Wet-Stable Lamellar Wood Sponge with High Elasticity and Fatigue Resistance Enabled by Chemical Cross-Linking

The excessive consumption of fossil-based plastics and the associated environmental concerns motivate the increasing exploitation of sustainable biomass-based materials for advanced applications. Natural wood-derived lamellar wood sponges via a top-down approach have recently attracted significant attention; however, the insufficient compressive fatigue resistance and lack of structural stability in water limit their wide applications. Here, we report a facile chemical cross-linking strategy to tackle these challenges, by which the cellulose fibrils in the lamellas are covalently bridged to enhance their connectivity. The cross-linked wood sponges demonstrate high compressibility up to 70% strain and exceptional compressive fatigue resistance (∼5% plastic deformation after 10,000 cycles at 50% strain). The interfibrillar cross-linking inhibits the swelling of cellulose fibrils and preserves the arch-shaped lamellas of the sponge in water, endowing the wood sponge with excellent wet stability. Such highly elastic and wet-stable lamellar wood sponges offer a sustainable alternative to synthetic polymer-based sponges used in diverse applications.

Structural insight into the ZFAND1-p97 interaction involved in stress granule clearance

Arsenite-induced stress granule (SG) formation can be cleared by the ubiquitin-proteasome system aided by the ATP-dependent unfoldase p97. ZFAND1 participates in this pathway by recruiting p97 to trigger SG clearance. ZFAND1 contains two An1-type zinc finger domains (ZF1 and ZF2), followed by a ubiquitin-like domain (UBL); but their structures are not experimentally determined. To shed light on the structural basis of the ZFAND1-p97 interaction, we determined the atomic structures of the individual domains of ZFAND1 by solution-state NMR spectroscopy and X-ray crystallography. We further characterized the interaction between ZFAND1 and p97 by methyl NMR spectroscopy and cryo-EM. 15N spin relaxation dynamics analysis indicated independent domain motions for ZF1, ZF2, and UBL. The crystal structure and NMR structure of UBL showed a conserved β-grasp fold homologous to ubiquitin and other UBLs. Nevertheless, the UBL of ZFAND1 contains an additional N-terminal helix that adopts different conformations in the crystalline and solution states. ZFAND1 uses the C-terminal UBL to bind to p97, evidenced by the pronounced line-broadening of the UBL domain during the p97 titration monitored by methyl NMR spectroscopy. ZFAND1 binding induces pronounced conformational heterogeneity in the N-terminal domain of p97, leading to a partial loss of the cryo-EM density of the N-terminal domain of p97. In conclusion, this work paved the way for a better understanding of the interplay between p97 and ZFAND1 in the context of SG clearance.

Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS

Chemical cross-linking with mass spectrometry provides low-resolution structural information on proteins in cells and tissues. Combined with quantitation, it can identify changes in the interactome between samples, for example, control and drug-treated cells or young and old mice. A difference can originate from protein conformational changes that alter the solvent-accessible distance separating the cross-linked residues. Alternatively, a difference can result from conformational changes localized to the cross-linked residues, for example, altering the solvent exposure or reactivity of those residues or post-translational modifications of the cross-linked peptides. In this manner, cross-linking is sensitive to a variety of protein conformational features. Dead-end peptides are cross-links attached only at one end to a protein with the other terminus being hydrolyzed. As a result, changes in their abundance reflect only conformational changes localized to the attached residue. For this reason, analyzing both quantified cross-links and their corresponding dead-end peptides can help elucidate the likely conformational changes giving rise to observed differences in cross-link abundance. We describe analysis of dead-end peptides in the XLinkDB public cross-link database and, with quantified mitochondrial data isolated from failing heart versus healthy mice, show how a comparison of abundance ratios between cross-links and their corresponding dead-end peptides can be leveraged to reveal possible conformational explanations.

Investigation of Cross-Linked Chitosan-Based Membranes as Potential Adsorbents for the Removal of Cu2+ Ions from Aqueous Solutions

Rapid industrialization has led to huge amounts of organic pollutants and toxic heavy metals into aquatic environment. Among the different strategies explored, adsorption remains until the most convenient process for water remediation. In the present work, novel cross-linked chitosan-based membranes were elaborated as potential adsorbents of Cu²⁺ ions, using as cross-linking agent a random water-soluble copolymer P(DMAM-co-GMA) of glycidyl methacrylate (GMA) and N,N-dimethylacrylamide (DMAM). Cross-linked polymeric membranes were prepared through casting aqueous solutions of mixtures of P(DMAM-co-GMA) and chitosan hydrochloride, followed by thermal treatment at 120 °C. After deprotonation, the membranes were further explored as potential adsorbents of Cu²⁺ ions from aqueous CuSO₄ solution. The successful complexation of copper ions with unprotonated chitosan was verified visually through the color change of the membranes and quantified through UV-vis spectroscopy. Cross-linked membranes based on unprotonated chitosan adsorb Cu²⁺ ions efficiently and decrease the concentration of Cu²⁺ ions in water to a few ppm. In addition, they can act as simple visual sensors for the detection of Cu²⁺ ions at low concentrations (~0.2 mM). The adsorption kinetics were well-described by a pseudo-second order and intraparticle diffusion model, while the adsorption isotherms followed the Langmuir model, revealing maximum adsorption capacities in the range of 66-130 mg/g. Finally, it was shown that the membranes can be effectively regenerated using aqueous H₂SO₄ solution and reused.

Engineered Living Bacteriophage-Enabled Self-Adjuvanting Hydrogel for Remodeling Tumor Microenvironment and Cancer Therapy

Due to the complexity and heterogeneity in the tumor microenvironment, the efficacy of breast cancer treatment has been significantly impeded. Here, we established a living system using an engineered M13 bacteriophage through chemical cross-linking and biomineralization to remodel the tumor microenvironment. Chemically cross-linking of the engineered bacteriophage gel (M13 Gel) could in situ synthesize photothermal palladium nanoparticles (PdNPs) on the pVIII capsid protein to obtain M13@Pd Gel. In addition, NLG919 was further loaded into a gel to form (M13@Pd/NLG gel) for down-regulating the expression of tryptophan metabolic enzyme indoleamine 2,3-dioxygenase 1 (IDO1). Both in vitro and in vivo studies showed that the M13 bacteriophage served not only as a cargo-loaded device but also as a self-immune adjuvant, which induced the immunogenic death of tumor cells effectively and down-regulated IDO1 expression. Such a bioactive gel system constructed by natural living materials could reverse immunosuppression and significantly improve the anti-breast cancer response.

AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome

Intrinsically disordered proteins/regions (IDPRs) are a very large and functionally important class of proteins that participate in weak multivalent interactions in protein complexes. They are recalcitrant for interrogations using X-ray crystallography and cryo-EM. The IDPRs observed at the interface of the photosynthetic pigment protein complexes (PPCs) remain much less clear, e.g., the major cyanobacterial light-harvesting complex (PBS) contains an unstructured PB-loop insertion in the phycocyanobilin domain (PB domain) of ApcE (the largest polypeptide in PBS). Here, a joint platform is built to probe such structural domains. This platform is characterized by two-round progressive justifications of in silico models by using the structural mass spectrometry data. First, the AlphaFold-generated 3D structure of the PB domain (containing PB-loop) was justified in the context of PBS. Second, docking the AlphaFold-generated ApcG (a ligand) into the first-step justified structure (a receptor). The final ligand-receptor complex was then subjected to a second-round justification, again, by using unequivocal isotopically-encoded cross-links identified in LC-MS/MS. This work reveals a full-length PB-loop structure modelled in the PBS basal cylinder, free from any spatial conflicts against the other subunits in PBS. The structure of PB domain highlights the close associations of the intrinsically disordered PB-loop with its binding partners in PBS, including ApcG, another IDPR. The PB-loop region involved in the binding of photosystem II (PSII) is also discussed in the context of excitation energy transfer regulation. This work calls attention to the highly disordered, yet interrogatable interface between the light-harvesting antenna complexes and the reaction centers.

