Random Coil Transition Research Articles

Improvement of gelation properties of Penaeus vannamei surimi by magnetic field-assisted freezing in combination with curdlan

Traditional methods of freezing and thawing may harm the quality of meat products. In order to reduce the negative impact of freezing on surimi products, the magnetic field-assisted freezing method is combined with various curdlan ratios to enhance the gelation characteristics of Penaeus vannamei surimi in this study. The results showed that the magnetic field-assisted freezing technique significantly improved the quality of thawed surimi compared with soaking freezing (SF), whereas the addition of curdlan further improved the gelation properties, and the gel strength, water-holding capacity, textural properties, whiteness, and G′ value were significantly improved when its content was increased to 0.6 %. However, excessive amounts of curdlan interfered with protein covalent cross-linking, leading to a decrease in gel quality. Additionally, the addition of magnetic field and curdlan encouraged the shift of the α-helix to the random coil and β-sheet transition, which stimulated the growth of myofibril molecules, exposed the hydrophobic groups and thiols, improved protein-molecule interactions, and promoted systematic gathering of proteins, leading to the formation of the microstructure of dense and small pores. It also resulted in a drop in water release, an increase in the proton density and a shift in the water condition from free water to more immobile water, which had higher sensory qualities. These effects together resulted in a reduction in thawing and cooking loss to 11.41 % and 13.83 %, respectively. These results also help to clarify the gelation process of shrimp surimi and help to regulate the gelation characteristics of shrimp surimi products.

Co-assembled whey protein and proanthocyanidins as a promising biocarrier for hydrophobic pterostilbene: Fabrication, characterization, and cellular antioxidant potential

The usage of food-derived polyphenols with different polarities has been limited by their instability and incompatibility. Therefore, a biocarrier was developed by co-assembly of whey protein isolate (WPI) and hydrophilic proanthocyanidin (PC) for loading hydrophobic pterostilbene (PTE). Such biocarrier has superior affinity for PTE than WPI alone, as determined by encapsulation efficiency and loading capacity assay, fluorescence quenching analysis, and molecular docking, whereas the assembly process was characterized by particle size and zeta potential, 3-dimensional fluorescence, and scanning electron microscopy. Circular dichroism and Fourier transform infrared spectroscopy spectra confirmed the α-helix to β-sheet and random coil transition of proteins during the formation of nanocomplexes. Whey protein isolate acted as a mediator through altering the binding mode of PC and PTE, allowing them to perform significant synergistic effects in enhancing 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and 2,2-diphenyl-1-picrylhydrazyl radical scavenging and reducing H2O2-induced cell damage. This research may serve to develop new protein/polyphenol co-loading systems and offer a reliable nutritional fortification.

Recognizing boiled bone-remains from the Boca de Lega archaeological site in Argentina through mechanical spectroscopy studies

A study in thermo-altered bone-remains recovered from the Boca de Lega archaeological site (Santa Fe, Argentina) is performed with the aim of distinguishing among the whole group of seven investigated bone-remains which ones were boiled during culinary activities. In fact, for the boiled-bone-remains, the damping spectra exhibited the appearance of the damping peaks related to the loss of free water, the loss of the crystallization water, and the peak related to the viscous movement of collagen fibrils, after the triple helix to random coil transition; at around 370 K, 420 K and 510 K, respectively. In addition, the dynamic modulus behaviour in boiled samples exhibited the peaked shape behaviour as a function of temperature, i.e., an increase from around 370 K up to around 450 K, which was already reported for experimental bones. The results from mechanical spectroscopy were corroborated through scanning electron microscopy studies at high resolution. Besides, differential thermal analysis, thermogravimetry, and energy dispersive spectroscopy, are used also as instrumental techniques and their obtained results are discussed in the present work too.

β-Sheet to Random Coil Transition in Self-Assembling Peptide Scaffolds Promotes Proteolytic Degradation.

