Random Coil State Research Articles

The human eIF4E:4E-BP2 complex structure for studying hyperphosphorylation.

The cap-dependent mRNA translation is dysregulated in many kinds of cancers. The interaction between eIF4E and eIF4G through a canonical eIF4E-binding motif (CEBM) determines the efficacy of the cap-dependent mRNA translation. eIF4E-binding proteins (4E-BPs) share the CEBM and compete with eIF4G for the same binding surface of eIF4E and then inhibit the mRNA translation. 4E-BPs function as tumor repressors in nature. Hyperphosphorylation of 4E-BPs regulates the structure folding and causes the dissociation of 4E-BPs from eIF4E. However, until now, there has been no structure of the full-length 4E-BPs in complex with eIF4E. The regulation mechanism of phosphorylation is still unclear. In this work, we first investigate the interactions of human eIF4E with the CEBM and an auxiliary eIF4E-binding motif (AEBM) in eIF4G and 4E-BPs. The results unravel that the structure and interactions of the CEBM are highly conserved between eIF4G and 4E-BPs. However, the extended CEBM (ECEBM) in 4E-BPs forms a longer helix than that in eIF4G. The residue R62 in the ECEBM of 4E-BP2 forms salt bridges with E32 and E70 of eIF4E. The residue R63 of 4E-BP2 forms two special hydrogen bonds with N77 of eIF4E. Both of these interactions are missing in eIF4G. The AEBM of 4E-BPs folds into a β-sheet conformation, which protects V81 inside a hydrophobic core in 4E-BP2. In eIF4G, the AEBM exists in a random coil state. The hydrophilic residues S637 and D638 of eIF4G open the hydrophobic core for solvents. The results show that the ECEBM and AEBM may be responsible for the competing advantage of 4E-BP2. Finally, based on our previous work (J. Zeng, F. Jiang and Y. D. Wu, J. Chem. Theory Comput., 2017, 13, 320), the human eIF4E:4E-BP2 complex (eIF4E:BP2P18-I88) including all reported phosphorylation sites is predicted. The eIF4E:BP2P18-I88 complex is different from the existing experimental eIF4E:eIF4G complex and provides an important structure for further studying the regulation mechanism of phosphorylation in 4E-BPs.

An In Silico Comparative Study of Eleven Wasp Venom Allergens: An Arena for Therapeutic Approach

Peptide toxins in animals as part of the chemical arsenal for predation and/or protection, and they can also safeguard the host from pathogenic infections. Insects including the hymenopterans generate a battery of toxic bactericidal or bacteriostatic molecules which are small multifunctional, linear peptides that cause pain, have antimicrobial effects, and inflammatory processes . The toxins under the experiment are active against gram-positive, gram-negative bacteria and fungi. The present in silico study aims to predict the physicochemical attributes like molecular weight, theoretical pI, amino acid composition, extinction co-efficient, estimated half-life, instability index, aliphatic index and grand average of hydropathy (gravy) of wasps’ (class: Insecta; order: Hymenoptera) 11 wasp venom allergens through Expasy Protparam & Pepstat software tools. The secondary structures of the toxins were predicted using psi-Blast-based secondary structure prediction GOR4 tools revealing the % α helix, extended β strand, random coil and ambiguous state reflecting a comparative picture of physicochemical parameters of these defensins. 3D Homology modelling of these toxins was accomplished through Swiss-model webserver tool and validated through various in silico tools like ANOLEA, ProSA-web, QMean4 determining Z score, PROCHEK establishing the 3D models of these toxins. Use of Inter Pro, CDD, PROSITE, P fam, Tox DL, PrDOS software predicted the protein family, protein toxicity, protein disorder respectively. Scratch Protein Predictor software tools predicted cysteine – cysteine bonds. Docking of the eleven (11) wasp venom allergens individually with bacterial cell wall component N-acetylglucosamine was done by CB DOCK webserver resulting negative affinity scores reflecting towards the strong binding between the mentioned 11 toxins and N-acetylglucosamine indicating that the mentioned wasps’ toxin molecules might be used as potential antibacterial therapeutic molecules binding to N-acetylglucosamine leading to an avenue to the probable bacterial drug discovery.

