Proportion Of Secondary Structure Research Articles

Gelation Behavior and Drug Sustained-Release Properties of a Helix Peptide Organohydrogel with pH Responsiveness.

Based on the typical similar repeat units (abcdefg)n of α-helical structure, the peptide H was designed to self-assemble into an organohydrogel in response to pH. Depending on the different pH, the proportions of secondary structure, microstructure, and mechanical properties of the gel were investigated. Circular dichroism (CD) and Fourier transform infrared (FT-IR) showed that the proportion of α-helical structure gradually increased to become dominant with the increase of pH. Combining transmission electron microscopy (TEM) and atomic force microscopy (AFM), it was found that the increase of the ordered α-helix structure promoted fiber formation. The further increase in pH changed the intermolecular forces, resulting in an increase in the α-helix content and the enhancement of helix-helix interaction, causing the gel fibers to converge into thicker and more dense ones. The temperature test showed the stable rheological properties of the organohydrogel between 20-60 °C. Drug release and cytotoxicity showed that the DOX-loaded organohydrogel could have a better release in an acidic environment, indicating its potential application as a drug local delivery carrier.

Characterization of active peptides derived from three leeches and comparison of their anti-thrombotic mechanisms using the tail vein thrombosis model in mice and metabonomics

Background and aims: The increasing incidence of cardiovascular diseases has created an urgent need for safe and effective anti-thrombotic agents. Leech, as a traditional Chinese medicine, has the effect of promoting blood circulation and removing blood stasis, but its real material basis and mechanism of action for the treatment of diseases such as blood stasis and thrombosis have not been reported.Methods: In this study, Whitmania Pigra Whitman (WPW), Hirudo nipponica Whitman (HNW) and Whitmania acranutata Whitman (WAW) were hydrolyzed by biomimetic enzymatic hydrolysis to obtain the active peptides of WPW (APP), the active peptides of HNW (APH) and the active peptides of WAW (APA), respectively. Then their structures were characterized by sykam amino acid analyzer, fourier transform infrared spectrometer (FT-IR), circular dichroism (CD) spectrometer and LC-MS. Next, the anti-thrombotic activities of APP, APH and APA were determined by carrageenan-induced tail vein thrombosis model in mice, and the anti-thrombotic mechanisms of high-dose APP group (HAPP), high-dose APH group (HAPH) and high-dose APA group (HAPA) were explored based on UHPLC-Q-Exactive Orbitrap mass spectrometry.Results: The results showed that the amino acid composition of APP, APH and APA was consistent, and the proportion of each amino acid was few different. The results of FT-IR and CD showed that there were no significant differences in the proportion of secondary structures (such as β-sheet and random coil) and infrared absorption peaks between APP, APH and APA. Mass spectrometry data showed that there were 43 common peptides in APP, APH and APA, indicating that the three have common material basis. APP, APH and APA could significantly inhibit platelet aggregation, reduce black-tail length, whole blood viscosity (WBV), plasma viscosity (PV), and Fibrinogen (FIB), and prolong coagulation time, including activated partial thrombin time (APTT), prothrombin time (PT) and thrombin time (TT). In addition, 24 metabolites were identified as potential biomarkers associated with thrombosis development. Among these, 19, 23, and 20 metabolites were significantly normalized after administration of HAPP, HAPH, and HAPA in the mice, respectively. Furthermore, the intervention mechanism of HAPP, HAPH and HAPA on tail vein thrombosis mainly involved in linoleic acid metabolism, primary bile acid biosynthesis and ether lipid metabolism.Conclusion: Our findings suggest that APP, APH and APA can exert their anti-blood stasis and anti-thrombotic activities by interfering with disordered metabolic pathways in vivo, and there is no significant difference in their efficacies.

Effect of ultrasonic thawing temperature on the quality of quick-frozen small yellow croaker (Larimichthys polyactis) and its possible mechanisms

Thawing temperature is an important factor affecting the thawing quality characteristics of quick-frozen small yellow croakers. The objective of this study was to reveal the effect of ultrasonic-assisted low-temperature (U-LT) thawing on the physicochemical quality and structural characteristics of myofibrillar protein (MPs) of quick-frozen small yellow croakers, and to select the optimal thawing temperature. The results showed that the color difference (ΔE) and total volatile basic nitrogen (TVB-N) value of the small yellow croakers gradually increased with the increase of the temperature (2 °C, 6 °C, 10 °C, 15 °C). Compared with other thawed groups, the thawed sample of U-LT 6 °C (20 kHz, 50 W/L) had the lowest thawing loss (5.44%), cooking loss (7.87%), and thiobarbituric acid-reactive substance (TBARS) value (0.24 mg MDA/kg). Moreover, the MPs obtained by U-LT 6 °C thawing had the highest total sulfhydryl content (107.84 μmol/g protein) and free amino content (275.27 mmol/g), and the proportion of secondary structure was closest to the fresh sample. Therefore, U-LT 6 °C thawing can guarantee less loss in quality of the samples than other thawing methods. Meanwhile, U-LT 6 °C thawing may ensure the quality parameters of the fish by reducing the structural changes of MPs.

