Biopolymers[JOURNAL]
Sun
200 papers
Exploring helix structures of γ-peptides based on 2-(aminomethyl)cyclopentanecarboxylic acid.
Park HS, Lee JY, Kang YK
Biopolymers · 2024 May · PMID 38465777 · Publisher ↗
Conformational search and density functional theory calculations were performed to explore the preferences of helical structures for chiro-specific oligo-γ-peptides of 2-(aminomethyl)cyclopentanecarboxylic acid (γAmc) wi...
Conformational search and density functional theory calculations were performed to explore the preferences of helical structures for chiro-specific oligo-γ-peptides of 2-(aminomethyl)cyclopentanecarboxylic acid (γAmc) with a cyclopentyl constraint on the C-C bond in solution. The dimer and tetramer of γAmc (1) with homochiral (1S, 2S) configurations exhibited a strong preference for the 9-membered helix foldamer in solution, except for the tetramer in water. However, the oligomers of γAmc (1) longer than tetramer preferentially adopted a right-handed (P)-2.6-helix (H-14) as the peptide sequence becomes longer and as solvent polarity increases. The high stabilities for H-14 foldamers of γAmc (1) in solution were ascribed to the favored solvation free energies. The calculated mean backbone torsion angles for H-14 helix foldamers of γAmc (1) were similar to those calculated for oligomers of other γ-residues with cyclopentane or cyclohexane rings. However, the substitution of cyclopentane constraints on the C-C bond of the γAmc (1) residue resulted in different conformational preferences and/or handedness of helix foldamers. In particular, the pyrrolidine-substituted analogs of the H-14 foldamers of γAmc (1) with adjacent amine diads substituted at a proximal distance are expected to be potential catalysts for the crossed aldol condensation in nonpolar and polar solvents.
Correlation between the activation energy of PLA respectively PLA/starch composites and mechanical properties with regard to differ accelerated aging conditions.
Reit M, Zarges JC, Heim HP
Biopolymers · 2024 May · PMID 38385628 · Publisher ↗
Within this research semi-crystalline polylactide and composites with 50 wt.% native potato starch were compounded and injection molded. The material was mechanically characterized by tensile, three-point bending, and Ch...
Within this research semi-crystalline polylactide and composites with 50 wt.% native potato starch were compounded and injection molded. The material was mechanically characterized by tensile, three-point bending, and Charpy impact tests. These tests were carried out in the freshly molded state and after 332 and 792 h of storage at accelerated temperature or humidity. The respective activation energy was calculated by applying the Flynn-Wall-Ozawa method. The focus of the study was to investigate the correlation between the activation energy and the related mechanical and thermal properties. The results showed that the addition of native potato starch as a filler prevents the decrease in activation energy over the course of the experiments. Thus, the PLA/starch composite is more resistant to the two aging conditions than the pure PLA. When considering the mechanical properties, the pure PLA showed a large deviation of results compared to the initial value in a range of +63.88% to -33.96% with regard to the respective aging conditions, whereas the PLA/starch composite properties nearly always remained at the initial values. Through the investigation of the mechanical and thermal properties, it was shown that the steady activation energies are consistent with the mechanical properties, as these have shown only a small deviation of the mechanical properties during the duration of experiments for the PLA/starch composite.
The energy landscape of the ribosome.
Byju S, Hassan A, Whitford PC
Biopolymers · 2024 Mar · PMID 38051695 · Publisher ↗
The ribosome is a prototypical assembly that can be used to establish general principles and techniques for the study of biological molecular machines. Motivated by the fact that the dynamics of every biomolecule is gove...
The ribosome is a prototypical assembly that can be used to establish general principles and techniques for the study of biological molecular machines. Motivated by the fact that the dynamics of every biomolecule is governed by an underlying energy landscape, there has been great interest to understand and quantify ribosome energetics. In the present review, we will focus on theoretical and computational strategies for probing the interactions that shape the energy landscape of the ribosome, with an emphasis on more recent studies of the elongation cycle. These efforts include the application of quantum mechanical methods for describing chemical kinetics, as well as classical descriptions to characterize slower (microsecond to millisecond) large-scale (10-100 Å) rearrangements, where motion is described in terms of diffusion across an energy landscape. Together, these studies provide broad insights into the factors that control a diverse range of dynamical processes in this assembly.