Application Of Wasps’ Defensins As Anti-Fungal Therapeutic Molecules: An In Silico Comparative Study

Animal peptide toxins as part of chemical arsenal for predation and/or protection that can safeguard host from pathogenic infections. Hymenopterans generate toxic bactericidal or bacteriostatic molecules, called defensins are small multifunctional, linear, polycationic peptides causing pain, have antimicrobial effects. Defensins are active against gram-positive, gram-negative bacteria and fungi. The present in silico study aims to predict the physicochemical attributes like molecular weight, theoretical pI, amino acid composition, extinction co-efficient, estimated half-life, instability index, aliphatic index and grand average of hydropathy (gravy) of 09 different wasps’ defensins using Expasy Protparam tool. The secondary structures of the toxins were predicted using psi-Blast-based PSIPRED, SOPMA tools revealing % α helix, extended β strand, random coil and ambiguous state reflecting a comparative physico-chemical parameters of these defensins. 3D Homology modelling of these toxins was accomplished through Swiss-model webserver and validated through ProSA-web, QMean4 determining Z score,PROCHEK establishing the 3D models of these defensins. Use of InterPro, CDD, ToxDL, PrDOS software predicted protein family, conserved domain, protein toxicity, protein disorder respectively. CYSCON and CYSPRED tools predicted cysteine-cysteine bonds. Docking of the nine (09) wasps’ defensins individually with fungal cellwall component 1,4 Beta-D-Glucan was done by DockThor webserver resulting negative affinity scores refleting strong binding between the defensins and 1,4 beta-D-Glucan indicating that the mentioned wasps’ defensin molecules might be used as potential antifungal therapeutic molecules binding to 1, 4 Beta-D-Glucan indicating an avenue to antifungal drug discovery.

Conformational and Structural Changes in Chickpea Proteins Caused by Simulated Salivary Alterations in the Elderly.

The impact of salivary alterations on chickpea protein structure in the elderly has not been well documented. This study aimed to understand the role of simulated salivary alterations in the conformational properties and secondary structure of the chickpea protein isolate (CPI). Whey protein isolate (WPI) was used as the reference. Protein dispersions (10%) were subjected to in vitro oral processing under simulated salivary conditions in both the elderly and adult subjects. Proteins and their oral counterparts were characterized in terms of their composition, charge, size, solubility, water absorption, molecular weight (MW), and secondary structure (Circular Dichroism and Raman spectroscopy). Under condition of simulated oral digestion in the elderly population, the ordered secondary protein structure was significantly affected, decreasing α-helix by ~36% and ~29% in CPI and WPI compared to the control (adult) population, respectively. An increase in the unordered random coil state was observed. These results could be attributed to an increase in electrolytes in the salivary composition. The structure of CPI is more stable than that of WPI because of its higher MW, more rigid structure, less charged surface, and different amino acid compositions. This study is meaningful in understanding how alterations in the elderly oral system affect protein conformation and is expected to improve the understanding of plant-based protein digestibility.

Characterization of pH-induced conformational changes in recombinant DENV NS2B-NS3pro

The increasing frequency of Dengue is a cause of severe epidemics and therefore demands strategies for effective prevention, diagnosis, and treatment. DENV-protease is being investigated as a potential therapeutic target. However, due to the flat and highly charged active site of the DENV-protease, designing orthosteric medicines is very difficult. In this study, we have done a thorough analysis of pH-dependent conformational changes in recombinantly expressed DENV protease using various spectroscopic techniques. Our spectroscopic study of DENV protease (NS2B-NS3pro) at different pH conditions gives important insights into the dynamicity of structural conformation. At physiological pH, the DENV-protease exists in a random-coiled state. Lowering the pH promotes the formation of alpha-helical and beta-sheet structures i.e. gain of secondary structure as shown by Far-UV CD. The light scattering and Thioflavin T (ThT)-binding assay proved the aggregation-prone tendency of DENV-protease at pH 4.0. Further, the confocal microscopy image intensity showed the amorphous aggregate formation of DENV protease at pH 4.0. Thus, the DENV protease acquires different conformations with changes in pH conditions. Together, these results have the potential to facilitate the design of a conformation destabilizer-based therapeutic strategy for dengue fever.

