Helix-coil Transition Research Articles

Helix-Coil Transition in Heterogeneous Biopolymers: Influence of Fixing Bond Scale

Helix-Coil Transition in Heterogeneous Biopolymers: Influence of Fixing Bond Scale

Application of the photothermal-responsive gelatin-based microspheres for controlled release of imidacloprid by helix-coil structural transition mechanism

Intelligent controlled release systems (ICRS) are recognized as a feasible and economical way for the highly efficient utilization of agrochemicals. In this work, we developed an intelligent photothermal-responsively controlled-release pesticide particle (IYGCP) based on imidacloprid (IMI, a model pesticide), yeast biochar (YB, adsorbent and photothermal material), gelatin (GE, temperature-responsive polymer), and Ca-alginate (CA, microsphere matrix). Therein, YB with high adsorption property and photothermal conversion capacity was used as a carrier of IMI to avoid the loss of active ingredients, and as an agent to endow the IYGCP platform with unique photothermal-responsive performance. After IMI loading, IMI/YB was scattered and anchored in CA/GE semi-interpenetrating hydrogels by the chelation of sodium alginate and Ca2+. Upon irradiation under simulated sunlight, YB with satisfactory photothermal conversion efficiency can effectively transfer solar energy into thermal energy, induing a free helix-coil structural transition of the un-crossed GE polymers, thereby resulting in changes in microstructure of hydrogel spheres and further enabling a controlled release of IMI encapsulated in the IYGCP. Besides, the composite displayed high control efficacy on corn borers. Consequently, this photothermal-responsive gelatin-based microsphere shows a bright prospect for controlling the release and loss of pesticides.

Highly sensitive tryptophan fluorescence probe for detecting rhythmic conformational changes of KaiC in the cyanobacterial circadian clock system.

KaiC, a core protein of the cyanobacterial circadian clock, consists of an N-terminal CI domain and a C-terminal CII domain, and assembles into a double-ring hexamer upon binding with ATP. KaiC rhythmically phosphorylates and dephosphorylates its own two adjacent residues Ser431 and Thr432 at the CII domain with a period of ∼24 h through assembly and disassembly with the other clock proteins, KaiA and/or KaiB. In this study, to understand how KaiC alters its conformation as the source of circadian rhythm, we investigated structural changes of an inner-radius side of the CII ring using time-resolved Trp fluorescence spectroscopy. A KaiC mutant harboring a Trp fluorescence probe at a position of 419 exhibited a robust circadian rhythm with little temperature sensitivity in the presence of KaiA and KaiB. Our fluorescence observations show a remarkable environmental change at the inner-radius side of the CII ring during circadian oscillation. Crystallographic analysis revealed that a side chain of Trp at the position of 419 was oriented toward a region undergoing a helix–coil transition, which is considered to be a key event to allosterically regulate the CI ring that plays a crucial role in determining the cycle period. The present study provides a dynamical insight into how KaiC generates circadian oscillation.

Length-Dependent Collective Vibrational Dynamics in Alpha-Helices.

Functions of protein molecules in nature are closely associated with their well-defined three-dimensional structures and dynamics in body fluid. So far, many efforts have been made to reveal the relation of protein structure, dynamics, and function, but the structural origin of protein dynamics, especially for secondary structures as building blocks of conformation transition, is still ambiguous. Here we theoretically uncover the collective vibrations of elastic poly-alanine α-helices and find vibration patterns that are distinctively different over residue numbers ranging from 20 to 80. Contrary to the decreasing vibration magnitude from ends to the middle region for short helices, the vibration magnitude for long helices takes the minimum at approximately 1/5 of helix length from ends but reaches a peak at the center. Further analysis indicates that major vibrational modes of helical structures strongly depend on their lengths, where the twist mode dominates in the vibrations of short helices while the bend mode dominates the long ones analogous to an elastic Euler beam. The helix-coil transition pathway is also affected by the alternation of the first-order mode in helices with different lengths. The dynamic properties of the helical polypeptides are promising to be harnessed for de novo design of protein-based materials and artificial biomolecules in clinical treatments.

