Interplay of Coil-Globule Transition and Surface Adsorption of a Lattice HP Protein Model.
Ontology highlight
ABSTRACT:
SUBMITTER: Luo MB
PROVIDER: S-EPMC4280116 | biostudies-other | 2014 Dec
REPOSITORIES: biostudies-other
Similar Datasets
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:We revived and implemented a method developed by Kuhn in 1934, originally only published in German, that is, the so-called "freely jointed chain" model. This approach turned out to be surprisingly useful for analyzing state-of-the-art computer simulations of the thermosensitive coil-globule transition of N-Isopropylacrylamide 20-mer. Our atomistic computer simulations are orders of magnitude longer than those of previous studies and lead to a reliable description of thermodynamics and kinetics at many different temperatures. The freely jointed chain model provides a coordinate system, which allows us to construct a Markov state model of the conformational transitions. Furthermore, this guarantees a reliable reconstruction of the kinetics in back-and-forth directions. In addition, we obtain a description of the high diversity and variability of both conformational states. Thus, we gain a detailed understanding of the coil-globule transition. Surprisingly, conformational entropy turns out to play only a minor role in the thermodynamic balance of the process. Moreover, we show that the radius of gyration is an unexpectedly unsuitable coordinate to comprehend the transition kinetics because it does not capture the high conformational diversity within the different states. Consequently, the approach presented here allows for an exhaustive description and resolution of the conformational ensembles of arbitrary linear polymer chains.
| S-EPMC8154620 | biostudies-literature
Project description:By using extensive all-atom molecular dynamics simulations of an atactic linear polymer chain, we provide microscopic insights into poly(N-isopropylacrylamide) (PNIPAM) coil-to-globule transition addressing the roles played by both temperature and pressure. We detect a coil-to-globule transition up to large pressures, showing a reentrant behavior of the critical temperature with increasing pressure in agreement with experimental observations. Furthermore, again confirming the experimental findings, we report the existence at high pressures of a new kind of globular state. It is characterized by a more structured hydration shell that is closer to PNIPAM hydrophobic domains, as compared to the globular state observed at atmospheric pressure. Our results highlight that temperature and pressure induce a PNIPAM coil-to-globule transition through different molecular mechanisms, opening the way for a systematic use of both thermodynamic variables to tune the location of the transition and the properties of the associated swollen/collapsed states.
| S-EPMC8247264 | biostudies-literature
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:The hydrophobic effect, i.e., the poor solvation of nonpolar parts of molecules, plays a key role in protein folding and more generally for molecular self-assembly and aggregation in aqueous media. The perturbation of the water structure accounts for many aspects of protein hydrophobicity. However, to what extent the dispersion interaction between molecular entities themselves contributes has remained unclear. This is so because in peptide folding interactions and structural changes occur on all length scales and make disentangling various contributions impossible. We address this issue both experimentally and theoretically by looking at the force necessary to peel a mildly hydrophobic single peptide molecule from a flat hydrophobic diamond surface in the presence of water. This setup avoids problems caused by bubble adsorption, cavitation, and slow equilibration that complicate the much-studied geometry with two macroscopic surfaces. Using atomic-force spectroscopy, we determine the mean desorption force of a single spider-silk peptide chain as F = 58 +/- 8 pN, which corresponds to a desorption free energy of approximately 5 k(B)T per amino acid. Our all-atomistic molecular dynamics simulation including explicit water correspondingly yields the desorption force F = 54 +/- 15 pN. This observation demonstrates that standard nonpolarizable force fields used in classical simulations are capable of resolving the fine details of the hydrophobic attraction of peptides. The analysis of the involved energetics shows that water-structure effects and dispersive interactions give contributions of comparable magnitude that largely cancel out. It follows that the correct modeling of peptide hydrophobicity must take the intimate coupling of solvation and dispersive effects into account.
| S-EPMC2268547 | biostudies-literature
Project description:The understanding of the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest in both fundamental research and applications such as nanotechnology. However, despite intense research, the mechanisms and the structural determinants of protein/surface interactions are still unclear. We developed a strategy consisting in identifying, in a mixture of hundreds of soluble proteins, those proteins that are adsorbed on the surface and those that are not. If the two protein subsets are large enough, their statistical comparative analysis must reveal the physicochemical determinants relevant for adsorption versus non-adsorption. This methodology was tested with silica nanoparticles. We found that the adsorbed proteins contain a higher number of charged amino acids, particularly arginine, which is consistent with involvement of this basic amino acid in electrostatic interactions with silica. The analysis also identified a marked bias toward low aromatic amino acid content (phenylalanine, tryptophan, tyrosine and histidine) in adsorbed proteins. Structural analyses and molecular dynamics simulations of proteins from the two groups indicate that non-adsorbed proteins have twice as many π-π interactions and higher structural rigidity. The data are consistent with the notion that adsorption is correlated with the flexibility of the protein and with its ability to spread on the surface. Our findings led us to propose a refined model of protein adsorption.
| S-EPMC3839912 | biostudies-literature