Revisiting the Ramachandran plot based on statistical analysis of static and dynamic characteristics of protein structures

Ramachandran plots, which describe protein structures by plotting the dihedral angle pairs of the backbone on a two-dimensional plane, have played an important role in structural biology over the past few decades. However, despite continued discovery of new protein structures to date, the Ramachandran plot is still constructed by only a small number of data points, and further it cannot reflect the steric information of proteins. Here, we investigated the secondary structure of proteins in terms of static and dynamic characteristics. As for static feature, the Ramachandran plot was revisited for the dataset consisting of 9,148 non-redundant high-resolution protein structures released in the protein data bank until April 1, 2022. By calculating amino acid propensities, it was found that the proportion of secondary structures with respect to residue depth is directly related to their hydrophobicity. As for dynamic feature, normal mode analysis (NMA) based on an elastic network model (ENM) was carried out for the dataset using our KOSMOS web server (http://bioengineering.skku.ac.kr/kosmos/). All ENM-based NMA results were stored in the KOSMOS database, allowing researchers to use them in various ways. In this process, it was commonly found that high B-factors appeared at the edge of the alpha helix region, which was elucidated by introducing residue depth. In addition, by investigating the change in dihedral angle, it was possible to quantitatively survey the contribution of structural change of protein on the Ramachandran plot. In conclusion, our statistical analysis of protein characteristics will provide insight into a range of protein structural studies.

Evaluation of formation and proportion of secondary structure in γ-polyglutamic acid by terahertz time-domain spectroscopy

The study of secondary structure is essential for understanding peptides and proteins. Here, we measured the terahertz (THz) spectra of γ-polyglutamic acid (γ-PGA) dominated by α-helix and random coil (RC) respectively. The α-helix has two absorption peaks in the THz region, but no absorption peak is observed in the RC conformation. We believe this is because the hydrogen bonding effect leads to a higher orientation in the helix-dominated γ-PGA. At lower pH, the absorption intensity of γ-PGA increases with the induction time. Similar changes were obtained in the Fourier infrared spectroscopy (FTIR). Through the correlation analysis of THz and IR spectroscopy, it is found that the characteristic peak at 1.2 THz can be used as a sensitive indicator of the intermediate conformation of the α-helical structure. In addition, the transformation of α-helix-RC conformation is related to the peak intensity at 1.99 THz (R2 = 0.991), which preliminarily indicates that terahertz time-domain spectroscopy (THz-TDS) has the potential to become a new effective method for characterizing and evaluating secondary structure.

Effect of heat-treated tea water-insoluble protein nanoparticles on the characteristics of Pickering emulsions

Tea water-insoluble protein nanoparticles (TWIPNs) can be used as Pickering particles. However, Pickering emulsions stabilized by heat-treated TWIPNs (TWIPNPEs) were not characterized clearly. Therefore, the effect of heat-treated TWIPNs on the characteristics of Pickering emulsions was analyzed. TWIPNs became small at 60 °C and reassembled at 100 and 120 °C. Disulfide bonds and noncovalent bonds synergistically participated in the intermolecular forces of heat-treated TWIPNs. The random coil content of heat-treated TWIPNs decreased from 0.24 to 0.13 and the contents of α-helices and β-sheets increased from 0.11 to 0.27 to 0.19 and 0.30 in the proportion of secondary structure with the increase in heat-treated TWIPN temperature. High temperature (100 °C/120 °C) on TWIPN accelerated the flocculation of emulsion droplets. A potential mechanism for the changes occurring in TWIPNPEs based on heat-treated TWIPNs was proposed to exhibit the instability of TWIPNPEs stabilized by heat-treated TWIPNs due to the structural rearrangements and enhanced intermolecular forces of TWIPNs at 100 and 120 °C. Besides, heat-treated TWIPNs at 30 and 40 g/L decreased the gel-like behavior of TWIPNPEs. These results can broaden our understanding of the characteristics of TWIPNPEs stabilized by heat-treated TWIPNs for utilizing tea by-products.

Comprehensive predictions of secondary structures for comparative analysis in different species

Protein structures are directly linked to biological functions. However, there is a gap of knowledge between the decoded genome and the structure. To bridge the gap, we focused on the secondary structure (SS). From a comprehensive analysis of predicted SS of proteins in different types of organisms, we have arrived at the following findings: The proportions of SS in genomes were different among phylogenic domains. The distributions of strand lengths indicated structural limitations in all of the species. Different from bacteria and archaea, eukaryotes have an abundance of α-helical and random coil proteins. Interestingly, there was a relationship between SS and post-translational modifications. By calculating hydrophobicity moments of helices and strands, highly amphipathic fragments of SS were found, which might be related to the biological functions. In conclusion, comprehensive predictions of SS will provide valuable perspectives to understand the entire protein structures in genomes and will help one to discover or design functional proteins.

Interface Adsorption Taking the Most Advantageous Conformation for Electron Transfer Between Graphene and Cytochrome c.

Most designed functions in biomedical nanotechnology are directly influenced by interactions of biological molecules with nano surfaces. Here, we explored and detected the most favorable adsorption conformation of cytochrome c on graphene by measuring the adsorption energy, the number of contact atoms, and the minimal distance between protein and surface. From the root mean square deviation of the protein backbone, the radius of gyration, and the proportion of secondary structure, it is revealed that cytochrome c does not deform significantly and the secondary structures are preserved to a large extent. The residues, Lys, Phe and Thr contribute significantly to the adsorption of cytochrome c to graphene. The long hydrophobic and flexible alkyl tail of Lys, the π-π stacking interaction between Phe and graphene, and the presence of abundant Thr constitute the driving force for the stable adsorption of cytochrome c on graphene. Cytochrome c is adsorbed to graphene with the group heme lying almost perpendicular to the graphene, and the distance between Fe atom and the graphene is 10.15 A, which is shorter than that between electron donor and receptor in many other biosystems. All the results suggest that the most favorable adsorption takes the most advantageous conformation for electron transfer, which promotes significantly the electron transfer between graphene and cytochrome c. The findings might provide new and important information for designs of biomedical devices or products with graphene-based nanomaterials.