Hydrophobic Homopolymer's Coil-Globule Transition and Adsorption onto a Hydrophobic Surface under Different Conditions.

Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we use Monte Carlo calculations of a coarse-grained model incorporating water's effects on the system's free energy. Following previous studies, we modeled an unstructured protein as a polymer chain. Because we are interested in investigating how it responds to thermodynamic changes near a hydrophobic surface under different conditions, we chose an entirely hydrophobic sequence to maximize the interaction with the interface. We show that a slit pore confinement without top-down symmetry enhances the unfolding and adsorption of the chain in both random coil and globular states. Moreover, we demonstrate that the hydration water modulates this behavior depending on the thermodynamic parameters. Our findings provide insights into how homopolymers and possibly unstructured proteins can sense and adjust to external stimuli such as nanointerfaces or stresses.

Chemical Shifts of Artificial Monomers Used to Construct Heterogeneous-Backbone Protein Mimetics in Random Coil and Folded States.

The construction of protein-sized synthetic chains that blend natural amino acids with artificial monomers to create so-called heterogeneous-backbones is a powerful approach to generate complex folds and functions from bio-inspired agents. A variety of techniques from structural biology commonly used to study natural proteins have been adapted to investigate folding in these entities. In NMR characterization of proteins, proton chemical shift is a straightforward to acquire, information-rich metric that bears directly on a variety of properties related to folding. Leveraging chemical shift to gain insight into folding requires a set of reference chemical shift values corresponding to each building block type (i.e., the 20 canonical amino acids in the case of natural proteins) in a random coil state and knowledge of systematic changes in chemical shift associated with particular folded conformations. Although well documented for natural proteins, these issues remain unexplored in the context of protein mimetics. Here, we report random coil chemical shift values for a library of artificial amino acid monomers frequently used to construct heterogeneous-backbone protein analogues as well as a spectroscopic signature associated with one monomer class, β3-residues bearing proteinogenic side chains, adopting a helical folded conformation. Collectively, these results will facilitate the continued utilization of NMR for the study of structure and dynamics in protein-like artificial backbones.

The Pressure Dependence of the Stability of the G-quadruplex Formed by d(TGGGGT).

The G-quadruplex (GQ), a tetrahelix formed by guanine-rich nucleic acid sequences, is a potential drug target for several diseases. Monomolecular GQs are stabilized by guanine tetrads and non-guanine regions that form loops. Hydrostatic pressure destabilizes the folded, monomolecular GQ structures. In this communication, we present data on the effect of pressure on the conformational stability of the tetramolecular GQ, d[5′-TGGGGT-3′]4. This molecule does not have loops linking the tetrads; thus, its physical properties presumably reflect those of the tetrads alone. Understanding the properties of the tetrads will aid in understanding the contribution of the other structural components to the stability of GQ DNA. By measuring UV light absorption, we have studied the effect of hydrostatic pressure on the thermal stability of the tetramolecular d[5′-TGGGGT-3′]4 in the presence of sodium ions. Our data show that, unlike monomolecular GQ, the temperature at which d[5′-TGGGGT-3′]4 dissociates to form the constituent monomers is nearly independent of pressure up to 200 MPa. This implies that there is no net molar volume difference (∆V) between the GQ and the unfolded random-coil states. This finding further suggests that the large negative ∆V values for the unfolding of monomolecular GQ are due to the presence of the loop regions in those structures.

