Globule State Research Articles

Molecular dynamics simulations of the folding structure of a thermoresponsive 2-dimethylaminoethyl methacrylate oligomer in the globule state

Molecular dynamics simulations of the folding structure of a thermoresponsive 2-dimethylaminoethyl methacrylate oligomer in the globule state

Switchable Anion Exchange in Polymer-Encapsulated APbX3 Nanocrystals Delivers Stable All-Perovskite White Emitters.

We report a one-step synthesis of halide perovskite nanocrystals embedded in amphiphilic polymer (poly(acrylic acid)-block-poly(styrene), PAA-b-PS) micelles, based on injecting a dimethylformamide solution of PAA-b-PS, PbBr2, ABr (A = Cs, formamidinium, or both) and “additive” molecules in toluene. These bifunctional or trifunctional short chain organic molecules improve the nanocrystal–polymer compatibility, increasing the nanocrystal stability against polar solvents and high flux irradiation (the nanocrystals retain almost 80% of their photoluminescence after 1 h of 3.2 w/cm2 irradiation). If the nanocrystals are suspended in toluene, the coil state of the polymer allows the nanocrystals to undergo halide exchange, enabling emission color tunability. If the nanocrystals are suspended in methanol, or dried as powders, the polymer is in the globule state, and they are inert to halide exchange. By mixing three primary colors we could prepare stable, multicolor emissive samples (for example, white emitting powders) and a UV-to-white color converting layer for light-emitting diodes entirely made of perovskite nanocrystals.

Molecular understanding of the LCST phase behaviour of P(MEO2MA-b-OEGMA) block copolymers

ABSTRACT The lower critical solution temperature (LCST) behaviour of block copolymer 2-(2-methoxyethoxy) ethyl methacrylate and oligo (ethylene glycol) methacrylate (P(MEO2MA-b-OEGMA)) was studied by molecular dynamics simulations. Our simulations show that the LCST of P(MEO2MA-b-OEGMA) is linear to its OEGMA block ratio, which is agreed with our previous experimental observations. Meanwhile, the mechanism of the LCST phase behaviour was also revealed by our simulations. The hydrophilic effect of copolymer and the entropy effect of water are the main factors of affecting the aggregate behaviours of copolymers and further affect their LCSTs. The hydrophilic effect is dominant and these water molecules are apt to gather around the copolymers and the copolymers exist in a coil state when the temperature is relatively lower. However, the entropy effect of water prevails and the copolymers tend to in a globule state when the temperature is higher. The coil-to-globule transition occurs when the temperature reaches a certain degree, namely LCST, at which the competition between the hydrophilic effect of copolymer and entropy effect of water reaches a balance.

Aggregation of poly(N-isopropylacrylamide) homopolymer by Cu2+ and Zn2+: Significance for ratiometric metal ion indicators

Aqueous transition metal dications Cu2+ and Zn2+ bind to the amide groups of the responsive polymer poly(N-isopropylacrylamide) (PNIPAm). Ratiometric detection by the response of PNIPAm is based on the effect of metal ion binding to ligands that are copolymerized into PNIPAm. Metal ions bound to copolymerized ligands cause a polarity change that shifts the ratio of coil and globule polymer phases, whereby the coil:globule state is monitored by the FRET process of a pair of fluorophores distributed throughout the polymer. This work shows that aqueous Cu2+ or Zn2+ ([M2+] = 2.5 × 10−2 M to 2.5 × 10−4 M) cause aggregation of the PNIPAm homopolymer (Mn = 8400 and 10,300) in the globule phase above 32 °C, as determined by second-order and dynamic light-scattering. Conditional formation constants (pH 6.3) for Cu2+ binding PNIPAm were measured as log Kc = 2.64 ± 0.07 and 4.02 ± 0.05 for PNIPAm concentrations of 1 mg/mL and 0.05 mg/mL, respectively. The interaction of Cu2+ and Zn2+ with PNIPAm is therefore in competition with the copolymerized ligands and when detecting millimolar to high micromolar concentrations, this interaction poses a potential interference to metal ion detection. Several aggregation processes are implicated based on Cu2+ or Zn2+ from 8 × 10−5 to 2.5 × 10−2 M. These processes are fully reversible by reducing the sample temperature.