Nanobodies and chemical cross-links advance the structural and functional analysis of PI3Kα

Nanobodies and chemical cross-linking were used to gain information on the identity and positions of flexible domains of PI3Kα. The application of chemical cross-linking mass spectrometry (CXMS) facilitated the identification of the p85 domains BH, cSH2, and SH3 as well as their docking positions on the PI3Kα catalytic core. Binding of individual nanobodies to PI3Kα induced activation or inhibition of enzyme activity and caused conformational changes that could be correlated with enzyme function. Binding of nanobody Nb3-126 to the BH domain of p85α substantially improved resolution for parts of the PI3Kα complex, and binding of nanobody Nb3-159 induced a conformation of PI3Kα that is distinct from known PI3Kα structures. The analysis of CXMS data also provided mechanistic insights into the molecular underpinning of the flexibility of PI3Kα.

Evaluation of Physically and/or Chemically Modified Chitosan Hydrogels for Proficient Release of Insoluble Nystatin in Simulated Fluids

To avoid fungal spreading in the bloodstream and internal organs, many research efforts concentrate on finding appropriate candidiasis treatment from the initial stage. This paper proposes chitosan-based physically or chemically cross-linked hydrogels aimed to provide sustained release of micronized nystatin (NYSm) antifungal drug, known for its large activity spectrum. Nystatin was demonstrated itself to provide hydrodynamic/mechanic stability to the chitosan hydrogel through hydrophobic interactions and H-bonds. For chemical cross-linking of the succinylated chitosan, a non-toxic diepoxy-functionalized siloxane compound was used. The chemical structure and composition of the hydrogels, also their morphology, were evidenced by infrared spectroscopy (FTIR), by energy dispersive X-ray (EDX) analysis and by scanning electron microscopy (SEM), respectively. The hydrogels presented mechanical properties which mimic those of the soft tissues (elastic moduli < 1 MPa), necessary to ensure matrix accommodation and bioadhesion. Maximum swelling capacities were reached by the hydrogels with higher succinic anhydride content at both pH 7.4 (429%) and pH 4.2 (471%), while higher amounts of nystatin released in the simulative immersion media (57% in acidic pH and 51% in pH 7.4) occurred from the physical cross-linked hydrogel. The release mechanism by non-swellable matrix diffusion and the susceptibility of three Candida strains make all the hydrogel formulations effective for NYSm local delivery and for combating fungal infections.

Novel Trends in Hydrogel Development for Biomedical Applications: A Review

Nowadays, there are still numerous challenges for well-known biomedical applications, such as tissue engineering (TE), wound healing and controlled drug delivery, which must be faced and solved. Hydrogels have been proposed as excellent candidates for these applications, as they have promising properties for the mentioned applications, including biocompatibility, biodegradability, great absorption capacity and tunable mechanical properties. However, depending on the material or the manufacturing method, the resulting hydrogel may not be up to the specific task for which it is designed, thus there are different approaches proposed to enhance hydrogel performance for the requirements of the application in question. The main purpose of this review article was to summarize the most recent trends of hydrogel technology, going through the most used polymeric materials and the most popular hydrogel synthesis methods in recent years, including different strategies of enhancing hydrogels’ properties, such as cross-linking and the manufacture of composite hydrogels. In addition, the secondary objective of this review was to briefly discuss other novel applications of hydrogels that have been proposed in the past few years which have drawn a lot of attention.

Improved Interpretation of Protein Conformational Differences and Ligand Occupancy in Large-Scale Cross-Link Data

Chemical cross-linking of proteins in complex samples, cells, or even tissues is emerging to provide unique structural information on proteins and complexes that exist within native or nativelike environments. The public database XLinkDB automatically maps cross-links to available structures based on sequence homology. Structures most likely to reflect protein conformations in the cross-linked sample are routinely identified by having cross-linked residues separated by Euclidean distances within the maximum span of the applied cross-linker. Solvent accessible surface distance (SASD), which considers the accessibility of the cross-linked residues and the path connecting them, is a better predictor of consistency than the Euclidean distance. However, SASDs of structures are not publicly available, and their calculation is computationally intensive. Here, we describe in XLinkDB version 4.0 the automatic calculation of SASDs using Jwalk for all cross-links mapped to structures, both with and without regard to ligands, and derive empirical maximum SASD spans for BDP-NHP and DSSO cross-linkers of 51 and 43 Å, respectively. We document ligands proximal to cross-links in structures and demonstrate how SASDs can be used to help infer sample protein conformations and ligand occupancy, highlighting cross-links sensitive to ADP binding in mitochondria isolated from HEK293 cells.

Cogel Strategy for the Preparation of a "Thorn"-Like Porous Halloysite/Gelatin Composite Aerogel with Excellent Mechanical Properties and Thermal Insulation

This work presents the preparation and property characterization of a biomass gelatin (GA)-based aerogel. Halloysite nanotubes (HNTs) were used to improve the mechanical strength, pore size distribution, and thermal stability of the aerogel. Polyethyleneimine (PEI) and (3-glycidyloxypropyl)trimethoxysilane (GPTMS) were utilized to increase the interfacial interaction between HNTs and GA through chemical cross-linking. Green, sustainable, and low-cost composite aerogels were prepared by "cogel" and freeze-drying techniques. The experimental results show that the HNTs/GA composite aerogel has a low density (31.98-57.48 mg/cm³), a high porosity (>95%), a low thermal conductivity (31.85-40.16 mW m^-1 K^-1), and superior moldability. In addition, the mechanical strength and thermal insulation properties of the HNTs/GA composite aerogels with a "thorn"-like lamellar porous network structure are different in the axial direction versus the radial direction. The maximum compressive strength, maximum compressive modulus, and corresponding specific modulus in the axial direction were 1.81 MPa, 5.45 MPa, and 94.8 kN m kg^-1, respectively. Therefore, the biomass/clay composite aerogel will be a sustainable and renewable functional material with high mechanical strength and thermal insulation properties, which is expected to further promote biomass and clay for high value utilization.

pH Dependence of Succinimide-Ester-Based Protein Cross-Linking for Structural Mass Spectrometry Applications

Within the research field of cross-linking mass spectrometry (XL-MS), the most commonly used cross-linking reagents are succinimide-ester-based (e.g., disuccinimidyl suberate (DSS)). These reagents primarily cross-link lysine side chains. So far, they have predominantly been used to investigate protein structures at neutral to slightly basic pH (7.0-8.5) to ensure the reactivity of the primary amine of the lysine side chain. However, disease-related molecular processes are not limited to such pH ranges; e.g., some important biological pathways are active in acidic intracellular compartments. The applicability of lysine-reactive cross-linking reagents to low-pH conditions remains unclear. Here, we cross-linked a mixture of eight model proteins at eight different pH conditions (pH 4.0-7.5) to investigate the pH dependency of DSS. DSS was able to cross-link proteins even at pH 4.0, but a clear decrease in the cross-linking efficiency was observed when the pH was lowered. Nevertheless, at pH 5.0, approximately half of the number of cross-links observed at pH 7.5 could still be identified. These findings highlight the ability of succinimide-based cross-linking reagents to be useful in probing the structure of proteins in a slightly acidic environment.