Salt effects on knot dynamics in polyelectrolyte solutions

ABSTRACT We study the dynamics of linear polyelectrolyte (PE) knot in solution with doping salt by molecular dynamics simulations. The molecular mechanisms of PE knot dynamics are explained. The knot dynamics are the coupling results by the moving effect of chain entanglement and by the breathing effect of knot fluctuations. The moving effect is important as the whole chain is in the random coil state and becomes weak as shrinking to the close-to-globule (CTG) state. Interestingly, as the chain in the CTG state, the knot swells with occupying more segments. The breathing effect dominates the knot dynamics in the CTG state. This nontrivial behaviour (in comparison to neutral polymer knot) is prominent for the cases of doping salt with high concentration or of doping high-valent salt, which attributes to the enhanced electrostatic interactions and long-range fluctuation effects.

Characterization of Weak Protein Domain Structure by Spin-Label Distance Distributions.

Function of intrinsically disordered proteins may depend on deviation of their conformational ensemble from that of a random coil. Such deviation may be hard to characterize and quantify, if it is weak. We explored the potential of distance distributions between spin labels, as they can be measured by electron paramagnetic resonance techniques, for aiding such characterization. On the example of the intrinsically disordered N-terminal domain 1–267 of fused in sarcoma (FUS) we examined what such distance distributions can and cannot reveal on the random-coil reference state. On the example of the glycine-rich domain 188–320 of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) we studied whether deviation from a random-coil ensemble can be robustly detected with 19 distance distribution restraints. We discuss limitations imposed by ill-posedness of the conversion of primary data to distance distributions and propose overlap of distance distributions as a fit criterion that can tackle this problem. For testing consistency and size sufficiency of the restraint set, we propose jack-knife resampling. At current desktop computers, our approach is expected to be viable for domains up to 150 residues and for between 10 and 50 distance distribution restraints.

Thermal inactivation scaling applied for SARS-CoV-2

Based on a model of protein denaturation rate limited by an entropy-related barrier, we derive a simple formula for virus inactivation time as a function of temperature. Loss of protein structure is described by two reaction coordinates: conformational disorder of the polymer and wetting by the solvent. These establish a competition between conformational entropy and hydrophobic interaction favoring random coil or globular states, respectively. Based on the Landau theory of phase transition, the resulting free energy barrier is found to decrease linearly with the temperature difference T − Tm, and the inactivation rate should scale as U to the power of T − Tm. This form recalls an accepted model of thermal damage to cells in hyperthermia. For SARS-CoV-2 the value of U in Celsius units is found to be 1.32. Although the fitting of the model to measured data is practically indistinguishable from Arrhenius law with an activation energy, the entropy barrier mechanism is more suitable and could explain the pronounced sensitivity of SARS-CoV-2 to thermal damage. Accordingly, we predict the efficacy of mild fever over a period of ∼24 h in inactivating the virus.

Helix-Coil Transition at a Glycine Following a Nascent α-Helix: A Synergetic Guidance Mechanism for Helix Growth.

A detailed understanding of forces guiding the rapid folding of a polypeptide from an apparently random coil state to an ordered α-helical structure following the rate-limiting preorganization of the initial three residue backbones into helical conformation is imperative to comprehending and regulating protein folding and for the rational design of biological mimetics. However, several details of this process are still unknown. First, although the helix-coil transition was proposed to originate at the residue level (J. Chem. Phys. 1959, 31, 526-535; J. Chem. Phys. 1961, 34, 1963-1974), all helix-folding studies have only established it between time-averaged bulk states of a long-lived helix and several transiently populated random coils, along the whole helix model sequence. Second, the predominant thermodynamic forces driving either this two-state transition or the faster helix growth following helix nucleation are still unclear. Third, the conformational space of the random coil state is not well-defined unlike its corresponding α-helix. Here we investigate the restrictions placed on the conformational space of a Gly residue backbone, as a result of it immediately succeeding a nascent α-helical turn. Analyses of the temperature-dependent 1D-, 2D-NMR, FT-IR, and CD spectra and GROMACS MD simulation trajectory of a Gly residue backbone following a model α-helical turn, which is artificially rigidified by a covalent hydrogen bond surrogate, reveal that: (i) the α-helical turn guides the ϕ torsion of the Gly exclusively into either a predominantly populated entropically favored α-helical (α-ϕ) state or a scarcely populated random coil (RC-ϕ) state; (ii) the α-ϕ state of Gly in turn favors the stability of the preceding α-helical turn, while the RC-ϕ state disrupts it, revealing an entropy-driven synergetic guidance for helix growth in the residue following helix nucleation. The applicability of a current synergetic guidance mechanism to explain rapid helix growth in folded and unfolded states of proteins and helical peptides is discussed.