Structural, material and antibacterial properties of quercetin incorporated soy protein isolate films and its binding behavior through molecular docking.
Rani P, Yadav PK, Singh AK … +3 more , Nayak S, Kumar KD, Kumar R
Biopolymers · 2024 Mar · PMID 37970979 · Publisher ↗
This study aimed to investigate the three different methods for the fabrication of quercetin (1%-3% w/w of protein) incorporated soy protein isolate (SPI) films and their effect on material properties. The quercetin inco...
This study aimed to investigate the three different methods for the fabrication of quercetin (1%-3% w/w of protein) incorporated soy protein isolate (SPI) films and their effect on material properties. The quercetin incorporated SPI films prepared by these methods were characterized by Fourier transform infrared (FTIR) spectroscopy, UV-Vis spectrophotometer, tensile properties, and water uptake and leaching properties. The cross-linking pattern was revealed by the FTIR spectrum that showed formation of an ester group because of interaction between the quercetin hydroxyl group and the carboxyl side chain of SPI amino acids. The tensile strength of SPI films were enhanced with the addition of quercetin as it increased to a maximum of 6.17 MPa while neat SPI film had tensile strength 4.13 MPa. The prepared films exhibit significant antibacterial activity against Listeria monocytogenes and Escherichia coli. The In-silico docking analysis demonstrates that covalent and non-covalent forces play crucial roles in binding interaction. It shows the formation of four hydrogen bonds, two salt bridges along with one pi-alkyl interaction. The simulation studies reflect the crucial amino acid residues involved in SPI-quercetin binding. The effect of quercetin binding with SPI on its stability and compactness is revealed by Root mean square deviation (RMSD) and radius of gyration studies.
Innovations in applications and prospects of non-isocyanate polyurethane bioplastics.
Mangal M, H S, Bose S … +1 more , Banerjee T
Biopolymers · 2023 Dec · PMID 37846654 · Publisher ↗
Currently, conventional plastics are necessary for a variety of aspects of modern daily life, including applications in the fields of healthcare, technology, and construction. However, they could also contain potentially...
Currently, conventional plastics are necessary for a variety of aspects of modern daily life, including applications in the fields of healthcare, technology, and construction. However, they could also contain potentially hazardous compounds like isocyanates, whose degradation has a negative impact on both the environment and human health. Therefore, researchers are exploring alternatives to plastic which is sustainable and environmentally friendly without compromising its mechanical and physical features. This review study highlights the production of highly eco-friendly bioplastic as an efficient alternative to non-biodegradable conventional plastic. Bioplastics are produced from various renewable biomass sources such as plant debris, fatty acids, and oils. Poly-addition of di-isocyanates and polyols is a technique employed over decades to produce polyurethanes (PUs) bioplastics from renewable biomass feedstock. The toxicity of isocyanates is a major concern with the above-mentioned approach. Novel green synthetic approaches for polyurethanes without using isocyanates have been attracting greater interest in recent years to overcome the toxicity of isocyanate-containing raw materials. The polyaddition of cyclic carbonates (CCs) and polyfunctional amines appears to be the most promising method to obtain non-isocyanate polyurethanes (NIPUs). This method results in the creation of polymeric materials with distinctive and adaptable features with the elimination of harmful compounds. Consequently, non-isocyanate polyurethanes represent a new class of green polymeric materials. In this review study, we have discussed the possibility of creating novel NIPUs from renewable feedstocks in the context of the growing demand for efficient and ecologically friendly plastic products.
Polymer properties of softwood organosolv lignins produced in two different reactor systems.