Developing sulfur-doped titanium oxide nanoparticles loaded chitosan/cellulose-based proangiogenic dressings for chronic ulcer and burn wounds healing

Development of biomaterials supporting angiogenesis are highly desired in medical applications. In current work, chitosan and cellulose were cross-linked by using triethyl orthoformate and loaded with sulfur-doped titanium oxide nanoparticles. A readily available and inexpensive titanium oxide was added as a potential proangiogenic agent based on our group findings and other reports on metal oxide nanoparticles activity to stimulate angiogenesis. A simple freeze gelation method led to the development of flexible, foldable, and porous membranes. To investigate the chemical characteristics of the synthesized membranes, Fourier-transform infrared spectroscopy was used. Scanning electron microscopy equipped with energy-dispersive X-ray microanalysis was employed for surface morphological investigations. The cross-linked membranes showed higher degree of swelling capacity compared to the same material with titania-loaded nanoparticles in vitro. The synthesized materials showed higher degree of degradation in H₂ O₂ as compared to phosphate-buffered saline and lysozyme. Chorioallantoic membrane assay was done to investigate the angiogenic potential. Titanium oxide nanoparticles loaded membranes (CLHTS-5 wt%) exhibited the best degree of angiogenesis in comparison to the other tested materials. In CLHTS-5 wt% experimental group, a good level of attachment and ingrowth of several blood vessels was observed. Interestingly, the same tested group (CLHTS-5 wt%) had shown the increasing trend of cellular metabolic rate of the seeded cells from Day 0 to Day 7 in vitro. These findings were further confirmed by the decline in lactate dehydrogenase enzyme release which was monitored until 72 h, indicating the promising ability of this biomaterial in wound healing applications.

Photoinduced Porcine Gelatin Cross-Linking by Homobi- and Homotrifunctional Tetrazoles

Gelatin is a costless polypeptide material of natural origin, able to form hydrogels that are potentially useful in biomaterial scaffold design for drug delivery, cell cultures, and tissue engineering. However, gelatin hydrogels are unstable at physiological conditions, losing their features only after a few minutes at 37 °C. Accordingly, treatments to address this issue are of great interest. In the present work, we propose for the first time the use of bi- and trifunctional tetrazoles, most of them unknown to date, for photoinduced gelatin cross-linking towards the production of physiologically stable hydrogels. Indeed, after UV-B irradiation, aryl tetrazoles generate a nitrilimine intermediate that is reactive towards different functionalities, some of them constitutively present in the amino acid side chains of gelatin. The efficacy of the treatment strictly depends on the structure of the cross-linking agent used, and substantial improved stability was observed by switching from bifunctional to trifunctional cross-linkers.

Deciphering the architecture and interactome of hnRNP proteins and enigmRBPs

RNA-binding proteins (RBPs) have conserved domains and consensus sequences that interact with RNAs and other proteins forming ribonucleoprotein (RNP) complexes. RNPs are involved in the regulation of several cellular processes, including transcription, pre-mRNA splicing, mRNA transport, localization, degradation and storage, and ultimately control of translation. Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RBPs that mediate transcription control and nuclear processing of transcripts. Some hnRNPs are part of the spliceosome complex, a dynamic machinery formed by RNPs that regulate alternative splicing of pre-mRNAs. Here, chemical crosslinking of proteins was applied to identify specific interacting regions and protein structural features of hnRNPs: hnRNPA1, hnRNPA2/B1, hnRNPC, and RALY. The results reveal interaction of these proteins within RNA-binding domains and conserved motifs, providing evidence of a coordinated action of known regulatory sequences of RBPs. Moreover, these crosslinking data enable structural model generation for RBPs, illustrating how crosslinking mass spectrometry can complement other structural methods.

Pharmacokinetic variables of medium molecular weight cross linked chitosan nanoparticles to enhance the bioavailability of 5-fluorouracil and reduce the acute oral toxicity

To prepare glutaraldehyde-based cross-linked medium molecular weight chitosan nanoparticles encapsulated with 5-Fluorouracil (5-FU), to overcome dosing frequency as well as reducing acute oral toxicity and poor bioavailability of the drug. Medium molecular weight chitosan nanoparticles (MMWCH-NPs) were prepared by reverse micelles method based on glutaraldehyde (GA) cross-linking and optimized by the process as well as formulation variables like a various drug to polymer ratio, cross-linker volumes, varying stirring speeds (rpm), different time of rotation/stirring, respectively and their effects on the mean particles size distribution and entrapment efficiency %EE and %LC of NPs. Characterization of formulations was done by FTIR studies, TEM, PXRD, TGA, Stability, and dissolution drug release studies were performed by dialysis bag technique at both pH (1.2 & 7.4) and acute oral toxicity studies in albino rabbits. The formulated nanoparticles showed a smooth morphology with smaller particle size distribution (230–550 nm), zeta potential (−15 to −18 mV) required to achieve enhanced permeation and retention effect (EPR), entrapment efficiency (%EE 12–59%). These NPs exhibited a controlled drug release profile with 84.36% of the drug over a period of 24 h. Drug release data were fitted to different kinetic models which predominantly followed Fickian diffusion mechanism (R² = 0.972–0.976, N = 0.326–0.256). The optimized formulation (5-FU6) was observed under DSC/TGA, TEM. PXRD curves, FTIR, which confirmed thermal stability, structural integrity, amorphous state, compatibility between drug and polymer of optimized (5-FU6) as well as reduced acute oral toxicity in albino rabbits. Cross-linked medium molecular weight chitosan nanoparticles are nontoxic, well-tolerated therefore could be the future candidate for therapeutic effects as novel drug delivery carrier for anticancer drug(s).

Construction of the Cellulose Nanofibers (CNFs) Aerogel Loading TiO2 NPs and Its Application in Disposal of Organic Pollutants

Aerogels have been widely used in the adsorption of pollutants because of their large specific surface area. As an environmentally friendly natural polysaccharide, cellulose is a good candidate for the preparation of aerogels due to its wide sources and abundant polar groups. In this paper, an approach to construct cellulose nanofibers aerogels with both the good mechanical property and the high pollutants adsorption capability through chemical crosslinking was explored. On this basis, TiO₂ nanoparticles were loaded on the aerogel through the sol-gel method followed by the hydrothermal method, thereby the enriched pollutants in the aerogel could be degraded synchronously. The chemical cross-linker not only helps build the three-dimensional network structure of aerogels, but also provides loading sites for TiO₂. The degradation efficiency of pollutants by the TiO₂@CNF Aerogel can reach more than 90% after 4 h, and the efficiency is still more than 70% after five cycles. The prepared TiO₂@CNF Aerogels have high potential in the field of environmental management, because of the high efficiency of treating organic pollutes and the sustainability of the materials. The work also provides a choice for the functional utilization of cellulose, offering a valuable method to utilize the large amount of cellulose in nature.