Formation of Higher Structural Levels in λ-Carrageenan Induced by the Antimalarial Drug Chloroquine.

The linear polysaccharide λ-carrageenan is the only one among the carrageenans not forming secondary, tertiary, and quaternary structures in the presence of inorganic ions. Chloroquine (CQ) is a well-established antimalaria drug also recently discussed in therapeutics against the COVID-19 pandemic. The interaction of this polysaccharide-ionic drug pair was investigated by combining UV-vis spectrophotometry and atomic force microscopy (AFM) imaging. A decrease of the UV peak assigned to free CQ and the occurrence of isosbestic points indicate the formation of complexes. High-resolution AFM height images revealed an increasing height of the single polysaccharide chains in the random coil state upon addition of CQ, indicating the formation of a secondary structure, followed by higher hierarchical aggregates. The disappearance of higher-ordered structures and the recovery of polysaccharide chains with primary structure were observed by introducing inorganic cations (Na+, K+, Ca2+), replacing the condensed CQ and paving the way to reversible ion-induced drug release.

Isolation, physical, structural characterization and in vitro prebiotic activity of a galactomannan extracted from endosperm splits of Chinese Sesbania cannabina seeds

The purpose of this study was to identify and determine the physical and structural characterization of the water-soluble galactomannan extracted from endosperm splits of Chinese S. cannabina seeds. The Sesbania galactomannan (SP) was extracted and purified using a novel method with a high yield (40.3 ± 7.2%). The molecular structure of SP was determined by monosaccharide composition, FTIR and NMR spectroscopy. The structural data showed that SP was galactomannan which composed by a β-(1/4)-linked mannose backbone with galactopyranosyl residues attached through α-(1/6) linkages. The constant mannose/galactose (M/G) ratio and average molecular weight (Mw) of SP was 1.6:1 and 2.16 × 105 g/mol, respectively. The physical results revealed that SP had many branches on the backbone and existed as a random coil state in aqueous solution. SP was a good biopolymer which had smooth and clearer surface with homogeneous composition, and had some degree of crystallinity and prebiotic activity. As a consequence, SP could be a potential prebiotic and was expected to be suitable for applications in food, pharmaceutical, biomedical or cosmetic industries as a promising new biomaterial.

Optical Detection of Thrombin on Nanoporous Anodic Alumina with Aptamer-Modified Surface