Comparison based on statistical thermodynamics between globule-to-coil transition of poly(N-isopropylacrylamide) and cold denaturation of a protein

When the temperature T becomes sufficiently low, poly(N-isopropylacrylamide) (PNIPAM) and a protein, respectively, cause the globule-to-coil transition and the cold denaturation (i.e., transitions to states comprising more extended structures). It is experimentally known for PNIPAM that the coil state is soluble in water but the globule state is insoluble. By contrast, both of the cold-denatured and native states of a protein are soluble. Using our recently developed statistical-mechanical theory combined with molecular models for water, we show that the two structural transitions share physically the same mechanism but still the difference between PNIPAM and a protein in terms of the solubilities of the two states can be reproduced. The solute hydration can be decomposed into the two processes: the creation of a cavity matching the solute structure at the atomic level in water (process 1: hydrophobic hydration); and the incorporation of solute–water van der Waals interaction potential followed by that of solute–water electrostatic interaction potential (process 2). The hydration free energies, energies, and entropies in processes 1 and 2 are denoted by μH,1 > 0 and μH,2 < 0, εVH,1 < 0 and εVH,2 < 0, and SVH,1 < 0 and SVH,2 < 0, respectively. We find that the excluded-volume (EV) terms in εVH,1 and SVH,1 are strongly dependent on T, whereas not only the sum of the water-accessible surface terms in εVH,1 and SVH,1 but also εVH,2 and SVH,2 remain essentially constant against a change in T. The EV term of SVH,1 becomes significantly smaller at low T, which is interpretable as the weakening of the hydrophobic effect and the trigger of the two structural transitions. The changes in structure and properties of water near PNIPAM or a protein upon the transition to a state comprising more extended structures are unimportant. Though μH,1 is a largely increasing function of T, |μH,2| is only very weakly dependent on T. μH,1/|μH,2| for PNIPAM is much larger than that for a protein, which is attributable to the lower electrostatic affinity of PNIPAM for water. As a consequence, μH(Coil) < 0 at low T but μH(Globule) ≫ 0 at high T for PNIPAM but μH(Denatured) ≪ 0 at low T and μH(Native) ≪ 0 at high T for a protein (μH = μH,1 + μH,2).

Mechanism of globule-to-coil transition of poly(N-isopropylacrylamide) in water: Relevance to cold denaturation of a protein

In water, poly(N-isopropylacrylamide) (PNIPAM) is in a soluble coil state below the lower critical soluble temperature (LCST) but in an insoluble globule state above LCST. Namely, as the temperature decreases, PNIPAM exhibits a globule-to-coil transition at LCST~305 K. We generate structural ensembles of coil and globule states by all-atom molecular dynamics simulations conducted at 273 and 323 K, respectively. We then calculate a variety of energetic and entropic components of thermodynamic quantities of the two states at the two temperatures using our recently developed, accurate statistical-mechanical method for solute hydration where molecular models are employed for water and the PNIPAM structure is taken into account at the atomic level. We identify the physical factors driving or opposing the transition and evaluate their relative magnitudes and temperature dependences. The presence of PNIPAM generates an excluded volume (EV) which is inaccessible to the centers of water molecules in the entire system. The presence of a water molecule also generates an EV for the other water molecules with the result that all of the water molecules are entropically correlated, causing water crowding. The globule state, where the EV is smaller and water crowding is less significant, is more favored in terms of the translational, configurational entropy of water. This effect always opposes the globule-to-coil transition. At low temperatures, however, this effect becomes significantly weaker, yielding to the factors driving it. The mechanism of the transition is physically the same as that of cold denaturation of a protein.

An insight into the biophysical characterization of different states of cefotaxime hydrolyzing β-lactamase 15 (CTX-M-15)

Cefotaxime hydrolyzing β-lactamase-15 (CTX-M-15) is encoded by blaCTX-M-15 gene present on plasmid of various Gram-negative bacteria, such as E. coli, E. cloacae, K. pneumoniae, etc. The widespread dissemination of CTX-M-15 harboring bacteria in hospital as well as community settings is a universal threat as they are resistant to various clinically significant antibiotics. In order to gain an insight into the folding mechanism of CTX-M-15, we carried out pH-induced denaturation study by monitoring Trp fluorescence, far-UV circular dichroism (CD), and ANS fluorescence. We found that the pH-induced denaturation of CTX-M-15 was a three-step process with the accumulation of two stable folding intermediates (XI at pH 2.5 and XII at pH 1.5) in the folding pathway. The intermediates were further characterized by far-UV and near-UV CD analysis, Trp fluorescence, ANS fluorescence, three-dimensional fluorescence, acrylamide quenching, dynamic light scattering, and thermal denaturation studies. We found that XI state lacked tertiary structure but retained most of the secondary structure, its Trp residues were partially exposed to the solvent and its hydrophobic patches were highly accessible to ANS. On the other hand, a complete disruption of tertiary structure along with more than 50% loss in secondary structure was observed in XII state. We conclude that the XI state of CTX-M-15 at pH 2.5 had all the characteristics of a molten globule (MG) state, while its XII state at pH 1.5 was more similar to pre-molten globule (PMG) state. ANS fluorescence also showed that the binding of ANS in XII state was lower than that in the XI state. We propose that the accumulation of MG- and PMG-states was due to separation (at pH 2.5) and then unfolding (at pH 1.5) of the αβα-fold of CTX-M-15, respectively.