Synthesis and Characterization of Biocompatible Methacrylated Kefiran Hydrogels: Towards Tissue Engineering Applications

Hydrogel application feasibility is still limited mainly due to their low mechanical strength and fragile nature. Therefore, several physical and chemical cross-linking modifications are being used to improve their properties. In this research, methacrylated Kefiran was synthesized by reacting Kefiran with methacrylic anhydride (MA). The developed MA-Kefiran was physicochemically characterized, and its biological properties evaluated by different techniques. Chemical modification of MA-Kefiran was confirmed by ¹H-NMR and FTIR and GPC-SEC showed an average Mw of 793 kDa (PDI 1.3). The mechanical data obtained revealed MA-Kefiran to be a pseudoplastic fluid with an extrusion force of 11.21 ± 2.87 N. Moreover, MA-Kefiran 3D cryogels were successfully developed and fully characterized. Through micro-CT and SEM, the scaffolds revealed high porosity (85.53 ± 0.15%) and pore size (33.67 ± 3.13 μm), thick pore walls (11.92 ± 0.44 μm) and a homogeneous structure. Finally, MA-Kefiran revealed to be biocompatible by presenting no hemolytic activity and an improved cellular function of L929 cells observed through the AlamarBlue^® assay. By incorporating methacrylate groups in the Kefiran polysaccharide chain, a MA-Kefiran product was developed with remarkable physical, mechanical, and biological properties, resulting in a promising hydrogel to be used in tissue engineering and regenerative medicine applications.

LinX: A Software Tool for Uncommon Cross-Linking Chemistry

Chemical cross-linking mass spectrometry has become a popular tool in structural biology. Although several algorithms exist that efficiently analyze data-dependent mass spectrometric data, the algorithm to identify and quantify intermolecular cross-links located at the interaction interface of homodimer molecules was missing. The algorithm in LinX utilizes high mass accuracy for ion identification. In contrast with standard data-dependent analysis, LinX enables the elucidation of cross-linked peptides originating from the interaction interface of homodimers labeled by ¹⁴N/¹⁵N, including their ratio or cross-links from protein-nucleic acid complexes. The software is written in Java language, and its source code and a detailed user's guide are freely available at https://github.com/KukackaZ/LinX or https://ms-utils.org/LinX. Data are accessible via the ProteomeXchange server with the data set identifier PXD023522.

Polyglycerol-based hydrogels and nanogels: from synthesis to applications

Hydrogels and nanogels have emerged as promising materials for biomedical applications owing to their large surface area and tunable mechanical and chemical properties. Their large surface area is well suited for bioconjugation, whilst the interior porous network can be utilized for the transport of valuable biomolecules. The use of biocompatible hydrophilic building blocks/linkers for the preparation of hydrogels and nanogels not only avoids undesired side effects within the biological system, but also retains high water content, thereby creating an environment which is very similar to extracellular matrix. Their tunable multivalency and hydrophilicity and excellent biocompatibility, together with ease of functionalization, makes polyglycerol macromonomers well suited for synthesizing cross-linked networks that can be used as extracellular matrix mimics. Here we provide an overview of the synthesis of polyglycerol-based hydrogels and nanogels for various biomedical applications.

Current Status in the Utilization of Biobased Polymers for 3D Printing Process: A Systematic Review of the Materials, Processes, and Challenges

Three-dimensional (3D) printing is a revolutionary additive manufacturing technique that allows rapid prototyping of objects with intricate architectures. This Review covers the recent state-of-the-art of biopolymers (protein and carbohydrate-based materials) application in pharmaceutical, bioengineering, and food printing and main reinforcement approaches of biomacromolecular structure for the development of 3D constructs. Some perspectives and main important limitations with the biomaterials utilization for advanced 3D printing procedures are also provided. Because of the improved the ink's flow behavior and enhance the mechanical strength of resulting printed architectures, biopolymers are the most used materials for 3D printing applications. Biobased polymers by taking advantage of modifying the ink viscosity could improve the resolution of deposited layers, printing precision, and consequently, develop well-defined geometries. In this regard, the rheological properties of printable biopolymeric-based inks and factors affecting ink flow behavior related to structural properties of printed constructs are discussed. On the basis of successful applications of biopolymers in 3D printing, it is suggested that other biomacromolecules and nanoparticles combined with the matrix can be introduced into the ink dispersions to enhance the multifunctionality of 3D structures. Furthermore, tuning the biopolymer's structural properties offers the most common and essential approach to attain the printed architectures with precisely tailored geometry. We finish the Review by giving a viewpoint of the upcoming 3D printing process and recognize some of the existing bottlenecks facing the blossoming 3D pharmaceutical, bioengineering, and food printing applications.

Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure

Biology is advanced by producing structural models of biological systems, such as protein complexes. Some systems are recalcitrant to traditional structure determination methods. In such cases, it may still be possible to produce useful models by integrative structure determination that depends on simultaneous use of multiple types of data. An ensemble of models that are sufficiently consistent with the data is produced by a structural sampling method guided by a data-dependent scoring function. The variation in the ensemble of models quantified the uncertainty of the structure, generally resulting from the uncertainty in the input information and actual structural heterogeneity in the samples used to produce the data. Here, we describe how to generate, assess, and interpret ensembles of integrative structural models using our open source Integrative Modeling Platform program (https://integrativemodeling.org).

Leveraging the Entirety of the Protein Data Bank to Enable Improved Structure Prediction Based on Cross-Link Data

XLinkDB is a fast-expanding public database now storing more than 100 000 distinct identified cross-linked protein residue pairs acquired by chemical cross-linking with mass spectrometry from samples of 12 species (J. Proteome Res. 2019, 18 (2), 753-758). Mapping identified cross-links to protein structures, when available, provides valuable guidance on protein conformations detected in the cross-linked samples. As more and more structures become available in the Protein Data Bank (Nucleic Acids Res. 2000, 28 (1), 235-242), we sought to leverage their utility for cross-link studies by automatically mapping identified cross-links to structures based on sequence homology of the cross-linked proteins with those within structures. This enables use of structures derived from organisms different from those of samples, including large multiprotein complexes and complexes in alternative states. We demonstrate utility of mapping to orthologous structures, highlighting a cross-link between two subunits of mouse mitochondrial Complex I that was mapped to 15 structures derived from five mammals, its distances there of 16.2 ± 0.4 Å indicating strong conservation of the protein interaction. We also show how multimeric structures enable reassessment of cross-links presumed to be intraprotein as potentially homodimeric interprotein in origin.

Structural Analysis of the Regulatory GAF Domains of cGMP Phosphodiesterase Elucidates the Allosteric Communication Pathway

Regulation of photoreceptor phosphodiesterase (PDE6) activity is responsible for the speed, sensitivity, and recovery of the photoresponse during visual signaling in vertebrate photoreceptor cells. It is hypothesized that physiological differences in the light responsiveness of rods and cones may result in part from differences in the structure and regulation of the distinct isoforms of rod and cone PDE6. Although rod and cone PDE6 catalytic subunits share a similar domain organization consisting of tandem GAF domains (GAFa and GAFb) and a catalytic domain, cone PDE6 is a homodimer whereas rod PDE6 consists of two homologous catalytic subunits. Here we provide the x-ray crystal structure of cone GAFab regulatory domain solved at 3.3 Å resolution, in conjunction with chemical cross-linking and mass spectrometric analysis of conformational changes to GAFab induced upon binding of cGMP and the PDE6 inhibitory γ-subunit (Pγ). Ligand-induced changes in cross-linked residues implicate multiple conformational changes in the GAFa and GAFb domains in forming an allosteric communication network. Molecular dynamics simulations of cone GAFab revealed differences in conformational dynamics of the two subunits forming the homodimer and allosteric perturbations on cGMP binding. Cross-linking of Pγ to GAFab in conjunction with solution NMR spectroscopy of isotopically labeled Pγ identified the central polycationic region of Pγ interacting with the GAFb domain. These results provide a mechanistic basis for developing allosteric activators of PDE6 with therapeutic implications for halting the progression of several retinal degenerative diseases.

