Biopolymers最新文献

Human papillomavirus (HPV) is recognized as the causative agent of cervical cancer in women, and it is associated with other anogenital and head/neck cancers. More than 120 types of HPV have been identified and many classified as high- or low-risk according to their oncogenic potential. One of its proteins, E6, has evolved to overcome the oncosuppressor functions of p53 by targeting this protein for degradation via interaction with the human ubiquitin-ligase E6AP. This study evaluates the correlation between the association strength of 40 HPV E6 types to the E6AP/p53 complex and the HPV oncogenesis risk using molecular simulations and machine and deep learning (ML/DL). In addition, a ML/DL-driven prediction is proposed for the HPV unclassified oncogenic risk type. The results indicate that thermodynamics play a pivotal role in the establishment of HPV-associated cancer and highlight the need to include some viral types in the HPV-related cancer surveillance and prevention strategies.

The biological functions of polysaccharides are influenced by their chemistry and chain conformation, which have resulted in various functional applications and new uses for polysaccharides in recent years. Sacran is an intriguing ampholytic polysaccharide with several key properties such as metal adsorption, anti-inflammatory nature, and transdermal drug-carrying capacity. It has an extremely high molecular weight over 10⁷ g/mol, which is much higher than those of the previously reported microbial polysaccharides. In particular, it has a remarkable self-orienting characteristic over a large length scale, which could produce a bundle with twisted morphologies from the nanoscale to the microscale with diameters of ~1 μm and lengths of >800 μm. In this review, morphological variations, as well as novel self-organization and hierarchical self-assembly are comprehensively discussed. Sacran fibers deform into various forms, such as two- and three-dimensional flexible fibers and micro–nano fragments, during their evaporation. The self-assembly and disassembly of the sacran are explained in terms of the preparation process and factors that influence the morphology. This review will pave the way for the development of novel modules such as humidity-sensitive actuators, micro-patterned cell scaffolds, and uniaxially oriented membranes.

Elastin-like peptides (ELPs) are thermoresponsive biopolymers inspired by the characteristic repetitive sequences of natural elastin. As ELPs exhibit temperature-dependent reversible self-assembly, they are expected to be biocompatible thermoresponsive materials for drug delivery carriers. One of the most widely studied ELPs in this field is the repetitive pentapeptide, (VPGXG)_n. We previously reported that phenylalanine-containing ELP (Fn) analogs, in which the former Val residue of the repetitive sequence (VPGVG)_n is replaced by Phe, show coacervation with a short chain length (n = 5). Owing to their short sequences, Fn analogs are easily modified in amino acid sequences via simple chemical synthesis, and are useful for investigating the relationship between peptide sequences and temperature responsiveness. In this study, we developed Fn analogs by replacing Phe residue(s) with other amino acids or introducing another amino acid at the N-terminus. The temperature responsiveness of the Fn analogs changed drastically with the substitution of a single Phe residue, suggesting that aromatic amino acids play an important role in their self-assembly. In addition, the self-assembling ability of Fn was enhanced by increasing the bulkiness of the N-terminal amino acids. Therefore, the N-terminal residue was considered to be important for hydrophobicity-induced intermolecular interactions between the peptides during coacervation.

The redeposition of lignin to the fiber surface after organosolv pretreatment was studied using two different reactor types. Results from the conventional autoclave reactor suggest that redeposition occurs during the cooling down stage. Redeposited particles appeared to be spherical in shape. The size and population density of the particles depends on the concentration of organosolv lignin in the cooking liquor, which is consistent with the hypothesis that reprecipitation of lignin occurs when the system is cooled down. The use of a displacement reactor showed that displacing the spent cooking liquor with fresh cooking liquor helps in reducing the redeposition and the inclusion of a washing stage with fresh cooking liquor reduced the reprecipitation of lignin, particularly on the outer fiber surfaces. Redeposition of lignin was still observed on regions that were less accessible to washing liquid, such as fiber lumens, suggesting that complete prevention of redeposition was not achieved.