Conformational transition of H-shaped branched polymers

We report dynamic Monte Carlo simulation on conformational transition of H-shaped branched polymers by varying main chain (backbone) and side chain (branch) length. H-shaped polymers in comparison with equivalent linear polymers exhibit a depression of theta temperature accompanying with smaller chain dimensions. We observed that the effect of branches on backbone dimension is more pronounced than the reverse, and is attributed to the conformational heterogeneity prevails within the molecule. With an increase in branch length, backbone is slightly stretched out in the coil and globule state. However, in the pre-collapsed (cf. crumpled globule) state, backbone size decreases with the increase of branch length. We attribute this non-monotonic behavior as the interplay between excluded volume interaction and intra-chain bead-bead attractive interaction during collapse transition. Structural analysis reveals that the inherent conformational heterogeneity promotes the formation of a collapsed structure with segregated backbone and branch units (resembles to "sandwich" or "Janus" morphology) rather an evenly distributed structure consisting of all the units. The shape of the collapsed globule becomes more spherical with increasing either backbone or branch length.

Meso-scale Simulations of Poly(N-isopropylacrylamide) Grafted Architectures

ABSTRACTPoly(N-isopropylacrylamide) (PNIPAM) is a thermosensitive polymer that is well-known for its behavior at a lower critical solution temperature (LCST) around 305 K. Below the LCST, PNIPAM is soluble in water, and above this temperature, polymer chains collapse and transform into a globule state. The conformational dynamics of single chains of polymer in a solution is known to be different from those of grafted structures that comprise of an ensemble of such single chains. In this study, we have carried out MD simulations of a mesoscopic nanostructure of PNIPAM polymer chains consisting of 60 monomer units grafted onto gold nanoparticles of different diameters, to study the effect of temperature and core particle size on the polymer conformations. Additionally, we have also studied the effect of grafting density on the coil-to-globule transition exhibited by PNIPAM through the LCST. The systems investigated consisted of ∼3 and ∼6 million atoms. Simulations were carried out below and above the LCST of PNIPAM, at 275K and 325K. Simulation trajectories were analyzed for radius of gyration of PNIPAM chains.

Guanidine hydrochloride-induced alkali molten globule model of horse ferrocytochrome c

This article compares structural, kinetic and thermodynamic properties of previously unknown guanidine hydrochloride (GdnHCl)-induced alkali molten globule (MG) state of horse 'ferrocytochrome c' (ferrocyt c) with the known NaCl-induced alkali-MG state of ferrocyt c. It is well known that Cl(-) arising from GdnHCl refolds and stabilizes the acid-denatured protein to MG state. We demonstrate that the GdnH(+) arising from GdnHCl (≤0.2 M) also transforms the base-denatured CO-liganded ferrocyt c (carbonmonoxycyt c) to MG state by making the electrostatic interactions to the negative charges of the protein. Structural and molecular properties extracted from the basic spectroscopic (circular dichroism (CD), fluorescence, FTIR and NMR) experiments suggest that the GdnH(+)- and Na(+)-induced MG states of base-denatured carbonmonoxycyt c are molecular compact states containing native-like secondary structures and disordered tertiary structures. Kinetic experiments involving the measurement of the CO association to the alkaline ferrocyt c in the presence of different GdnHCl and NaCl concentrations indicate that the Na(+)-induced MG state is more constrained relative to that of GdnH(+)-induced MG state. Analyses of thermal (near UV-CD) denaturation curves of the base-denatured protein in the presence of different GdnHCl and NaCl concentration also indicate that the Na(+)-induced MG state is thermally more stable than the GdnH(+)-induced MG state.