Joseph P, Tanase-Opedal M, Moe ST
Biopolymers · 2023 Dec · PMID 37795978 · Publisher ↗
Lignin, the second most abundant biopolymer on earth and with a predominantly aromatic structure, has the potential to be a raw material for valuable chemicals and other bio-based chemicals. In industry, lignin is underu...
Lignin, the second most abundant biopolymer on earth and with a predominantly aromatic structure, has the potential to be a raw material for valuable chemicals and other bio-based chemicals. In industry, lignin is underutilized by being used mostly as a fuel for producing thermal energy. Valorization of lignin requires knowledge of the structure and different linkages in the isolated lignin, making the study of structure of lignin important. In this article, lignin samples isolated from two types of reactors (autoclave reactor and displacement reactor) were analyzed by FT-IR, size exclusion chromatography, thermogravimetric analysis (TGA), and Py-GC-MS. The average molecular mass of the organosolv lignins isolated from the autoclave reactor decreased at higher severities, and FT-IR showed an increase in free phenolic content with increasing severity. Except for molecular mass and molecular mass dispersity, there were only minor differences between lignins isolated from the autoclave reactor and lignins isolated from the displacement reactor. Carbohydrate analysis, Py-GC-MS and TGA showed that the lignin isolated using either of the reactor systems is of high purity, suggesting that organosolv lignin is a good candidate for valorization.
Recent advancements in bionanomaterial applications of peptide nucleic acid assemblies.
Sarkar S
Biopolymers · 2024 Mar · PMID 37792292 · Publisher ↗
Peptide nucleic acid (PNA) is a unique combination of peptides and nucleic acids. PNA can exhibit hydrogen bonding interactions with complementary nucleobases like DNA/RNA. Also, its polyamide backbone allows easy incorp...
Peptide nucleic acid (PNA) is a unique combination of peptides and nucleic acids. PNA can exhibit hydrogen bonding interactions with complementary nucleobases like DNA/RNA. Also, its polyamide backbone allows easy incorporation of biomolecules like peptides and proteins to build hybrid molecular constructs. Because of chimeric structural properties, PNA has lots of potential to build diverse nanostructures. However, progress in the PNA material field is still immature compared with its massive applications in antisense oligonucleotide research. Examples of well-defined molecular assemblies have been reported with PNA amphiphiles, self-assembling guanine-PNA monomers/dimers, and PNA-decorated nucleic acids/ polymers/ peptides. All these works indicate the great potential of PNA to be used as bionanomaterials. The review summarizes the recent reports on PNA-based nanostructures and their versatile applications. Additionally, this review shares a perspective to promote a better understanding of controlling molecular assembly by the systematic structural modifications of PNA monomers.
Experimental and theoretical estimation of the Hansen solubility parameters of paramylon esters based on the degrees of substitution and chain lengths of their acyl groups.
Ata S, Shibakami M
Biopolymers · 2023 Nov · PMID 37635653 · Publisher ↗
Paramylon is a natural hydrophilic polysaccharide produced in the pyrenoids of euglenoids, and esterification may render paramylon hydrophobic. Esterification imparts not only thermoplasticity, but also potential compati...
Paramylon is a natural hydrophilic polysaccharide produced in the pyrenoids of euglenoids, and esterification may render paramylon hydrophobic. Esterification imparts not only thermoplasticity, but also potential compatibilities with other polymer resins and fillers. However, the dependence of the compatibility on the structure of the polymer ester has not yet been systematically studied. To estimate the affinities between paramylon esters and hydrophobic organic solvents/resins, the dependences of their Hansen solubility parameters, which are association indices, on the degrees of substitution and chain lengths of the ester groups were investigated. Experimental and theoretical investigations were conducted using the dissolution and Fedors methods, respectively. Esterification decreased the solubility parameter from 49 (paramylon) to approximately 18 MPa (paramylon esters), indicating that the potential affinities of paramylon esters for hydrophobic organic solvents/polymers increased. A multiple regression analysis was also performed to investigate the effects of acyl chain length and degree of substitution with acyl groups on the solubility parameter. The solubility parameters of the paramylon derivatives were continuously variable from hydrophilic to -phobic. Hence, esterification with various acyl groups may control the hydrophobicities of paramylon esters, enhancing their miscibilities with various hydrophobic organic solvents and resins.