Cellular Interactome Dynamics during Paclitaxel Treatment

Cell-cycle inhibitors, including paclitaxel, are among the most widely used and effective cancer therapies. However, several challenges limit the success of paclitaxel, including drug resistance and toxic side effects. Paclitaxel is thought to act primarily by stabilizing microtubules, locking cells in a mitotic state. However, the resulting cytotoxicity and tumor shrinkage rates observed cannot be fully explained by this mechanism alone. Here we apply quantitative chemical cross-linking with mass spectrometry analysis to paclitaxel-treated cells. Our results provide large-scale measurements of relative protein levels and, perhaps more importantly, changes to protein conformations and interactions that occur upon paclitaxel treatment. Drug concentration-dependent changes are revealed in known drug targets including tubulins, as well as many other proteins and protein complexes involved in apoptotic signaling and cellular homeostasis. As such, this study provides insight into systems-level changes to protein structures and interactions that occur with paclitaxel treatment.

Chavez et al. reveal interactome changes in cells treated with mitotic inhibitors using quantitative cross-linking and mass spectrometry. Cross-links reflect interaction/conformational changes specific for drug type and concentration, which are not evident by protein expression levels. Microtubule stabilization, cytoskeletal alteration, and changes to mitochondrial function are visualized in cross-link levels.

Addressing the Molecular Mechanism of Longitudinal Lamin Assembly Using Chimeric Fusions

The molecular architecture and assembly mechanism of intermediate filaments have been enigmatic for decades. Among those, lamin filaments are of particular interest due to their universal role in cell nucleus and numerous disease-related mutations. Filament assembly is driven by specific interactions of the elementary dimers, which consist of the central coiled-coil rod domain flanked by non-helical head and tail domains. We aimed to investigate the longitudinal 'head-to-tail' interaction of lamin dimers (the so-called A_CN interaction), which is crucial for filament assembly. To this end, we prepared a series of recombinant fragments of human lamin A centred around the N- and C-termini of the rod. The fragments were stabilized by fusions to heterologous capping motifs which provide for a correct formation of parallel, in-register coiled-coil dimers. As a result, we established crystal structures of two N-terminal fragments one of which highlights the propensity of the coiled-coil to open up, and one C-terminal rod fragment. Additional studies highlighted the capacity of such N- and C-terminal fragments to form specific complexes in solution, which were further characterized using chemical cross-linking. These data yielded a molecular model of the A_CN complex which features a 6.5 nm overlap of the rod ends.

Chemically Cross-Linked Cellulose Nanocrystal Aerogels for Effective Removal of Cation Dye

In this study, porous aerogels were prepared by directional freeze-drying via cross-linking cellulose nanocrystals (CNCs) with poly(methyl vinyl ether-co-maleic acid) (PMVEMA) and poly(ethylene glycol) (PEG). The thermal properties and physical adsorption performance toward cation methylene blue dye of the obtained CNC aerogels were investigated. The maximum degradation temperature was increased from 324°C of CNCs to 355°C of cross-linked CNC aerogels. The dye adsorption isotherm results showed that the maximum methylene blue adsorption capacity of CNC aerogels was 116.2 mg g⁻¹, according to the Langmuir model, which was mainly due to the electrostatic attractions between negatively charged carboxyl groups or sulfonate groups on the CNC aerogles and cation MB molecules. The reusability test showed that the CNC aerogels contained the same dye adsorption performance in five adsorption/desorption cycles. Overall, this study described an ideal alternative for water purification with high dye adsorption capacity and enhanced physical performance.

Evidence of Allosteric Coupling between Substrate Binding and Adx Recognition in the Vitamin D Carbon-24 Hydroxylase CYP24A1

Metabolic inactivation of 1,25(OH)2D3 requires molecular recognition between the mitochondrial enzyme cytochrome P450 24A1 (CYP24A1) and its cognate redox partner adrenodoxin (Adx). Recent evidence supports a model of CYP24A1 function in which substrate binding and Adx recognition are structurally linked. However, the details of this allosteric connection are not clear. In this study, we utilize chemical cross-linking coupled to mass spectrometry, nuclear magnetic resonance (NMR) spectroscopy, and CYP24A1 functional assays to inform a working model of a CYP24A1-Adx complex. We report that differential cross-linking internal to CYP24A1 points toward an Adx-induced conformational change that perturbs the F and G helices, which are required for substrate binding. Moreover, the modeled complex suggests that a semiconserved nonpolar interaction at the interface may influence CYP24A1 regioselectivity. Taken together, these findings contribute to our understanding of Adx recognition in a critical vitamin D-inactivating enzyme and provide broader insight regarding the variability inherent in CYP-Adx interactions.

A PEGDA/DNA Hybrid Hydrogel for Cell-Free Protein Synthesis

Cell-free protein synthesis (CFPS) has the advantage of rapid expression of proteins and has been widely implemented in synthetic biology and protein engineering. However, the critical problem limiting CFPS industrial application is its relatively high cost, which partly attributes to the overexpense of single-use DNA templates. Hydrogels provide a possible solution because they can preserve and reutilize the DNA templates in CFPS and have great potential in elevating the protein production yield of the CFPS. Here, we presented a low-cost hybrid hydrogel simply prepared with polyethylene glycol diacrylate (PEGDA) and DNA, which is capable of high-efficient and repeated protein synthesis in CFPS. Parameters governing protein production specific to hybrid hydrogels were optimized. Structures and physical properties of the hybrid hydrogel were characterized. Transcription and expression kinetics of solution phase system and gel phased systems were investigated. The results showed that PEGDA/DNA hydrogel can enhance the protein expression of the CFPS system and enable a repeated protein production for tens of times. This PEGDA/DNA hybrid hydrogel can serve as a recyclable gene carrier for either batch or continuous protein expression, and paves a path toward more powerful, scalable protein production and cell-free synthetic biology.

The Isotope-Labeled, MS-Cleavable Cross-Linker Disuccinimidyl Dibutyric Urea for Improved Cross-Linking/Mass Spectrometry Studies

Previous studies have shown the benefits of the amine-reactive, CID-MS/MS-cleavable cross-linker disuccinimidyl dibutyric urea (DSBU) for structural proteomics studies via cross-linking/MS (XL-MS). To further facilitate the automation of XL-MS experiments, we synthesized a deuterated (D₁₂) version of the DSBU cross-linker combining the advantages of MS-cleavable linkers and isotope labeling. The rationale of conducting XL-MS with a mixture of unlabeled and stable isotope-labeled DSBU is to obtain characteristic mass differences at the MS level indicating cross-linked species. These cross-linked species can then be selected for fragmentation by collisional activation. At the MS/MS level, the characteristic 26-u doublets arising from cleavage of the central urea group in DSBU confirm the amino acid sequences of cross-linked peptides as well as the exact cross-linking sites. D₁₂-labeled DSBU was tested on three systems with increasing complexity: (i) bovine serum albumin as purified protein, (ii) Escherichia coli ribosome as large, multimeric protein assembly, and (iii) Drosophila embryo extract as complete proteome. We demonstrate the benefits arising from the use of isotope-labeled DSBU for an automated assignment of cross-linked products. Combining isotope labeling and MS cleavability in one cross-linker resulted in higher cross-link identification numbers especially for highly complex protein mixtures.