Additivity in the helix-coil transition of alpha-helical peptides with varying length

The mechanical unfolding of alanine-rich helices with various lengths and sequences has been characterized using Adaptive Steered Molecular Dynamics (ASMD). We have found that the potential of mean force (PMF) and hydrogen bonding profiles for these various helices exhibit a correspondence between different chains, and the required energetics for the overall unfolding process is additive with respect to the chain length. [Biophys. J, 120, 2009 (2021)] Polyalanine peptides were used to guide the hypotheses because of their high helix propensity for helical formation, and the low computational cost needed to simulate them.

Dual-sensitive antibacterial peptide nanoparticles prevent dental caries.

Background: Dental caries is the most prevalent bacterial biofilm-induced disease. Current clinical prevention and treatment agents often suffer from adverse effects on oral microbiota diversity and normal tissues, predominately arising from the poor biofilm-targeting property of the agents.Methods: To address this concern, we herein report dual-sensitive antibacterial peptide nanoparticles pHly-1 NPs upon acid and lipid-binding for treatment of dental caries. Amino acid substitutions were performed to design the peptide pHly-1. The potential, morphology and secondary structure of pHly-1 were characterized to elucidate the mechanisms of its pH and lipid sensitivity. Bacterial membrane integrity assay and RNA-seq were applied to uncover the antimicrobial mechanism of peptides under acidic condition. The in vitro and ex vivo antibiofilm assays were used to determine the antibiofilm performance of pHly-1 NPs. We also carried out the in vivo anti-caries treatment by pHly-1 NPs on dental caries animal model. Oral microbiome and histopathological analyses were performed to assess the in vivo safety of pHly-1 NPs.Results: The pHly-1 peptide underwent the coil-helix conformational transition upon binding to bacterial membranes in the acidic cariogenic biofilm microenvironment, thereby killing cariogenic bacteria. Under normal physiological conditions, pHly-1 adopted a β-sheet conformation and formed nanofibers, resulting in negligible cytotoxicity towards oral microbes. However, in acidic solution, pHly-1 NPs displayed reliable antibacterial activity against Streptococcus mutans, including standard and clinically isolated strains, mainly via cell membrane disruption, and also suppressed in vitro and human-derived ex vivo biofilm development. Compared to the clinical agent chlorhexidine, in vivo topical treatment with pHly-1 NPs showed an advanced effect on inhibiting rat dental caries development without adverse effects on oral microbiota diversity and normal oral or gastric tissues.Conclusion: Our results demonstrated the high efficacy of dual-sensitive antimicrobial peptides for the selective damage of bacterial biofilms, providing an efficient strategy for preventing and treating dental caries.

Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25

SUMMARYSNAP-25 (synaptosomal-associated protein of 25 kDa) is a prototypical intrinsically disordered protein (IDP) that is unstructured by itself but forms coiled-coil helices in the SNARE complex. With high conformational heterogeneity, detailed structural dynamics of unbound SNAP-25 remain elusive. Here, we report an integrative method to probe the structural dynamics of SNAP-25 by combining replica-exchange discrete molecular dynamics (rxDMD) simulations and label-based experiments at ensemble and single-molecule levels. The rxDMD simulations systematically characterize the coil-to-molten globular transition and reconstruct structural ensemble consistent with prior ensemble experiments. Label-based experiments using Förster resonance energy transfer and double electron-electron resonance further probe the conformational dynamics of SNAP-25. Agreements between simulations and experiments under both ensemble and single-molecule conditions allow us to assign specific helix-coil transitions in SNAP-25 that occur in submillisecond timescales and potentially play a vital role in forming the SNARE complex. We expect that this integrative approach may help further our understanding of IDPs.

Description of Helix-Coil Transition in Heteropolymers in Frame of GMPC

Description of Helix-Coil Transition in Heteropolymers in Frame of GMPC

Optical-Dissymmetry Phase Transitions in an Achiral Helical-Spring Polymer through Controlled Noncovalent Interactions.