One of the most desirable properties that biomaterials designed for tissue engineering or drug delivery applications should fulfill is biodegradation and resorption without toxicity. Therefore, there is an increasing interest in the development of biomaterials able to be enzymatically degraded once implanted at the injury site or once delivered to the target organ. In this paper, we demonstrate the protease sensitivity of self-assembling amphiphilic peptides, in particular, RAD16-I (AcN-RADARADARADARADA-CONH2), which contains four potential cleavage sites for trypsin. We detected that when subjected to thermal denaturation, the peptide secondary structure suffers a transition from β-sheet to random coil. We also used Matrix-Assisted Laser Desorption/Ionization-Time-Of-Flight (MALDI-TOF) to detect the proteolytic breakdown products of samples subjected to incubation with trypsin as well as atomic force microscopy (AFM) to visualize the effect of the degradation on the nanofiber scaffold. Interestingly, thermally treated samples had a higher extent of degradation than non-denatured samples, suggesting that the transition from β-sheet to random coil leaves the cleavage sites accessible and susceptible to protease degradation. These results indicate that the self-assembling peptide can be reduced to short peptide sequences and, subsequently, degraded to single amino acids, constituting a group of naturally biodegradable materials optimal for their application in tissue engineering and regenerative medicine.

Exploring polymer solubility with thermally‐responsive Diels‐Alder monomers: Revisiting the monkey's fist

AbstractThermo‐responsive monomers were designed to contain a Diels‐Alder (DA) adduct such that cyclo‐reversion would yield either the maleimide or the furan unit attached to the polymer chain. These thermally responsive monomers were then copolymerized with N‐isopropylacrylamide (NIPAM) via reversible addition‐fragmentation chain‐transfer (RAFT) polymerization to yield linear gradient‐copolymer structures as a comparison to existing nanogel/starlike systems to understand how polymer topology and composition influence solution‐state properties. Using UV–Vis spectroscopy, it was determined that solution‐state properties were thermally dependent and influenced by a number of variables such as comonomer feed ratio, polymer chain end functionality, and polymer backbone length and composition. Manipulation of the feed ratio allowed for control over the cloud point, including the breadth and location of phase separation. Thermal treatment of these copolymers revealed tunable and predictable variations in previously observed transitions, directly correlated to cleavage of the DA adducts and change in polymer backbone composition. Finally, on cooling cycles, a double sigmoid was sometimes observed, indicating a complex globule to random coil transition correlated to polymer chain end composition. These studies help understand how to untie the “monkey's fist.”

Determining the temperatures to which the bone was heated in archaeological contexts. Distinguishing between boiled and grilled bones

A study carried out in fresh cow (Bos taurus) cortical-femur bones which allows determining the maximum annealing temperature to which a bone was subjected is shown. It is focused on temperatures near the ones used in culinary activities. Mechanical spectroscopy, optical microscopy, differential thermal analysis and thermogravimetry studies are used in the present work. The study takes into account the behaviour of the thermal denaturation processes from the remnant collagen as a function of temperature. The survey of the relaxation process related to the triple helix to random coil transition from the residual collagen which occurs at 510 K/237 °C, is proposed as a potentially useful tool for determining that the bone was not previously heated above this temperature. In addition, by using mechanical spectroscopy a procedure for discriminating between grilled- and boiled-bones is shown. Likewise, a reference chart of the thermodynamic states of denaturation of collagen in the bone as a function both of temperature and cooking mode is reported. The relationships between the denaturation stages and the responses from mechanical spectroscopy and differential thermal analysis are also shown.

Prospects of Silk Sericin as an Adsorbent for Removal of Ibuprofen from Aqueous Solution

This Article presents removal of ibuprofen from aqueous solution using commercially available silk sericin as an adsorbent in an integrated adsorbent-membrane process. The adsorption study was performed at different physiological conditions, such as adsorbent concentration (1–10g), ibuprofen concentration (10–70 mg/L), temperatures (20, 30, and 40 °C), and pH (5, 6, 7, and 8). The occurrence of adsorption before membrane separation was confirmed by performing analysis of sericin–ibuprofen interaction and complex formation. Sericin–ibuprofen interaction and complex formation was investigated using FTIR, FESEM, fluorescence spectroscopy, XRD, and ITC. Sericin and ibuprofen interaction is spontaneous and endothermic in nature, while random coil transition of Sericin governed the adsorption system. ITC analysis exhibited a binding affinity (Kb) value of 2.51 × 104 ± 1.4 and one binding site (n ≈ 1) per molecule at 27 °C, revealing moderate binding of ibuprofen to the sericin protein. Complete removal of ibupr...