Investigation of biodegradability and cellular activity of PCL/PLA and PCL/PLLA electrospun webs for tissue engineering applications.
Oztemur J, Ozdemir S, Tezcan-Unlu H … +3 more , Cecener G, Sezgin H, Yalcin-Enis I
Biopolymers · 2023 Nov · PMID 37614178 · Publisher ↗
Biodegradability and cellular activity are key performance indicators that should be prioritized for tissue engineering applications. Biopolymer selection, determination of necessary structural properties, and their syne...
Biodegradability and cellular activity are key performance indicators that should be prioritized for tissue engineering applications. Biopolymer selection, determination of necessary structural properties, and their synergistic interactions play an active role in obtaining the expected biodegradability and biological activity from scaffolds. In this study, it is aimed to produce electrospun webs with improved biocompatibility by blending polycaprolactone (PCL) with polylactic acid (PLA) and poly-l-lactide (PLLA), and examine the effect of biopolymer selection and blend ratio on the biodegradability and cellular activity of surfaces. In this context, fibrous webs are produced from PCL/PLA and PCL/PLLA blends with a weight ratio of 80/20 and 50/50 and pure polymers of PCL, PLA, and PLLA by electrospinning method and subjected to morphological and biological analyses. The biodegradation tests are carried out hydrolytically while the cell viability and cell proliferation analyses are performed with adult human primary dermal fibroblasts and human umbilical endothelial cells (HUVECs). The results show that the fiber diameters of the fabricated webs ranged from 0.747 to 1.685 μm. At the end of the 5th month, it is observed that the biodegradation rates of the webs blended 50% with PLA and PLLA, in comparison to PCL ones, increase from 3.7% to 13.33% and 7.69%, respectively. On the other hand, cell culture results highlight that the addition of 20% PLA and PLLA improves the cellular activity of both cell types, but increased PLA or PLLA ratio in PCL webs has a negative effect as it makes the structure stiff and brittle.
Chemical and biological conjugation strategies for the development of multivalent protein vaccine nanoparticles.
Park J, Pho T, Champion JA
Biopolymers · 2023 Aug · PMID 37490564 · Full text
The development of subunit vaccine platforms has been of considerable interest due to their good safety profile and ability to be adapted to new antigens, compared to other vaccine typess. Nevertheless, subunit vaccines...
The development of subunit vaccine platforms has been of considerable interest due to their good safety profile and ability to be adapted to new antigens, compared to other vaccine typess. Nevertheless, subunit vaccines often lack sufficient immunogenicity to fully protect against infectious diseases. A wide variety of subunit vaccines have been developed to enhance antigen immunogenicity by increasing antigen multivalency, as well as stability and delivery properties, via presentation of antigens on protein nanoparticles. Increasing multivalency can be an effective approach to provide a potent humoral immune response by more strongly engaging and clustering B cell receptors (BCRs) to induce activation, as well as increased uptake by antigen presenting cells and their subsequent T cell activation. Proper orientation of antigen on protein nanoparticles is also considered a crucial factor for enhanced BCR engagement and subsequent immune responses. Therefore, various strategies have been reported to decorate highly repetitive surfaces of protein nanoparticle scaffolds with multiple copies of antigens, arrange antigens in proper orientation, or combinations thereof. In this review, we describe different chemical bioconjugation methods, approaches for genetic fusion of recombinant antigens, biological affinity tags, and enzymatic conjugation methods to effectively present antigens on the surface of protein nanoparticle vaccine scaffolds.
Purification effects show seed and root mucilage's ability to respond to changing rhizosphere conditions.