Hydrodynamic Selection of the Kinetic Pathway of a Polymer Coil-Globule Transition

Recently, the role of hydrodynamic interactions in the selection of a kinetic pathway for phase transitions has attracted considerable attention. Here we study this problem numerically by taking as an example a coil-globule transition of a single polymer, which is a prototype model of protein folding. When a swollen polymer collapses into a globule state, hydrodynamic interactions accelerate the transition. We find, on the other hand, that when a rather compact polymer collapses into the same final state, hydrodynamic interactions decelerate the transition due to a slow squeezing process of the solvent. We reveal that the degree of the initial enhancement of anisotropy of the polymer configuration determines whether hydrodynamic interactions accelerate or decelerate the collapsing dynamics. We also discuss the possible relevance of squeezing flow effects in protein folding.

Reversibility and “pH– T phase diagrams” of Rapana venosa hemocyanin and its structural subunits

We have studied the stability and reassociation behaviour of native molecules of Rapana venosa hemocyanin and its two subunits, termed RvH1 and RvH2. In the presence of different concentrations of Ca 2+ and Mg 2+ ions and pH values, the subunits differ not only in their reassociation behaviour, but also in their formation of helical tubules and multidecamers. RvH1 revealed a greater stability at higher pH values compared to RvH2. Overall, the stability of reassociated RvH and its structural subunits was found to be pH-dependent. The increasing stability of native Hc and its subunits, shown by pH-induced CD transitions (acid and alkaline denaturation), can be explained with the formation of quaternary structure. The absence of a Cotton effect at temperatures 20–40 °C in the pH-transition curves of RvH2 indicates that this subunit is stabilized by additional “factors”, e.g.: non-ionic/hydrophobic stabilization and interactions of carbohydrate moieties. A similar behaviour was observed for the T-transition curves in a wide pH interval for RvH and its structural subunits. At higher temperatures, many of the secondary structural elements are preserved especially at neutral pH, even at extreme high temperatures above 90 °C the protein structures resemble a “globule state”.

Organic Solvent and Acid Induced Conformational Modification of Model Peptide : Lysozyme

The conformational modification of model peptide (lysozyme), which was solubilized in various concentrations of aqueous-ethanolic solutions (0-99% v/v), were characterized by circular dichroism and fluorometry. It was found that at 80% v/v ethanol, lysozyme changed its conformation to molten globule (MG) state. After HCl was introduced to achieve a solution of pH~2, only 35% v/v ethanol was required in order to initiate MG state. However, MG state was not generated when acidic solution was used alone without ethanol. This conformational change from native state to MG state was found to be reversible by simple aqueous dilution.

Discontinuous molecular dynamics simulation study of polymer collapse

Discontinuous molecular dynamics simulations were used to study the coil-globule transition of a polymer in an explicit solvent. Two different versions of the model were employed, which are differentiated by the nature of monomer-solvent, solvent-solvent, and nonbonded monomer-monomer interactions. For each case, a model parameter lambda determines the degree of hydrophobicity of the monomers by controlling the degree of energy mismatch between the monomers and solvent particles. We consider a lambda-driven coil-globule transition at constant temperature. The simulations are used to calculate average static structure factors, which are then used to determine the scaling exponents of the system in order to determine the theta-point values lambda(theta) separating the coil from the globule state. For each model we construct coil-globule phase diagrams in terms of lambda and the particle density rho. Additionally, we explore for each model the effects of varying the range of the attractive interactions on the phase boundary separating the coil and globule phases. The results are analyzed in terms of a simple Flory-type theory of the collapse transition.

Simulation of protein misfolding using a lattice model

Misfolding during protein self-assembly is the cause of numerous human and animal diseases. Understanding of the mechanism that underlies the protein folding into a normal or abnormal form can enhance the search for pathogen inhibitors and drug design. We used Monte Carlo dynamics to study the folding of a 27-membered heteropolymer on a cubic lattice. This lattice protein had a stable compact (“latent”) state that competed with the native state. It appeared that the free-energy surface of the system studied consisted of three basins, which corresponded to the semicompact globule, latent, and native states. We determined the bifurcation regions in the protein kinetic trajectories where the protein took a native or a latent structure and the probabilities of these structures to be formed. The effects of mutations on the probability of native state and the rate of its formation were modeled.

Salt-Controlled Intrachain/Interchain Segregation in DNA Complexed with Polycation of Natural Origin

A coil−globule transition in individual double-stranded DNA triggered by chitosan polycations was directly observed by fluorescence microscopy. It was shown that the character of the conformational transition depends essentially on the amount of added low-molecular-weight salt. At low salt content the collapse proceeds via the formation of an intermediate necklace structure, which is stabilized by Coulomb repulsion between uncompensated charges of DNA chains. By contrast, at high salt content, when the electrostatic repulsion is sufficiently screened, the collapse proceeds directly between coil and globule states without intermediate structures. Also, salt affects the collapsed state of chitosan/DNA complexes: it decreases the size of single globules and favors the interglobular aggregation.