Physicochemical responses of lysozyme on interaction with the ionic liquid (IL), 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4] in aqueous phosphate buffer medium

This study entails physicochemical responses of lysozyme on interaction with the ionic liquid, [BMIM] [BF4] in phosphate buffer medium at pH 6 and 8. Methods used for evaluation were UV–vis and fluorescence spectroscopy, circular dichroism, and molecular docking. Interaction of the ionic liquid (IL) with the tryptophan moieties in the protein was monitored to understand the interaction features of the IL-lysozyme combine. The process thermodynamics were evaluated from the fluorescence spectral data. The interaction was observed to occur in stages, and was pH dependent. The structural changes in the interaction process like α-helix to random coil transition, and β-sheet forms were also found from CD spectral results. Molecular docking was done to get information on the location of the interacted [BMIM] [BF4] in the enzyme. Such studies are not commonly found in literature.

Nonmonotonic Hydration Behavior of Bovine Serum Albumin in Alcohol/Water Binary Mixtures: A Terahertz Spectroscopic Investigation.

We report the experimental observation of nonmonotonic changes in the collective hydration of bovine serum albumin (BSA) in the presence of alcohols of varying carbon-chain lengths, that is, ethanol, 2-propanol, and tert-butyl alcohol (TBA), by using terahertz (THz) time domain spectroscopy. We measured the THz absorption coefficient (α) of the protein solutions, and it was observed that α fluctuated periodically as a function of alcohol concentration at a fixed protein concentration. For a fixed alcohol concentration, an increase in the protein concentration resulted in nonmonotonic changes in α; thus, it first decreased rapidly and then increased, which was followed by a shallow decrease. An alcohol-induced α helix to random coil transition of the protein secondary structure was revealed by circular dichroism spectroscopy measurements, and the effect was most prominent in TBA. The anomalous change in the hydration was found to be a delicate balance between the various interactions present in the three-component system.

Structural studies on aqueous gelatin solutions: Implications in designing a thermo-responsive nanoparticulate formulation

Gelatin as a polymer has found extensive application in the pharmaceutical industry. It is also being used, as a matrix molecule, for nanoparticle based drug delivery applications. Gelatin nanoparticles synthesised, keeping the native structure intact, show interesting properties. Synthesizing such nanoparticles requires an understanding of the structural features of gelatin under conditions of nanoparticle synthesis and preserving them during the process. To address this we have carried out an extensive characterization of gelatin using circular dichroism (CD) spectroscopy, differential scanning calorimetry (DSC) and scanning electron microscopy (SEM) under various reaction conditions that are utilized in the desolvation method for gelatin nanoparticle synthesis. We investigated the gel-sol transition, hysteresis and gelatin fibre morphology under different pH and temperature conditions. We also investigated the temperature and pH dependence of triple-helix to random-coil transition in gelatin. We finally demonstrate the synthesis of gelatin nanoparticles with native gelatin. These nanoparticles show shrinkage in size (∼90nm) with increase in temperature from 30°C (369.4 ±19.8) to 40°C (282.3±9.8). Our results suggest that by carefully selecting the reaction conditions, it is possible to synthesise nanoparticles having partially folded structures and with a varying degree of sensitivity towards temperature and pH.

Reactive molecular dynamics study of the pH-dependent dynamic structure of α-helix.

We have studied the α-helix to random coil transition using ReaxFF reactive molecular dynamics as a function of pH. Urea binding to peptides and associated interference with backbone H-bonds and charged side chains interactions, which can both denature the helices, have been studied previously using nonreactive force fields (Topol, I. A. J. Am. Chem. Soc. 2001, 123, 6054-6060). This study reveals new proton-transfer mechanisms related to the denaturation of α-helical structures, which cannot be captured by nonreactive molecular dynamics. In addition, we show that proton transfer between the solution and the peptide can break the α-helix hydrogen bonds, and consequently, at extreme pHs, a significant amount of helix will unravel. We also compare the effects of temperature in the denaturation mechanism. The ReaxFF findings are in significantly better agreement with ab initio calculations than previous nonreactive force field results, indicating the relevance of the reactive component on helical loss.