Noncovalent chemistry may offer diversity in the functions and applications for artificial polymers by allowing various ordered-disordered phase transitions in a precisely controlled manner. To verify this notion from a fundamental perspective, we examined an achiral poly(phenylacetylene) derivative with an α-helical structure as a helical-spring polymer for revealing phase changes through control of intramolecular hydrogen bonding with the chiral solvent and temperature. When an amine capable of hydrogen bonding was used as the chiral solvent, either an irreversible helix-helix or a reversible helix-coil phase change occurred in an optically dissymmetric manner according to the amount of the chiral solvent added and ambient temperature. Considering the hydrogen-bonding strength values of the solvent mixture and the thermodynamic parameters, we could predict if the optical-dissymmetry phase changes would occur and, if so, how they occur. Our results were similar to those see for the denaturation of proteins, induced by solvent and temperature, based on helix-coil phase transition.

Synthesis of polypyrrole-modified gelatin/poly (acrylic acid) semi-interpenetrating network hydrogel and its controlled release of agrochemicals based on helix–coil transition of gelatin

Synthesis of polypyrrole-modified gelatin/poly (acrylic acid) semi-interpenetrating network hydrogel and its controlled release of agrochemicals based on helix–coil transition of gelatin

Out of equilibrium coil-helix transition driven by chemical fuels

The coil-helix transition of biopolymers is an important secondary structure reconstruction and plays crucial role in biological events. It is known that under thermodynamic equilibrium, the coil-helix transition of polypeptides can be well controlled by external stimulus. In the current study, we are able to manipulate the conformation of PLG to transfer between α-helix and random coil conformation utilizing contiuns supply of the chemical energy flow, which is away from chemical equilibrium. We found that in the presence of EDC/NHS, carboxylate with negative charge on PLG side chains will be firstly activated by EDC and then converted into their corresponding electroneutral NHS-esters, followed by hydrolysis to form carboxylate and NHS again. Using this reaction cycle, we are able to control the charge interaction between side chains of PLG and switch the system from random coil conformation with low free energy to α-helical structure with high free energy in the presence of chemical fuel. Moreover, the lifetime and content of the transient α-helices can be tuned by adjusting the amount of chemical fuels and nucleophile. The fuel-mediated coil-helix transition of polypeptides presented here may provide an efficient strategy for mimicry the behavior of dynamic proteins found in natural systems and bring intriguing opportunities for future adaptive materials.

Helix-coil transition and conformational deformity in Aβ 42-monomer: a case study using the Zn2+ cation

The metal ions (like Fe Zn2+, Cu) are known to influence the amyloid beta (Aβ) aggregation. In this study, we have examined the conformational and dynamical changes during the coordination of Aβ-monomer with the Zn ion using all-atom molecular dynamics (MD) simulations using explicit solvent models. We have probed the unfolding of the full-length Aβ 42 monomer both inclusive and exclusive of the Zn cation, with 1:1 ratio of the peptide and the Zn cation. The inclusion of the Zn cation shows differential intra-peptide interactions which has been probed using various analyses. The Helix – Coil transition of the wild type A monomer is studied using the steered molecular dynamics simulations by taking the end-to-end C-α distance across the peptide. This gives an idea of the unequal intra – peptide and peptide – water interactions being found across the length of the Aβ monomer. The transition of an α-helix dominated wild-type (WT) Aβ structure to the unfolded coil structure gives significant evidence of the intra-peptide hydrogen bonding shifts in the presence of the Zn cation. This accounts for the structural and the dynamical variations that take place in the Aβ monomer in the presence of the Zn cation to mimic the conditions/environment at the onset of fibrillation. Communicated by Ramaswamy H. Sarma

Integrative Structural Dynamics Probing of the Conformational Heterogeneity in Synaptosomal-Associated Protein 25