Nanoporous anodic alumina (NAA) attracts interest in nanotechnology[1]. Its physical and chemical properties combined with a cost-effective and scalable production make it a good for nanotechnology-related applications. Its high and tuneable surface-to-volume ratio as well as its interesting optical properties[2] have been used as the basis of different biosensing schemes. Biosensing, and specifically optical biosensing is of great interest in health and environmental applications. The reflection interference spectroscopy (RIfS) method based on NAA has demonstrated its ability in detecting many kinds of molecules [3,4].Biosensors engineered with aptamers as a bioreceptor are called aptabiosensors. Thrombin Binding Aptamer (TBA) has a well-known binding process and high affinity and is one of the most studied aptamers. Thrombin is the key factor of blood coagulation, whose activity is important in wounds and in blood circulation. The free thrombin-binding aptamer remains as a random-coil state in the absence of thrombin, while in the presence of thrombin the protein attaches to the aptamer changing its conformation to quadruplex. In this study we assess the capabilities of NAA with the inner pore surfaces modified with TBA to detect specifically the thrombin protein by means of the RIfS method.We prepared NAA with the usual anodization conditions under oxalic acid electrolyte to obtain porous layers with uniform pore diameter and with a thickness that permits the measurement with RIfS in a flow-cell where the different species in solution can be introduced. The experiments consisted of monitoring the change in effective optical thickness (EOT, the quantitative characteristic parameter obtained from RIfS) in the different steps of the biosensing process. Figure 1 shows SEM pictures of the NAA platforms prepared.The NAA pore surfaces were initially functionalized with (3-aminopropyl)triethoxysilane (APTES) and then the surface mas modified in a three-step procedure monitored in real time thanks to the RIfS method. Figure 2 shows the change in EOT as a function of time during the surface functionalization of NAA: the covalent attachment of Sulfo-NHS-Biotin and subsequent streptavidin attachment (stages 1 and 2 in the figure) and the final immobilization of TBA in the pore walls of NAA (step 3 in the plot).. First, the flow of the Sulfo-NHS-Biotin solution produced a considerable increase in EOT. Then, a further increase in EOT is observed with the infiltration of streptavidin. Finally, EOT also shows clearly the immobilization of biotinylated TBA.The aptamer-functionalized NAA substrates were employed to detect human thrombin protein. For this purpose, different substrates were used in RIfS experiments with human thrombin protein at different concentrations. Figure 3 shows one example of the evolution of the EOT signal upon infiltration of a 1.35 µM thrombin solution. Results show that after obtaining a baseline with constant EOT corresponding to the flow of binding buffer, the thrombin solution is injected causing a rapid increase in EOT, at a rate of 0,05 nm/s. After this increase a stable value is reached after 3600 s, with an absolute change in EOT of ∆EOT = 28 nm. The experiment corresponding to Figure 3 has been repeated for a set of concentrations to obtain a sensitivity curve of the aptamer-functionalized NAA and to determine the lower limit of detection. With this, the dissociation constant of the aptamer-thrombin reaction is determined as Kd = 0,9 µM, the sensitivity to be m = 45.5 nm/µM and the LOD = 72 nM.Finally, in order to demonstrate the specificity of the NAA platform, experiments replacing the flow of thrombin by the flow of a different but similar protein, Bovine Serum Albumin (BSA) were conducted showing a much lower response. Furthermore, thrombin flow experiments with NAA lacking the aptamer functionalization step were also performed to demonstrate the protein does not bind non-specifically to the NAA inner pore walls.[1] Josep Ferré-Borrull, et al., Nanomaterials, vol. 7, p. 5225 (2014).[2] Josep Ferré-Borrull et al., in NANOPOROUS ALUMINA: FABRICATION, STRUCTURE, PROPERTIES AND APPLICATIONS, Springer Series in Materials Science, vol. 219, p. 185 (2015).[3] Laura Pol et al., Nanomaterials, vol. 9, p.478 (2019).[4] Laura Pol et al, Sensors, vol. 19, p. 4543 (2019). Figure 1

Potential energy landscape and thermodynamic transitions of coarse-grained protein models revealed by the multicanonical generalized hybrid Monte Carlo method.

In the present study, thermodynamic properties of coarse-grained protein models have been studied by an extended ensemble method. Two types of protein model were analyzed; one is categorized into a fast folder and the other into a slow folder. Both models exhibit the following thermodynamic transitions: the collapse transition between random coil states and spatially compact, but non-native states and the folding transition between the collapsed states and the folded native states. Caloric curve for the fast folder shows strong statistical ensemble dependence, while almost no ensemble dependence is found for the slow folder. Microcanonical caloric curve for the fast folder exhibits S-shaped temperature dependence on the internal energy around the collapse transition which is reminiscent of the van der Waals loop observed for the first order transition; at the transition temperature, the collapsed and random coil states coexist dynamically. The corresponding microcanonical heat capacity is found to have negative region around the transition. This kind of exotic behaviors could be utilized to distinguish fast folding proteins.

Structure and mode of action of a novel antibacterial peptide from the blood of Andrias davidianus.