Protein Backbone and Average Particle Dynamics in Reconstituted Discoidal and Spherical HDL Probed by Hydrogen Deuterium Exchange and Elastic Incoherent Neutron Scattering

Lipoproteins are supramolecular assemblies of proteins and lipids with dynamic characteristics critically linked to their biological functions as plasma lipid transporters and lipid exchangers. Among them, spherical high-density lipoproteins are the most abundant forms of high-density lipoprotein (HDL) in human plasma, active participants in reverse cholesterol transport, and associated with reduced development of atherosclerosis. Here, we employed elastic incoherent neutron scattering (EINS) and hydrogen-deuterium exchange mass spectrometry (HDX-MS) to determine the average particle dynamics and protein backbone local mobility of physiologically competent discoidal and spherical HDL particles reconstituted with human apolipoprotein A-I (apoA-I). Our EINS measurements indicated that discoidal HDL was more dynamic than spherical HDL at ambient temperatures, in agreement with their lipid-protein composition. Combining small-angle neutron scattering (SANS) with contrast variation and MS cross-linking, we showed earlier that the most likely organization of the three apolipoprotein A-I (apoA-I) chains in spherical HDL is a combination of a hairpin monomer and a helical antiparallel dimer. Here, we corroborated those findings with kinetic studies, employing hydrogen-deuterium exchange mass spectrometry (HDX-MS). Many overlapping apoA-I digested peptides exhibited bimodal HDX kinetics behavior, suggesting that apoA-I regions with the same amino acid composition located on different apoA-I chains had different conformations and/or interaction environments.

A biuret-derived, MS-cleavable cross-linking reagent for protein structural analysis: A proof-of-principle study

Chemical cross-linking combined with mass spectrometry (XL-MS) and computational modeling has evolved as an alternative method to derive protein 3D structures and to map protein interaction networks. Special focus has been laid recently on the development and application of cross-linkers that are cleavable by collisional activation as they yield distinct signatures in tandem mass spectra. Building on our experiences with cross-linkers containing an MS-labile urea group, we now present the biuret-based, CID-MS/MS-cleavable cross-linker imidodicarbonyl diimidazole (IDDI) and demonstrate its applicability for protein cross-linking studies based on the four model peptides angiotensin II, MRFA, substance P, and thymopentin.

Mechanically Reinforced Gelatin Hydrogels by Introducing Slidable Supramolecular Cross-Linkers

Tough mechanical properties are generally required for tissue substitutes used in regeneration of damaged tissue, as these substitutes must be able to withstand the external physical force caused by stretching. Gelatin, a biopolymer derived from collagen, is a biocompatible and cell adhesive material, and is thus widely utilized as a component of biomaterials. However, the application of gelatin hydrogels as a tissue substitute is limited owing to their insufficient mechanical properties. Chemical cross-linking is a promising method to improve the mechanical properties of hydrogels. We examined the potential of the chemical cross-linking of gelatin hydrogels with carboxy-group-modified polyrotaxanes (PRXs), a supramolecular polymer comprising a poly(ethylene glycol) chain threaded into the cavity of α-cyclodextrins (α-CDs), to improve mechanical properties such as stretchability and toughness. Cross-linking gelatin hydrogels with threading α-CDs in PRXs could allow for freely mobile cross-linking points to potentially improve the mechanical properties. Indeed, the stretchability and toughness of gelatin hydrogels cross-linked with PRXs were slightly higher than those of the hydrogels with the conventional chemical cross-linkers 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC)/N-hydroxysuccinimide (NHS). In addition, the hysteresis loss of gelatin hydrogels cross-linked with PRXs after repeated stretching and relaxation cycles in a hydrated state was remarkably improved in comparison with that of conventional cross-linked hydrogels. It is considered that the freely mobile cross-linking points of gelatin hydrogels cross-linked with PRXs attenuates the stress concentration. Accordingly, gelatin hydrogels cross-linked with PRXs would provide excellent mechanical properties as biocompatible tissue substitutes exposed to a continuous external physical force.

Parylene-Coated Polytetrafluoroethylene-Membrane-Based Portable Urea Sensor for Real-Time Monitoring of Urea in Peritoneal Dialysate

A portable urea sensor for use in fast flow conditions was fabricated using porous polytetrafluoroethylene (PTFE) membranes coated with amine-functionalized parylene, parylene-A, by vapor deposition. The urea-hydrolyzing enzyme urease was immobilized on the parylene-A-coated PTFE membranes using glutaraldehyde. The urease-immobilized membranes were assembled in a polydimethylsiloxane (PDMS) fluidic chamber, and a screen-printed carbon three-electrode system was used for electrochemical measurements. The success of urease immobilization was confirmed using scanning electron microscopy, and fourier-transform infrared spectroscopy. The optimum concentration of urease for immobilization on the parylene-A-coated PTFE membranes was determined to be 48 mg/mL, and the optimum number of membranes in the PDMS chamber was found to be eight. Using these optimized conditions, we fabricated the urea biosensor and monitored urea samples under various flow rates ranging from 0.5 to 10 mL/min in the flow condition using chronoamperometry. To test the applicability of the sensor for physiological samples, we used it for monitoring urea concentration in the waste peritoneal dialysate of a patient with chronic renal failure, at a flow rate of 0.5 mL/min. This developed urea biosensor is considered applicable for (portable) applications, such as artificial kidney systems and portable dialysis systems.

Investigation on Rheological Properties and Storage Stability of Modified Asphalt Based on the Grafting Activation of Crumb Rubber

Acrylamide with a double bond and amide group can not only copolymerize with macromolecules of crumb rubber but also react with acidic groups in asphalt, so it was selected as a modifier to activate crumb rubber through chemical graft action. The purpose is to improve the compatibility between crumb rubber and asphalt and thus improve the rheological properties and storage stability of rubber asphalt. Infrared spectroscopy (IR) and scanning electron microscopy (SEM) were used to characterize the crumb rubbers and their modified asphalt. It was found that the crumb rubber of grafting acrylamide had better compatibility in asphalt due to its larger specific surface area and chemical reaction with asphalt. In addition, the high temperature rheological test, low temperature creep test, and polymer separation test were carried out to study the effect of grafted activated crumb rubber on the properties of modified asphalt. The results showed that compared with modified asphalt with common crumb rubber (CRMA), the rheological properties and storage stability of modified asphalt with grafting activated crumb rubber (A–G–R) were improved significantly. The results of microscopic and macroscopic tests show that the activated rubber particles have a larger contact area with asphalt due to a rougher surface and the chemical cross-linking between rubber particles and asphalt further strengthens their interaction. Therefore, there is a relatively stable blend system formed in modified asphalt, and its performance of modified asphalt has been improved.

