoparticles (NPs), typically through covalent attachment of the polymer chains to the NP surface, can add additional functionality and tunability to such hybrid materials. The versatility of these thermoresponsive polymer/nanoparticle materials has been shown previously; however, significant and important differences exist in the published literature between virtually identical materials. Here we use poly(N-isopropylacrylamide) (PNIPAm)-AuNPs as a model system to understand the aggregation behavior of thermoresponsive polymer-coated nanoparticles in pure water, made by either grafting-to or grafting-from methods. We show that, contrary to popular belief, the aggregation of PNIPAm-coated AuNPs, and likely other such materials, relies on the size and concentration of unbound "free" PNIPAm in solution. It is this unbound polymer that also leads to an increase in solution turbidity, a characteristic that is typically used to prove nanoparticle aggregation. The size of PNIPAm used to coat the AuNPs, as well as the concentration of the resultant polymer-AuNP composites, is shown to have little effect on aggregation. Without free PNIPAm, contraction of the polymer corona in response to increasing temperature is observed, instead of nanoparticle aggregation, and is accompanied by no change in solution turbidity or color. We develop an alternative method for removing all traces of excess free polymer and develop an approach for analyzing the aggregation behavior of such materials, which truly allows for heat-triggered aggregation to be studied.
| S-EPMC4838950 | biostudies-literature