Simulation study of the coil-globule transition of a polymer in solvent

Molecular dynamics simulations are used to study the coil-globule transition for a system composed of a bead-spring polymer immersed in an explicitly modeled solvent. Two different versions of the model are used, which are differentiated by the nature of monomer-solvent, solvent-solvent, and nonbonded monomer-monomer interactions. For each case, a model parameter lambda determines the degree of hydrophobicity of the monomers by controlling the degree of energy mismatch between the monomers and solvent particles. We consider a lambda-driven coil-globule transition at constant temperature. The simulations are used to calculate average static structure factors, which are then used to determine the scaling exponents of the system in order to determine the theta-point values lambdatheta separating the coil from the globule states. For each model we construct coil-globule phase diagrams in terms of lambda and the particle density rho. The results are analyzed in terms of a simple Flory-type theory of the collapse transition. The ratio of lambdatheta for the two models converges in the high density limit exactly to the value predicted by the theory in the random mixing approximation. Generally, the predicted values of lambdatheta are in reasonable agreement with the measured values at high rho, though the accuracy improves if the average chain size is calculated using the full probability distribution associated with the polymer-solvent free energy, rather than merely using the value obtained from the minimum of the free energy.

Slow Expansion of a Single Polymer Chain from the Knotted Globule

Knot formation in a single polymer chain was studied by measuring chain expansion processes from a globule to a coil state. Dilute solutions of poly(methyl methacrylate) in the mixed solvent tert-butyl alcohol + water(2.5 vol %) were preserved in a globule state at 25.0 °C for a time period tp and given a fast temperature jump to the θ temperature 41.5 °C to measure the chain expansion process by static light scattering. The chain expansion occurred slower with increasing tp for the molecular weight Mw = 1.22 × 107. For the constant time period tp = 7200 min, the expansion process became slower with increasing Mw from 4 × 106 to 1.5 × 107. These observations disclose the knot formation in a single polymer chain.

KINETIC ANALYSIS OF PROTEIN FOLDING LATTICE MODELS

Based on two-dimensional square lattice models of proteins, the relation between folding time and temperature is studied by Monte Carlo simulation. The results can be represented by a kinetic model with three states — random coil, molten globule, and native state. The folding process is composed of nonspecific collapse and final searching for the native state. At high temperature, it is easy to escape from local traps in the folding process. With decreasing temperature, because of the trapping in local traps, the final searching speed decreases. Then the folding shows chevron rollover. Through the analysis of the fitted parameters of the kinetic model, it is found that the main difference between the energy landscapes of the HP model and the Go model is that the number of local minima of the Go model is less than that of the HP model.

The application of fluorescence correlation spectroscopy in detecting DNA condensation

We report the application of fluorescence correlation spectroscopy (FCS) in characterizing conformational changes (condensation) of chemically well-defined DNA plasmids. The plasmids: pHβAPr-1-neo (10 kbp, contour length 3.4 μm) and pBluescript SKt (2.96 kbp, contour length 1.02 μm) were imaged by a confocal fluorescence microscope using two fluorescent probes: ethidium bromide (EtBr) and propidium iodide (PrIo). It became clear that the DNA molecule exhibits discrete conformational change between the coil and globule states with the addition of a small amount (the order of magnitude being 10 −5 M) of cationic surfactant, spermine and hexadecyltrimethyl ammonium bromide (HTAB). When the concentrations of both condensing agents are smaller than 6.0×10 −6 M and 2.0×10 −6 M for the 10 and 2.96 kbp, both plasmids are in the extended coil state with diffusion constants D 10 kbp=9.6×10 −13 m 2 s −1 and D 2.96 kbp=2.5×10 −12 m 2 s −1, respectively. When the condensing agent in a concentration higher than 1.10×10 −5 M is added to pHβAPr-1-neo (10 kbp), plasmids are in the condensed globular state and their diffusion constants are D 10 kbp=8.0×10 −12 m 2 s −1 (spermine) and D 10 kbp=5.5×10 −12 m 2 s −1 (HTAB). The globular state of the pBluescript SKt (2.96 kbp) plasmids is characterized by diffusion constants equal to D 2.96 kbp=9.2×10 −12 m 2 s −1 (spermine) and D 2.96 kbp=8.2×10 −12 m 2 s −1 (HTAB).