SNAP-25 (synaptosomal-associated protein of 25 kDa) is a prototypical intrinsically disordered protein (IDP) that is unstructured in its unbound form but forms coiled-coil helices in the SNARE complex. With high conformational heterogeneity, detailed structural dynamics of unbound SNAP-25 remains elusive. Here, we present an integrative method to probe the structural dynamics of SNAP-25 by combining replica-exchange discrete molecular dynamics (rxDMD) simulations and label-based experiments at ensemble and single-molecule levels. The rxDMD simulation allows us to systematically characterize the coil-to-molten-globular transition and reconstruct structural ensemble consistent with prior ensemble experiments. Label-based experiments using Forster Resonance Energy Transfer and Double Electron Electron Resonance further probe the conformational dynamics of SNAP-25. Agreements between simulations and experiments under both ensemble and single-molecule conditions allow us to assign specific helix-coil transitions in SNAP-25 that occur in sub-millisecond timescales and potentially play a vital role in forming the SNARE complex. We expect this integrative approach would help further our understanding of IDPs.

Mechanisms controlling wheat starch gelatinization and pasting behaviour in presence of sugars and sugar replacers: Role of hydrogen bonding and plasticizer molar volume

The effect of sugars and sugar replacers (i.e. plasticizers) on the gelatinization and pasting behaviour of wheat starch was studied. The intrinsic properties of the plasticizers, i.e. the molar volume density of effective hydroxyl groups NOH,s/vs, and the volumetric density of hydrogen bonds in the sugar solutions treated as a single solvent, i.e. Φw,eff, were proposed as factors controlling swelling (i.e. pasting) and gelatinization behaviour. Different classes of plasticizers were used including sugars, polyols, amino acids, soluble fibres such as oligofructoses, and mixtures thereof. The onset, peak and end temperature of starch gelatinization obtained by differential scanning calorimetry could be well described by Φw,eff for all solutions, following predictions from an adapted Flory-Huggins model for polymer melting. The multiple transitions involved in starch gelatinization could be well related to different ranges of Φw,eff following a side chain liquid crystalline model for starch. Deviations from the model predictions were observed mainly for Tonset in conditions of intermediate and excess solvent with high sugar concentrations (50% w/w). In such conditions phase separation likely occurs, increasing the effective starch concentration and consequently gelatinization temperatures. Pasting behaviour related to swelling, i.e. peak viscosity, was found to be a sigmoidal Fermi function of NOH,s/vs of the plasticizers. Plasticizers with high NOH,s/vs enhanced swelling compared to water while those with low NOH,s/vs had an inhibition effect. Overall, a comprehensive mechanism of starch plasticization, swelling and melting is proposed. Swelling associated with solvent ingress and helix-helix dissociation is affected by kinetic factors related to size and viscosity of the plasticizers (both described by NOH,s/vs) and by thermodynamic factors related to sugar partitioning and H-bonding ability (both related to Φw,eff). Melting of crystalline domains associated to helix-coil transition is controlled by thermodynamics, based on solvent H-bonding ability Φw,eff.

Photo/thermal response of polypyrrole-modified calcium alginate/gelatin microspheres based on helix-coil structural transition and the controlled release of agrochemicals

Responsive controlled-release systems can not only improve the efficiency of agrochemical utilization but also increase crop yield and reduce environmental pollution caused by excessive use of agrochemicals. In this paper, the helix-coil structural transition of gelatin was adopted to construct a novel stimuli-responsive controlled-release system called polypyrrole/Ca-alginate/gelatin (PPy/Ca-alginate/Gel). In PPy/Ca-alginate/Gel, Ca-alginate and gelatin form a semi-interpenetrating network in which uncross-linked gelatin can undergo a free helix-coil structural transition due to the photothermal effect of PPy. The structural transition of gelatin will lead to changes in the functional groups and microstructure of semi-interpenetrating hydrogels and furthermore achieve the release of template agrochemical molecules embedded in hydrogels. By using carbendazim as a template molecule, the photothermal conversion and controlled release of PPy/Ca-alginate/Gel were systematically studied. After 600 s of light irradiation, its temperature could be increased by 17 ℃. The release of carbendazim in microspheres reached 91.8 % after 8 h of light irradiation, while it was only 13.3 % in the dark. The results indicated that PPy/Ca-alginate/Gel have excellent controlled-release and sustained-release properties and broad application potential in agriculture.