Allosteric Regulation of Rod Photoreceptor Phosphodiesterase 6 (PDE6) Elucidated by Chemical Cross-Linking and Quantitative Mass Spectrometry

Photoreceptor phosphodiesterase (PDE6) is the central effector enzyme in the visual excitation pathway in rod and cone photoreceptors. Its tight regulation is essential for the speed, sensitivity, recovery, and adaptation of visual signaling. The rod PDE6 holoenzyme (Pαβγ₂) is composed of a catalytic heterodimer (Pαβ) that binds two inhibitory γ subunits. Each of the two catalytic subunits (Pα and Pβ) contains a catalytic domain responsible for cGMP hydrolysis and two tandem GAF domains, one of which binds cGMP noncatalytically. Unlike related GAF-containing PDEs where cGMP binding allosterically activates catalysis, the physiological significance of cGMP binding to the GAF domains of PDE6 is unknown. To elucidate the structural determinants of PDE6 allosteric regulators, we biochemically characterized PDE6 complexes in various allosteric states (Pαβ, Pαβ-cGMP, Pαβγ₂, and Pαβγ₂-cGMP) with a quantitative cross-linking/mass spectrometry approach. We employed a normalization strategy to dissect the cross-linking reactivity of individual residues in order to assess the spatial cross-linking propensity of detected pairs. In addition to identifying cross-linked pairs that undergo conformational changes upon ligand binding, we observed an asymmetric binding of the inhibitory γ-subunit and the noncatalytic cGMP to the GAFa domains of rod PDE6, as well as a stable open conformation of Pαβ catalytic dimer in different allosteric states. These results advance our understanding of the exquisite regulatory control of the lifetime of rod PDE6 activation/deactivation during visual signaling, as well as providing a structural basis for interpreting how mutations in rod PDE6 subunits can lead to retinal diseases.

Functionalized DNA Hydrogels Produced by Polymerase-Catalyzed Incorporation of Non-Natural Nucleotides as a Surface Coating for Cell Culture Applications

Cells from most mammalian tissues require an extracellular matrix (ECM) for attachment and proper functioning. In vitro cell cultures therefore must be supplied with an ECM that satisfies both the biological needs of cells used and the technical demands of the experimental setup. The latter include matrix functionalization for cell attachment, favorable microscopic properties, and affordable production costs. Here, modified DNA materials are therefore developed as an ECM mimic. The material is prepared by chemical cross-linking of commonly available salmon sperm DNA. To render the material cell-compatible, it is enzymatically modified by DNA polymerase I to provide versatile attachment points for peptides, proteins, or antibodies via a modular strategy. Different cells specifically attach to the material, even from mixed populations. They can be mildly released for further cell studies by DNase I-mediated digestion of the DNA material. Additionally, neural stem cells not only attach and survive on the material but also differentiate to a neural lineage when prompted. Furthermore, the DNA material can be employed to capture and retain cells under flow conditions. The simple preparation of the DNA material and its wide scope of applications open new perspectives for various cell study challenges and medical applications.

Analysis of the Effect of Processing Conditions on Physical Properties of Thermally Set Cellulose Hydrogels

Cellulose-based hydrogels were prepared by dissolving cellulose in aqueous sodium hydroxide (NaOH)/urea solutions and casting it into complex shapes by the use of sacrificial templates followed by thermal gelation of the solution. Both the gelling temperatures used (40–80 °C), as well as the method of heating by either induction in the form of a water bath and hot press or radiation by microwaves could be shown to have a significant effect on the compressive strength and modulus of the prepared hydrogels. Lower gelling temperatures and shorter heating times were found to result in stronger and stiffer gels. Both the effect of physical cross-linking via the introduction of additional non-dissolving cellulosic material, as well as chemical cross-linking by the introduction of epichlorohydrin (ECH), and a combination of both applied during the gelation process could be shown to affect both the mechanical properties and microstructure of the hydrogels. The added cellulose acts as a physical-cross-linking agent strengthening the hydrogen-bond network as well as a reinforcing phase improving the mechanical properties. However, chemical cross-linking of an unreinforced gel leads to unfavourable bonding and cellulose network formation, resulting in drastically increased pore sizes and reduced mechanical properties. In both cases, chemical cross-linking leads to larger internal pores.

High Axial Ratio Nanochitins for Ultrastrong and Shape-Recoverable Hydrogels and Cryogels via Ice Templating

High yield (>85%) and low-energy deconstruction of never-dried residual marine biomass is proposed following partial deacetylation and microfluidization. This process results in chitin nanofibrils (nanochitin, NCh) of ultrahigh axial size (aspect ratios of up to 500), one of the largest for bioderived nanomaterials. The nanochitins are colloidally stable in water (ζ-potential = +95 mV) and produce highly entangled networks upon pH shift. Viscoelastic and strong hydrogels are formed by ice templating upon freezing and thawing with simultaneous cross-linking. Slow supercooling and ice nucleation at -20 °C make ice crystals grow slowly and exclude nanochitin and cross-linkers, becoming spatially confined at the interface. At a nanochitin concentration as low as 0.4 wt %, highly viscoelastic hydrogels are formed, with a storage modulus of ∼16 kPa, at least an order of magnitude larger compared to those measured for the strongest chitin-derived hydrogels reported so far. Moreover, the water absorption capacity of the hydrogels reaches a value of 466 g g^-1. Lyophilization is effective in producing cryogels with a density that can be tailored in a wide range of values, from 0.89 to 10.83 mg·cm^-3, and corresponding porosity, between 99.24 and 99.94%. Nitrogen adsorption results indicate reversible adsorption and desorption cycles of macroporous structures. A fast shape recovery is registered from compressive stress-strain hysteresis loops. After 80% compressive strain, the cryogels recovered fast and completely upon load release. The extreme values in these and other physical properties have not been achieved before for neither chitin nor nanocellulosic cryogels. They are explained to be the result of (a) the ultrahigh axial ratio of the fibrils and strong covalent interactions; (b) the avoidance of drying before and during processing, a subtle but critical aspect in nanomanufacturing with biobased materials; and (c) ice templating, which makes the hydrogels and cryogels suitable for advanced biobased materials.

Novel Chemical Cross-Linked Ionogel Based on Acrylate Terminated Hyperbranched Polymer with Superior Ionic Conductivity for High Performance Lithium-Ion Batteries

A new family of chemical cross-linked ionogel is successfully synthesized by photopolymerization of hyperbranched aliphatic polyester with acrylate terminal groups in an ionic liquid of 1-butyl-3-methylimidazolium tetrafluoroborate (BMIMBF₄). The microstructure, viscoelastic behavior, mechanical property thermal stability, and ionic conductivities of the ionogels are investigated systematically. The ionogels exhibit high mechanical strength (up to 1.6 MPa) and high mechanical stability even at temperatures up to 200 °C. It is found to be thermally stable up to 371.3 °C and electrochemically stable above 4.3 V. The obtained ionogels show superior ionic conductivity over a wide temperature range (from 1.2 × 10^-3 S cm^-1 at 20 °C up to 5.0 × 10^-2 S cm^-1 at 120 °C). Moreover, the Li/LiFePO₄ batteries based on ionogel electrolyte with LiBF₄ show a higher specific capacity of 153.1 mAhg^-1 and retain 98.1% after 100 cycles, exhibiting very stable charge/discharge behavior with good cycle performance. This work provides a new method for fabrication of novel advanced gel polymer electrolytes for applications in lithium-ion batteries.