Diehl D, Knott M, Schaumann GE
Biopolymers · 2023 Aug · PMID 37435955 · Publisher ↗
Mucilage, a polysaccharide-containing hydrogel, is hypothesized to play a key role in the rhizosphere as a self-organized system because it may vary its supramolecular structure with changes in the surrounding solution....
Mucilage, a polysaccharide-containing hydrogel, is hypothesized to play a key role in the rhizosphere as a self-organized system because it may vary its supramolecular structure with changes in the surrounding solution. However, there is currently limited research on how these changes are reflected in the physical properties of real mucilage. This study examines the role of solutes in maize root, wheat root, chia seed, and flax seed mucilage in relation to their physical properties. Two purification methods, dialysis and ethanol precipitation, were applied to determine the purification yield, cation content, pH, electrical conductivity, surface tension, viscosity, transverse H relaxation time, and contact angle after drying of mucilage before and after purification. The two seed mucilage types contain more polar polymers that are connected to larger assemblies via multivalent cation crosslinks, resulting in a denser network. This is reflected in higher viscosity and water retention ability compared to root mucilage. Seed mucilage also contains fewer surfactants, making them better wettable after drying compared to the two root mucilage types. The root mucilage types, on the other hand, contain smaller polymers or polymer assemblies and become less wettable after drying. However, wettability not only depends on the amount of surfactants but also on their mobility, as well as the strength and mesh size of the network structure. The changes in physical properties and cation composition observed after ethanol precipitation and dialysis suggest that the polymer network of seed mucilage is more stable and specialized in protecting the seeds from unfavorable environmental conditions. In contrast, root mucilage is characterized by fewer cationic interactions and its network relies more on hydrophobic interactions. This allows root mucilage to be more flexible in responding to changing environmental conditions, facilitating nutrient and water exchange between root surfaces and the rhizosphere soil.
Influence of kepok banana bunch as new cellulose source on thermal, mechanical, and biodegradability properties of Thai cassava starch/polyvinyl alcohol hybrid-based bioplastic.
Autha N, Siregar FED, Harmiansyah … +2 more , Mahardika M, Nurfani E
Biopolymers · 2023 Sep · PMID 37435944 · Publisher ↗
Bioplastics were developed to overcome environmental problems that are difficult to decompose in the environment. This study analyzes Thai cassava starch-based bioplastics' tensile strength, biodegradability, moisture ab...
Bioplastics were developed to overcome environmental problems that are difficult to decompose in the environment. This study analyzes Thai cassava starch-based bioplastics' tensile strength, biodegradability, moisture absorption, and thermal stability. This study used Thai cassava starch and polyvinyl alcohol (PVA) as matrices, whereas Kepok banana bunch cellulose was employed as a filler. The ratios between starch and cellulose are 10:0 (S1), 9:1 (S2), 8:2 (S3), 7:3 (S4), and 6:4 (S5), while PVA was set constant. The tensile test showed the S4 sample's highest tensile strength of 6.26 MPa, a strain of 3.85%, and a modulus of elasticity of 166 MPa. After 15 days, the maximum soil degradation rate in the S1 sample was 27.9%. The lowest moisture absorption was found in the S5 sample at 8.43%. The highest thermal stability was observed in S4 (316.8°C). This result was significant in reducing the production of plastic waste for environmental remediation.
Fabrication and characterization of chlorhexidine gluconate loaded poly(vinyl alcohol)/45S5 nano-bioactive glass nanofibrous membrane for guided tissue regeneration applications.
Keçeciler-Emir C, Başaran-Elalmiş Y, Şahin YM … +2 more , Buluş E, Yücel S
Biopolymers · 2023 Oct · PMID 37421643 · Publisher ↗
Polymeric barrier membranes are used in periodontal applications to prevent fibroblastic cell migration into the cavities of bone tissue and to properly guide the proliferation of tissues. In this study, the fabrication,...