Aggregation and network formation in self-assembly of protein (H3.1) by a coarse-grained Monte Carlo simulation.

Multi-scale aggregation to network formation of interacting proteins (H3.1) are examined by a knowledge-based coarse-grained Monte Carlo simulation as a function of temperature and the number of protein chains, i.e., the concentration of the protein. Self-assembly of corresponding homo-polymers of constitutive residues (Cys, Thr, and Glu) with extreme residue-residue interactions, i.e., attractive (Cys-Cys), neutral (Thr-Thr), and repulsive (Glu-Glu), are also studied for comparison with the native protein. Visual inspections show contrast and similarity in morphological evolutions of protein assembly, aggregation of small aggregates to a ramified network from low to high temperature with the aggregation of a Cys-polymer, and an entangled network of Glu and Thr polymers. Variations in mobility profiles of residues with the concentration of the protein suggest that the segmental characteristic of proteins is altered considerably by the self-assembly from that in its isolated state. The global motion of proteins and Cys polymer chains is enhanced by their interacting network at the low temperature where isolated chains remain quasi-static. Transition from globular to random coil transition, evidenced by the sharp variation in the radius of gyration, of an isolated protein is smeared due to self-assembly of interacting networks of many proteins. Scaling of the structure factor S(q) with the wave vector q provides estimates of effective dimension D of the mass distribution at multiple length scales in self-assembly. Crossover from solid aggregates (D ∼ 3) at low temperature to a ramified fibrous network (D ∼ 2) at high temperature is observed for the protein H3.1 and Cys polymers in contrast to little changes in mass distribution (D ∼ 1.6) of fibrous Glu- and Thr-chain configurations.

Thermoresponsive Gelatin Nanogels.

We present a novel tunable thermoresponsive gelatin nanogel that shows a volume transition at ∼32 °C. A thermally induced volume reduction of more than 30× is observed due to the helix to random coil transition of gelatin chains confined in the nanogels. The physical process and key factors influencing thermoresponsive properties are investigated using dynamic light scattering (DLS), transmission electron microscopy (TEM), and polarimetry. The thermoresponsive properties of this nanogel can be exploited in the development of new types of stimuli-responsive, biomedically relevant materials based on natural polymers.

Conformational changes in polypeptides and proteins

AbstractWe consider the process of α‐helix↔random coil transition in alanine polypeptides. For this, we suggest a novel theoretical method based on the statistical mechanics. We apply the developed formalism for the description of the thermodynamical properties of alanine polypeptides of different length. We analyze the essential thermodynamical properties of the system such as heat capacity, the phase transition temperature, and the latent heat of the phase transition. Alternatively, we have obtained same thermodynamical characteristics from the molecular dynamics simulations and compared the results with the results of statistical mechanics calculations. The comparison proves the validity of the statistical mechanics approach and establishes its accuracy. We extend the developed formalism for the description of the α‐helix↔random coil transition in the presence of the effects of solvent. The performed analysis explains prominent decrease of the phase transition temperature of the polypeptide in water solution. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

Phase transitions in polypeptides: analysis of energy fluctuations

The helix↔random coil transition in alanine, valine, and leucine polypeptides consisting of 30 amino acids is studied in vacuo using the Langevin molecular dynamics approach. The influence of side chain radicals on internal energy and heat capacity of the polypeptides is discussed. The heat capacity of these polypeptides is calculated as a function of temperature using two different methods, namely, as the derivative of the energy with respect to temperature, and on the basis of energy fluctuations in the system. The convergence of the fluctuations based approach is analyzed as a function of simulation time. This study provides a comparison of methods for the description of structural transitions in polypeptides.