Single-molecule mechanics of synthetic aromatic amide helices: Ultrafast and robust non-dissipative winding

Summary Because of proteins’ many degrees of conformational freedom, programming protein folding dynamics, overall elasticity, and motor functions remains an elusive objective. Instead, smaller and simpler objects, such as synthetic foldamers, may be amenable to design. However, little is known about their mechanical performance. Here, we show that reducing molecular size may not compromise mechanical properties. We report that helical aromatic oligoamides as small as 1 nm possess outstanding elasticity and outperform most natural helices. Using single-molecule force spectroscopy, we characterize their folding trajectories and intermediate states. We show that they cooperatively and reversibly unwind at high forces. They extend up to 3.8 times their original length and rewind against considerable forces on a timescale of 10 μs. Pulling and relaxing cycles follow the same trace up to a very high loading rate, indicating that the mechanical energy accumulated during the stretching does not dissipate and is immediately reusable.

Construction of shape memorable imprinted cavities for protein recognition using oligo-l-lysine-based peptide crosslinker

Protein-imprinted polymers are artificial receptors capable of recognizing protein. They are highly promising for applications in important bio-related areas, however, their development was severely retarded by two problems: difficult template removal and low imprinting efficiency. The two problems could be overcome by constructing shape-memorable imprinted cavities using peptide crosslinker. Here a new oligo-l-lysine-based peptide crosslinker was designed and synthesized. A novel cytochrome c (Cyt C)-imprinted polymer was synthesized using the new peptide crosslinker. When switching pH between 12 and 7.4, the peptide segments incorporated in the polymer underwent reversible helix-coil transition. Because of the precise folding of the peptide segments, the imprinted cavities in the polymer could be enlarged when lowering pH to 7.4 to release the template protein, but restore their original size and shape at pH 12 to recognize the template protein. Therefore complete template removal was achieved under mild conditions. Meanwhile the imprinting efficiency was improved significantly. Compared to polymer crosslinked with the commonly used crosslinker N, N-methylenebisacrylamide, the imprinting efficiency of the peptide-crosslinked polymer was increased by 15 times. The new imprinted polymer presented not only a high adsorption capacity (454.4 mgg−1), a high imprinting factor (6.3), high selectivity towards Cyt C, and excellent reusability, but also could preserve the fragile secondary structure of the eluted protein, and therefore had high potential in bioseparation. As a demonstration, Cyt C added into fetal bovine serum was separated from the sample using the polymer via a simple adsorption-desorption cycle. The recovery rate was as high as 92.7%.

Human serum albumin-imprinted polymers with high capacity and selectivity for abundant protein depletion

Depletion of human serum albumin (HSA), the most abundant protein in human plasma, from serum/plasma is a prerequisite before their proteomic analysis. Molecularly imprinted polymers (MIPs) using HSA as a template have been designed for this purpose, but suffer from a low sorption capacity and low selectivity. Here, a new HSA-imprinted polymer was synthesized using N-isopropylacrylamide (NIPAM) as the main monomer; acrylamide (AAm), methacrylic acid (MAA), and dimethylaminoethyl methacrylate (DMAEMA) as functional monomers; and oligoglutamic acid-based peptide crosslinker (PC) as a crosslinker at pH 5.5. When pH is adjusted to 7.4, the peptide chains in the polymer change from a helical conformation to an extended coil conformation, and the polymer swells. Consequently, the template protein is removed completely. When pH is adjusted back to 5.5, the peptide chains fold back precisely to the helical conformation. Both the size and shape of the imprint cavities are restored. Therefore, the polymer rebinds the template protein selectively. Highest imprinting factor (IF) was observed at pH 5.5 at which the polymer was synthesized. The IF increases with the increasing number of glutamic acid residues in the PCs because of their increased degree of helicity at pH 5.5. No improvement in imprinting effect was observed when using a peptide crosslinker containing both L- and D-glutamic acid residues and hence incapable of folding into α-helix, further confirming the key role of the pH-induced helix-coil transition of the peptide chains. The MIP synthesized here presents a much higher affinity to HSA than the nontemplate proteins. It could be used repeatedly without evident decrease in sorption capacity. Because of the mild eluting conditions, the secondary structure of the extracted HSA protein remains unchanged. Finally, the MIP was used to deplete HSA from human serum. Because of its high sorption capacity and high selectivity, HSA was depleted completely and selectively. Statement of significanceA new molecularly imprinted polymer (MIP) using human serum albumin (HSA) as a template was synthesized using N-isopropylacrylamide (NIPAM) as the main monomer; acrylamide (AAm), methacrylic acid (MAA), and dimethylaminoethyl methacrylate (DMAEMA) as functional monomers; and oligoglutamic acid-based peptide crosslinker as a crosslinker. Because of the reversible and precise pH-induced helix-coil transition of the peptide chains, the template protein was removed facilely and completely under mild conditions. Simultaneously, a significant improvement in imprinting efficiency was obtained. The sorption capacity was as high as 648.05 mg/g and the imprinting factor was 7.9. Because of its high selectivity and high binding capacity, the MIP synthesized here is highly promising for the depletion of HSA, the most abundant protein in serum, which is a prerequisite for its proteomic analysis. For the first time, complete and selective depletion of HSA from human serum was achieved using a protein-imprinted polymer.