Polymeric barrier membranes are used in periodontal applications to prevent fibroblastic cell migration into the cavities of bone tissue and to properly guide the proliferation of tissues. In this study, the fabrication, characterization, bioactivity, and in vitro biological properties of polyvinyl alcohol-based nanofibrous membranes containing nano-sized 45S5 bioactive glass (BG) loaded with chlorhexidine (CH) gluconate with biocompatible, bioactive, and antibacterial properties for using as dental barrier membranes were investigated. Nanofibrous membranes with an average fiber diameter, pore size, and porosity of 210 nm, 24.73 μm, and 12.42%, respectively, were loaded with 1% and 2% CH, and the release profile was investigated. The presence of BG in the membranes promoted fibroblastic proliferation and the presence of CH provided antibacterial properties. Nanofibrous membranes exhibit a high ability to restrict bacterial growth while fulfilling the necessary conditions for use as a dental barrier thanks to their low swelling rates, significant surface bioactivities, and appropriate degradation levels.
Protocols for in vitro reconstitution of the cyanobacterial circadian clock.
Chavan A, Heisler J, Chang YG … +3 more , Golden SS, Partch CL, LiWang A
Biopolymers · 2024 Mar · PMID 37421636 · Full text
Circadian clocks are intracellular systems that orchestrate metabolic processes in anticipation of sunrise and sunset by providing an internal representation of local time. Because the ~24-h metabolic rhythms they produc...
Circadian clocks are intracellular systems that orchestrate metabolic processes in anticipation of sunrise and sunset by providing an internal representation of local time. Because the ~24-h metabolic rhythms they produce are important to health across diverse life forms there is growing interest in their mechanisms. However, mechanistic studies are challenging in vivo due to the complex, that is, poorly defined, milieu of live cells. Recently, we reconstituted the intact circadian clock of cyanobacteria in vitro. It oscillates autonomously and remains phase coherent for many days with a fluorescence-based readout that enables real-time observation of individual clock proteins and promoter DNA simultaneously under defined conditions without user intervention. We found that reproducibility of the reactions required strict adherence to the quality of each recombinant clock protein purified from Escherichia coli. Here, we provide protocols for preparing in vitro clock samples so that other labs can ask questions about how changing environments, like temperature, metabolites, and protein levels are reflected in the core oscillator and propagated to regulation of transcription, providing deeper mechanistic insights into clock biology.
Conformational fluctuations and phases in fused in sarcoma (FUS) low-complexity domain.
Thirumalai D, Kumar A, Chakraborty D … +2 more , Straub JE, Mugnai ML
Biopolymers · 2024 Mar · PMID 37399327 · Full text
The well-known phenomenon of phase separation in synthetic polymers and proteins has become a major topic in biophysics because it has been invoked as a mechanism of compartment formation in cells, without the need for m...
The well-known phenomenon of phase separation in synthetic polymers and proteins has become a major topic in biophysics because it has been invoked as a mechanism of compartment formation in cells, without the need for membranes. Most of the coacervates (or condensates) are composed of Intrinsically Disordered Proteins (IDPs) or regions that are structureless, often in interaction with RNA and DNA. One of the more intriguing IDPs is the 526-residue RNA-binding protein, Fused in Sarcoma (FUS), whose monomer conformations and condensates exhibit unusual behavior that are sensitive to solution conditions. By focussing principally on the N-terminus low-complexity domain (FUS-LC comprising residues 1-214) and other truncations, we rationalize the findings of solid-state NMR experiments, which show that FUS-LC adopts a non-polymorphic fibril structure (core-1) involving residues 39-95, flanked by fuzzy coats on both the N- and C-terminal ends. An alternate structure (core-2), whose free energy is comparable to core-1, emerges only in the truncated construct (residues 110-214). Both core-1 and core-2 fibrils are stabilized by a Tyrosine ladder as well as hydrophilic interactions. The morphologies (gels, fibrils, and glass-like) adopted by FUS seem to vary greatly, depending on the experimental conditions. The effect of phosphorylation is site-specific. Simulations show that phosphorylation of residues within the fibril has a greater destabilization effect than residues that are outside the fibril region, which accords well with experiments. Many of the peculiarities associated with FUS may also be shared by other IDPs, such as TDP43 and hnRNPA2. We outline a number of problems for which there is no clear molecular explanation.