Three and Counting

Three and Counting

Ab initio theory of helix↔coil phase transition

In this paper, we suggest a theoretical method based on the statistical mechanics for treating the α-helix↔random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely on fundamental physical principles. It describes essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated as a function of two dihedral angles, responsible for the polypeptide twisting. The suggested theory is general and with some modification can be applied for the description of phase transitions in other complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters, fullerenes).

α-helix↔random coil phase transition: analysis of ab initio theory predictions

In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [Eur. Phys. J. D, DOI: 10.1140/epjd/e2007-00328-9] and perform detail analysis of α-helix↔random coil transition in alanine polypeptides of different length. We have calculated the potential energy surfaces of polypeptides with respect to their twisting degrees of freedom and construct a parameter–free partition function of the polypeptide using the suggested method [Eur. Phys. J. D, DOI: 10.1140/epjd/e2007-00328-9]. From the build up partition function we derive various thermodynamical characteristics for alanine polypeptides of different length as a function of temperature. Thus, we analyze the temperature dependence of the heat capacity, latent heat and helicity for alanine polypeptides consisting of 21, 30, 40, 50 and 100 amino acids. Alternatively, we have obtained same thermodynamical characteristics from the use of molecular dynamics simulations and compared them with the results of the new statistical mechanics approach. The comparison proves the validity of the statistical mechanic approach and establishes its accuracy.

Infrared Spectroscopic Discrimination between the Loop and α-Helices and Determination of the Loop Diffusion Kinetics by Temperature-Jump Time-Resolved Infrared Spectroscopy for Cytochrome c

The infrared (IR) absorption of the amide I band for the loop structure may overlap with that of the α-helices, which can lead to the misassignment of the protein secondary structures. A resolution-enhanced Fourier transform infrared (FTIR) spectroscopic method and temperature-jump (T-jump) time-resolved IR absorbance difference spectra were used to identify one specific loop absorption from the helical IR absorption bands of horse heart cytochrome c in D 2O at a pD around 7.0. This small loop consists of residues 70–85 with Met-80 binding to the heme Fe(III). The FTIR spectra in amide I′ region indicate that the loop and the helical absorption bands overlap at 1653 cm −1 at room temperature. Thermal titration of the amide I′ intensity at 1653 cm −1 reveals that a transition in loop structural change occurs at lower temperature ( T m = 45°C), well before the global unfolding of the secondary structure ( T m ≈ 82°C). This loop structural change is assigned as being triggered by the Met-80 deligation from the heme Fe(III). T-jump time-resolved IR absorbance difference spectra reveal that a T-jump from 25°C to 35°C breaks the Fe-S bond between the Met-80 and the iron reversibly, which leads to a loop (1653 cm −1, overlap with the helical absorption) to random coil (1645 cm −1) transition. The observed unfolding rate constant interpreted as the intrachain diffusion rate for this 16 residue loop was ∼3.6 × 10 6 s −1.

Capillary electrophoresis is a sensitive monitor of the hairpin–random coil transition in DNA oligomers

Capillary electrophoresis (CE) has been used to characterize the hairpin–random coil transition of four octamers in the GCxxxxGC minihairpin family, where xxxx is GAAA, TTTC, TTTT, or AAAA. The transition can be monitored by CE because differences in the frictional coefficients of the hairpin and coil forms of each octamer lead to a difference of approximately 9% in the free solution mobilities of the two conformations. The GAAA octamer is unusually stable, with a melting temperature of 65 °C. The TTTT octamer forms a minihairpin with a melting temperature of 29 °C, the TTTC octamer has a melting temperature of 16 °C, and the AAAA octamer has a melting temperature below 0 °C. The thermal transitions of the TTTT, TTTC, and AAAA octamers are well fitted by a structure prediction algorithm; however, the GAAA minihairpin is considerably more stable than predicted. The melting temperature of the GAAA minihairpin is reduced to 47 °C in aqueous buffers containing 7.2 M urea and to 33 °C in buffers containing 7.2 M urea plus 40% (v/v) formamide. The combined results indicate that CE is a sensitive technique for monitoring conformational transitions in small DNA molecules.