Two different regimes in alcohol-induced coil-helix transition: effects of 2,2,2-trifluoroethanol on proteins being either independent of or enhanced by solvent structural fluctuations.

Inhomogeneous distribution of constituent molecules in a mixed solvent has been known to give remarkable effects on the solute, e.g., conformational changes of biomolecules in an alcohol-water mixture. We investigated the general effects of 2,2,2-trifluoroethanol (TFE) on proteins/peptides in a mixture of water and TFE using melittin as a model protein. Fluctuations and Kirkwood-Buff integrals (KBIs) in the TFE-H2O mixture, quantitative descriptions of inhomogeneity, were determined by small-angle X-ray scattering investigation and compared with those in the aqueous solutions of other alcohols. The concentration fluctuation for the mixtures ranks as methanol < ethanol ≪ TFE < tert-butanol < 1-propanol, indicating that the inhomogeneity of molecular distribution in the TFE-H2O mixture is unexpectedly comparable to those in the series of mono-ols. On the basis of the concentration dependence of KBIs between the TFE molecules, it was found that a strong attraction between the TFE molecules is not necessarily important to induce helix conformation, which is inconsistent with the previously proposed mechanism. To address this issue, by combining the KBIs and the helix contents reported by the experimental spectroscopic studies, we quantitatively evaluated the change in the preferential binding parameter of TFE to melittin attributed to the coil-helix transition. As a result, we found two different regimes on TFE-induced helix formation. In the dilute concentration region of TFE below ∼2 M, where the TFE molecules are not aggregated among themselves, the excess preferential binding of TFE to the helix occurs due to the direct interaction between them, namely independent of the solvent fluctuation. In the higher concentration region above ∼2 M, in addition to the former effect, the excess preferential binding is significantly enhanced by the solvent fluctuation. This scheme should be held as general cosolvent effects of TFE on proteins/peptides.

Иммобилизованные в матрицу геллана противоопухолевые препараты и наночастицы металлов: достижения и перспективы применения

A review is devoted to recent achievements in development of anticancer drugs based on natural polysaccharide – gellan that possesses coil-helix conformational transition, sol-gel phase transition, thermo- and salt sensitivity. The characteristics of high- and low-acyl gellan are briefly given and the influence of mono- and multivalent metal ions on the gelation efficiency is described. The mucoadhesive properties of gellan and its modified derivatives are briefly considered in the context of application in pharmacy as oral, buccal, nasal, ophthalmologic, vaginal forms. The main attention is paid to anticancer drugs, gold and silver nanoparticles immobilized within gellan matrix by chemical bonds, physical adsorption and chemosorption. The state-of-the art and perspectives of development of plasmonic photothermal therapy of cancer cells that is one of the promising direction of nanomedicine in diagnosis and treatment of oncological diseases are highlighted. It is outlined that the further strategy of development and application of plasmonic photothermal therapy into clinical practice is due to selection of metal nanoparticles with optimal sizes, high concentration, low cytotoxicity and suitable optical characteristics.