The aims of this study were to analyze the plasticizing effect of Apis mellifera honey on the mechanical, physicochemical and optical properties of whey protein isolate (WPI) films and to compare the results collected with the plasticizing effect of glycerol on WPI-films. Response surface was applied to optimize the amounts of WPI and glycerol in order to obtain films with higher tensile strength (TS), moderate elongation, and lower water vapor permeability so that they could be used as reference films. Honey was added at different concentrations (60%, 80%, and 100%) of g honey/100 g WPI, as a plasticizer to the WPI-films. In comparison to glycerol-plasticized films, an increase in the percentage of honey produced a reduction of 20 ± 10 to 48 ± 0.5% of TS, a 66 ± 0.5% lower in Young's modulus (WPI-films with 100% honey), and an increase of 186 ± 11% in elongation at break in the WPI-films with 100% honey. Honey-plasticized WPI-films were from 29 ± 11 to 43 ± 3% less permeable to water vapor than glycerol-plasticized WPI films. The mechanical characteristics of the 80% honey formulation did not differ significantly from those of the reference film (p > 0.05). Findings from this study indicate that honey has great potential as a plasticizer in WPI-films.

Translocation of positively charged cell penetrating peptides (CPP) through cell membrane is important in drug delivery. Here we report all-atom molecular dynamics simulations to investigate how a biphosphate salt in a solvent affects the interaction of a CPP, HIV-1 Tat peptide with model dipalmitoylphosphatidylcholine (DPPC) lipid bilayer. Tat peptide has a large number of basic arginines and a couple of polar glutamines. We observe that in absence of salt, the basic residues of the polypeptide get localized in the vicinity of the membrane without altering the bilayer properties much; polypeptide induce local thinning of the bilayer membrane at the area of localization. In presence of biphosphate salt, the basic residues, dressed by the biphosphate ions, are repelled by the phosphate head groups of the lipid molecules. However, polar glutamine prefers to stay in the vicinity of the bilayer. This leads to larger local bilayer thickness at the contact point by the polar residue and non-uniform bilayer thickness profile. The thickness deformation of bilayer structure disappears upon mutating the polar residue, suggesting importance of the polar residue in bilayer deformation. Our studies point to control bilayer deformation by appropriate peptide sequence and solvent conditions.

Specific recognition of DNA base sequences by proteins is vital for life-cycles of all organisms. In a large number of crystal structures of protein–DNA complexes, DNA conformation significantly deviates from the canonical B-DNA structure. A key question is whether such alternate conformations exist prior to protein binding and one is selected for complexation or the structure observed is induced by protein binding. Non-canonical base pairs, such as Hoogsteen base pairs, are often observed in crystal structures of protein–DNA complexes. We decided to explore whether the occurrence of such non-canonical base pairs in protein–DNA complexes is induced by the protein or is selected from pre-existing conformations. Detailed quantum chemical calculations with dispersion-corrected density functional theory (DFT-D) indicated that most of the non-canonical base pairs with DNA bases are stable even in the absence of the interacting amino acids. However, the G:G Hoogsteen base pair, which also appears in the telomere structure, appears to be unstable in the absence of other stabilizing agents, such as positively charged amino acids. Thus, the stability of many of the non-canonical base pair containing duplexes may be close to the canonical B-DNA structure and hence energetically accessible in the ground state; suggesting that the selection from pre-existing conformations may be an important mechanism for observed non-canonical base pairs in protein–DNA complexes.

Article First Published: 19 October 2021.

DOI: 10.1002/bip.23477

[Article in Biopolymers DOI: 10.1002/bip.23477]

In the published article above, there was an error in reference 136.

Non-viral gene carriers have shown noticeable potential in gene delivery because of limited side effects, biocompatibility, simplicity, and the ability to take advantage of electrostatic interactions. However, the low transfection rate of non-viral vectors under physiological conditions is controversial. This study aimed to decrease the transfection time using a static magnetic field. We used self-assembled cationic polysaccharides based on dextran–stearic acid–spermine (DSASP) conjugates associated with Fe₃O₄ superparamagnetic nanoparticles to investigate their potential as gene carriers to promote the target delivery. Our findings illustrate that the magnetic nanoparticles are spherical with a positive surface charge and exhibit superparamagnetic behavior. The DSASP–pDNA/Fe₃O₄ complexes offered a strong pDNA condensation, protection against DNase degradation, and significant cell viability in HEK 293T cells. Our results demonstrated that although conjugation of stearic acid could play a role in transfection efficiency, DSASP magnetic carriers with more spermine derivatives showed better affinity between the amphiphilic polymer and the negatively charged cell membrane.