Beyond traditional therapy: Mucoadhesive polymers as a new frontier in oral cancer management.
Das S, Bhattacharya K, Blaker JJ … +2 more , Singha NK, Mandal M
Biopolymers · 2023 Sep · PMID 37341448 · Publisher ↗
In recent times mucoadhesive drug delivery systems are gaining popularity in oral cancer. It is a malignancy with high global prevalence. Despite significant advances in cancer therapeutics, improving the prognosis of la...
In recent times mucoadhesive drug delivery systems are gaining popularity in oral cancer. It is a malignancy with high global prevalence. Despite significant advances in cancer therapeutics, improving the prognosis of late-stage oral cancer remains challenging. Targeted therapy using mucoadhesive polymers can improve oral cancer patients' overall outcome by offering enhanced oral mucosa bioavailability, better drug distribution and tissue targeting, and minimizing systemic side effects. Mucoadhesive polymers can also be delivered via different formulations such as tablets, films, patches, gels, and nanoparticles. These polymers can deliver an array of medicines, making them an adaptable drug delivery approach. Drug delivery techniques based on these mucoadhesive polymers are gaining traction and have immense potential as a prospective treatment for late-stage oral cancer. This review examines leading research in mucoadhesive polymers and discusses their potential applications in treating oral cancer.
Efficient production of fluorophore-labeled CC chemokines for biophysical studies using recombinant enterokinase and recombinant sortase.
Guan W, Zhang N, Bains A … +3 more , Sadqi M, Dupureur CM, LiWang PJ
Biopolymers · 2024 Mar · PMID 37341434 · Full text
Chemokines are important immune system proteins, many of which mediate inflammation due to their function to activate and cause chemotaxis of leukocytes. An important anti-inflammatory strategy is therefore to bind and i...
Chemokines are important immune system proteins, many of which mediate inflammation due to their function to activate and cause chemotaxis of leukocytes. An important anti-inflammatory strategy is therefore to bind and inhibit chemokines, which leads to the need for biophysical studies of chemokines as they bind various possible partners. Because a successful anti-chemokine drug should bind at low concentrations, techniques such as fluorescence anisotropy that can provide nanomolar signal detection are required. To allow fluorescence experiments to be carried out on chemokines, a method is described for the production of fluorescently labeled chemokines. First, a fusion-tagged chemokine is produced in Escherichia coli, then efficient cleavage of the N-terminal fusion partner is carried out with lab-produced enterokinase, followed by covalent modification with a fluorophore, mediated by the lab-produced sortase enzyme. This overall process reduces the need for expensive commercial enzymatic reagents. Finally, we utilize the product, vMIP-fluor, in binding studies with the chemokine binding protein vCCI, which has great potential as an anti-inflammatory therapeutic, showing a binding constant for vCCI:vMIP-fluor of 0.37 ± 0.006 nM. We also show how a single modified chemokine homolog (vMIP-fluor) can be used in competition assays with other chemokines and we report a K for vCCI:CCL17 of 14 μM. This work demonstrates an efficient method of production and fluorescent labeling of chemokines for study across a broad range of concentrations.
Alginate/chitosan hydrogels as perspective transport systems for cefotaxime.
Shilova SV, Mirgaleev GM, Romanova KA … +1 more , Galyametdinov YG
Biopolymers · 2023 Oct · PMID 37318946 · Publisher ↗
This work reports synthesis of pH-responsive alginate/chitosan hydrogel spheres with the average diameter of 2.0 ± 0.05 mm, which contain cefotaxime that is an antibiotic of the cefalosporine group. The spheres provided...