Andrias davidianus is widely recognized in traditional medicine as a cure-all to treat a plethora of ailments. In a previous study, a novel antibacterial peptide named andricin B was isolated from A. davidianus blood. In this study, we investigated andricin B structure and its mode of action. Circular dichroism spectra suggested that andricin B adopts a random coil state in aqueous solution and a more rigid conformation in the presence of bacteria. Moreover propidium iodide/fluorescein diacetate double staining indicated that bacteria treated with andricin B were not immediately eliminated. Rather, there is a gradual bacterial death, followed by a sublethal stage. Scanning electronic microscope imaging indicates that andricin B might form pores on cell membranes, leading to the release of cytoplasmic contents. These results were consistent with flow cytometry analysis. Furthermore, Fourier transform infrared spectroscopy suggests that andricin B induces changes in the chemical properties in the areas surrounding these "pores" on the cell membranes. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study suggested the new perspectives about the mode of action of antimicrobial peptide (AMP) active against sensitive bacteria. The AMP was able to be in a random coiled state in aqueous solution but to change to a more rigid one in the presence of sensitive bacteria. Exposure to AMP might not lead to immediate death of treated bacteria, rather bacteria concentration decreased gradually flattening at a sublethal stage. These findings will help people to understand better how the AMPs activate against sensitive bacteria.

Collapse Transition‐Assisted Crystallization in P3HT Solution

ABSTRACTUnderstanding the multiple phase transitions such as collapse transition, phase separation, and crystallization in solutions is of fundamental importance to control the solution structure of conjugated polymers in device processing. Combining in situ synchrotron radiation small and wide‐angle X‐ray scattering, ultrasensitive differential scanning calorimetry, ultraviolet–visible absorption spectroscopy, and polarized optical microscopy, we investigate the order–disorder transitions in poly(3‐hexylthiophene)/toluene solutions during cooling and heating processes. We demonstrate the occurrence of collapse transition of polymer chains from a random coil state to a lower dimensional network prior to the onset of crystallization during cooling in solution. This conformational preordering can lead to the formation of a lyotropic liquid crystalline phase, which is of great significance to the crystallization and ordering in polymer films, and further to promote its electric performance. It is examined that the mobility of films cast from chain‐collapsed solutions can be one order of magnitude higher than that from isotropic solutions with random‐coiled conformations. Thus, the conformational preordering in solutions is proposed to be a more efficient way than the postannealing of films to improve the electric performance of conjugated polymer films. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019, 57, 1105–1114

Adsorption of polymer chains on heterogeneous surfaces with random adsorption sites

The adsorption time τads of a linear polymer chain onto a heterogeneous surface with randomly distributed adsorption sites decreases with increasing the fraction of adsorption sites ρ but increases with increasing the intra-polymer attraction strength EPP. The scaling behavior of τads with the polymer length N, τads ~ Nα, is independent of ρ but is dependent on EPP. We find α = 1.6 for polymer in random coil state at small EPP and α = 2.0 for polymer in compacted globule state at large EPP. An interesting finding is that τads increases with EPS at small ρ but decreases with EPS at large ρ, indicating that the adsorption mechanism is dependent on the surface property. The adsorption of polymer is accompanied by the extension of polymer conformation as the equilibrium apparent size <R2g,xy>eq is increased after adsorption. However, at moderate ρ and large EPS, we find <R2g,xy>eq decreases with increasing ρ, in agreement with experimental observation for DNA adsorption.

Effect of temperature on the escape of charged polymer chain from a repulsive nanopore

ABSTRACTThe effect of temperature on the escape of a charged polymer chain from a repulsive nanopore is studied by Langevin dynamics simulations. The conformation properties of the charged polymer chain are dependent on the temperature as it is in random coil state at high temperature and in compact globule state at low temperature. The scaling behaviour between the escape time and polymer length is independent of temperature, while the escape time decreases with increasing the temperature in an exponential way. Different temperature-dependent behaviours are observed for the escape time in three temperature regimes: low temperature where the polymer is in compact globule state, intermediate temperature around the coil-to-globule transition temperature, and high temperature where the polymer is in the random coil state. We further find that, with a decrease in the temperature, the total number of moving steps for the escape increases sharply in the low-temperature regime while the time duration for each moving step increases sharply in the intermediate temperature regime.