This work reports synthesis of pH-responsive alginate/chitosan hydrogel spheres with the average diameter of 2.0 ± 0.05 mm, which contain cefotaxime that is an antibiotic of the cefalosporine group. The spheres provided the cefotaxime encapsulation efficiency of 95 ± 1%. An in vitro release of cefotaxime from the spheres in the media that simulate human biological fluids in peroral delivery conditions was found to be a pH-dependent process. The analysis of cefotaxime release kinetics by the Korsmeyer-Peppas model revealed a non-Fickian mechanism of its diffusion, which may be related to intermolecular interactions occurring between the antibiotic and chitosan. Conductometry, UV spectroscopy, and IR spectroscopy were used to study complexation of chitosan with cefotaxime in aqueous media with varied pH, characterize the composition of the complexes, and calculate their stability constants. The composition of the cefotaxime-chitosan complexes was found to correspond to the 1.0:4.0 and 1.0:2.0 molar ratios of the components at pH 2.0 and 5.6, respectively. Quantum chemical modeling was used to evaluate energy characteristics of chitosan-cefotaxime complexation considering the influence of a solvent.
New insights from modelling studies and molecular dynamics simulations of the DI extracellular linker of the skeletal muscle sodium channel NaV1.4.
Robinson A, Tao E, Neeman T … +2 more , Kaehler B, Corry B
Biopolymers · 2023 Jul · PMID 37254962 · Publisher ↗
In the CryoEM-structure of the hSkMNaV1.4 ion channel (PDB:6AGF), the 59-residue DI linker peptide was omitted due to absence of electron density. This peptide is intriguing - comprised of unique sequence and found only...
In the CryoEM-structure of the hSkMNaV1.4 ion channel (PDB:6AGF), the 59-residue DI linker peptide was omitted due to absence of electron density. This peptide is intriguing - comprised of unique sequence and found only in mammalian skeletal muscle sodium ion channels. To probe potential physiological and evolutionary significance, we constructed an homology model of the complete hSkMNaV1.4 channel. Rather than a flexible random coil potentiating drift across the channel, the linker folds into a compact configuration through self-assembling secondary structural elements. Analogous sequences from 48 mammalian organisms show hypervariability with between 40% and 100% sequence similarity. To investigate structural implications, sequences from 14 representative organisms were additionally modelled. All showed highly conserved N-and C-terminal residues closely superimposed, suggesting a critical functional role. An optimally located asparagine residue within the conserved region was investigated for N-linked glycosylation and MD simulations carried out. Results suggest a complex glycan added at this site in the linker may form electrostatic interactions with the DIV voltage sensing domain and be mechanistically involved in channel gating. The relationship of unique sequence, compact configuration, potential glycosylation and MD simulations are discussed relative to SkMNaV1.4 structure and function.
Analyzing paramagnetic NMR data on target DNA search by proteins using a discrete-state kinetic model for translocation.
Yu B, Iwahara J
Biopolymers · 2024 Mar · PMID 37254885 · Full text
Before reaching their targets, sequence-specific DNA-binding proteins nonspecifically bind to DNA through electrostatic interactions and stochastically change their locations on DNA. Investigations into the dynamics of D...
Before reaching their targets, sequence-specific DNA-binding proteins nonspecifically bind to DNA through electrostatic interactions and stochastically change their locations on DNA. Investigations into the dynamics of DNA-scanning by proteins are nontrivial due to the simultaneous presence of multiple translocation mechanisms and many sites for the protein to nonspecifically bind to DNA. Nuclear magnetic resonance (NMR) spectroscopy can provide information about the target DNA search processes at an atomic level. Paramagnetic relaxation enhancement (PRE) is particularly useful to study how the proteins scan DNA in the search process. Previously, relatively simple two-state or three-state exchange models were used to explain PRE data reflecting the target search process. In this work, using more realistic discrete-state stochastic kinetics models embedded into an NMR master equation, we analyzed the PRE data for the HoxD9 homeodomain interacting with DNA. The kinetic models that incorporate sliding, dissociation, association, and intersegment transfer can reproduce the PRE profiles observed at some different ionic strengths. The analysis confirms the previous interpretation of the PRE data and shows that the protein's probability distribution among nonspecific sites is nonuniform during the target DNA search process.
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