Evaluation of Different Stationary Phases in the Separation of Inter-Cross-Linked Peptides

Chemical cross-linking coupled with mass spectrometry (MS) is becoming a routinely and widely used technique for depicting and constructing protein structures and protein interaction networks. One major challenge for cross-linking/MS is the determination of informative low-abundant inter-cross-linked products, generated within a sample of high complexity. A C18 stationary phase is the conventional means for reversed-phase (RP) separation of inter-cross-linked peptides. Various RP stationary phases, which provide different selectivities and retentions, have been developed as alternatives to C18 stationary phases. In this study, two phenyl-based columns, biphenyl and fluorophenyl, were investigated and compared with a C18 phase for separating BS³ (bis(sulfosuccinimidyl)suberate) cross-linked bovine serum albumin (BSA) and myoglobin by bottom-up proteomics. Fractions from the three columns were collected and analyzed in a linear ion trap (LIT) mass spectrometer for improving detection of low abundant inter-cross-linked peptides. Among these three columns, the fluorophenyl column provides additional ion-exchange interaction and exhibits unique retention in separating the cross-linked peptides. The fractioned data was analyzed in pLink, showing the fluorophenyl column consistently obtained more inter-cross-linked peptide identifications than both C18 and biphenyl columns. For the BSA cross-linked sample, the identified inter-cross-linked peptide numbers of the fluorophenyl to C18 column are 136 to 102 in "low confident" results and 11 to 6 in "high confident" results. The fluorophenyl column could potentially be a better alternative for targeting the low stoichiometric inter-cross-linked peptides.

Graphene Quantum Dots-Doped Thin Film Nanocomposite Polyimide Membranes with Enhanced Solvent Resistance for Solvent-Resistant Nanofiltration

The core of the organic solvent nanofiltration (OSN) technology is solvent-resistant nanofiltration (SRNF) membranes. Till now, relative poor performance of solvent resistance is still the bottleneck of industrial application of SRNF membranes. This work reports a novel polyimide (PI)-based thin-film nanocomposite (TFN) membrane which was embedded with graphene quantum dots (GQDs) and showed an improved solvent resistance for OSN application. This kind of SRNF membrane, termed (PI-GQDs/PI)_XA, was synthesized via serial processes of interfacial polymerization (IP), imidization, cross-linking, and solvent activation. The IP process was performed between an aqueous m-phenylenediamine solution doped with GQDs, having an average size of 1.9 nm, and an 1,2,4,5-benzenetetracarboxylic acyl chloride n-hexane solution on the PI substrate surface. The prepared (PI-GQDs-50/PI)_X SRNF membranes without organic solvent activation achieved an ethanol permeance of nearly 50% higher than those of the GQD-free membranes under the same preparation conditions, while no compromise of the dye rejection was observed. Further, after the solvent activation using N, N-dimethylformamide (DMF) at 80 °C for 30 min, the ethanol permeance achieved about an 8-folds increment, from 2.84 to 22.6 L m^-2 h^-1 MPa^-1. Interestingly, the rejection of rhodamine B also increased from 97.8 to 98.6%. A long-term permeation test of more than 100 h using rose bengal (RB, 1017 Da)/DMF solution at room temperature demonstrated that the synthesized (PI-GQDs-50/PI)_XA membranes could maintain the DMF permeance and the RB rejection as high as 18.3 L m^-2 h^-1 MPa^-1 and 99.9%, respectively. Moreover, the immersion test of the prepared (PI-GQDs-50/PI)_XA SRNF membranes in both DMF and ethanol at room temperature for about one year also demonstrated the long-term organic solvent stability, indicating their good potential for OSN application.

Gelatin-Based Hydrogels through Homobifunctional Triazolinediones Targeting Tyrosine Residues

Gelatin is a biopolymer with interesting properties that can be useful for biomaterial design for different applications such as drug delivery systems, or 3D scaffolds for tissue engineering. However, gelatin suffers from poor mechanical stability at physiological temperature, hence methods for improving its properties are highly desirable. In the present work, a new chemical cross-linking strategy based on triazolinedione ene-type chemistry towards stable hydrogel is proposed. Two different homobifunctional 1,2,4-triazoline-3,5(4H)-diones, namely 4,4'-hexane-1,6-diylbis(3H-1,2,4-triazoline-3,5(4H)-dione) 1 and 4,4'-[methylenebis(4,1-phenylene)]bis(3H-1,2,4-triazoline-3,5(4H)-dione) 2 were used as cross-linkers in different ratio to tyrosine residues in gelatin. The reaction was proved effective in all experimented conditions and hydrogels featured with different thermal stability were obtained. In general, the higher the cross-linker/tyrosine ratio, the more thermostable the hydrogel. The swelling properties are strictly dependent upon the chemical nature of the cross-linker.

Synthesis and Characterization of Shell-Cross-Linked Glycopolymer Bilayer Vesicles

Vesicles composed of self-assembled lipids or amphiphilic polymers have significant potential in applications such as delivery of cargo for therapeutics. However, they are fragile under physiological conditions such as inside living cells or the bloodstream, in which a vast number of other molecules are present in high concentrations. This is because vesicles are in dynamic equilibrium between unimers and vesicles. Therefore, the development of more robust vesicles by covalent cross-linking of the shell was focused on. Cross-linked polymer vesicles were prepared by the self-assembly of maltopentaose-b-poly(propylene glycol) followed by the reaction between divinyl sulfone and the hydroxyl group in a maltopentaose unit. It was found that two equivalents of DVS to the polymer is an optimal condition for the cross-linking without changing in size. The bilayer structures were retained after the cross-linking reactions. Importantly, the cross-linked polymer vesicles retained their size and polydispersity even in 50:50 v/v methanol/water solution. This work highlights the potential of the divinyl sulfone shell cross-link as a promising tool for stabilization of glycopolymer vesicles.

The Role of Mass Spectrometry in Structural Studies of Flavin-Based Electron Bifurcating Enzymes

For decades, biologists and biochemists have taken advantage of atomic resolution structural models of proteins from X-ray crystallography, nuclear magnetic resonance spectroscopy, and more recently cryo-electron microscopy. However, not all proteins relent to structural analyses using these approaches, and as the depth of knowledge increases, additional data elucidating a mechanistic understanding of protein function is desired. Flavin-based electron bifurcating enzymes, which are responsible for producing high energy compounds through the simultaneous endergonic and exergonic reduction of two intercellular electron carriers (i.e., NAD⁺ and ferredoxin) are one class of proteins that have challenged structural biologists and in which there is great interest to understand the mechanism behind electron gating. A limited number of X-ray crystallography projects have been successful; however, it is clear that to understand how these enzymes function, techniques that can reveal detailed in solution information about protein structure, dynamics, and interactions involved in the bifurcating reaction are needed. In this review, we cover a general set of mass spectrometry-based techniques that, combined with protein modeling, are capable of providing information on both protein structure and dynamics. Techniques discussed include surface labeling, covalent cross-linking, native mass spectrometry, and hydrogen/deuterium exchange. We cover how biophysical data can be used to validate computationally generated protein models and develop mechanistic explanations for regulation and performance of enzymes and protein complexes. Our focus will be on flavin-based electron bifurcating enzymes, but the broad applicability of the techniques will be showcased.

Tertiary structure of apolipoprotein A-I in nascent high-density lipoproteins

Understanding the function of high-density lipoprotein (HDL) requires detailed knowledge of the structure of its primary protein, apolipoprotein A-I (APOA1). However, APOA1 flexibility and HDL heterogeneity have confounded decades of efforts to determine high-resolution structures and consistent models. Here, molecular dynamics simulations totaling 30 μs on two nascent HDLs, each with 2 APOA1 and either 160 phospholipids and 24 cholesterols or 200 phospholipids and 20 cholesterols, show that residues 1-21 of the N-terminal domains of APOA1 interact via strong salt bridges. Residues 26-43 of one APOA1 in the smaller particle form a hinge on the disc edge, which displaces the C-terminal domain of the other APOA1 to the phospholipid surface. The proposed structures are supported by chemical cross-linking, Rosetta modeling of the N-terminal domain, and analysis of the lipid-free ∆185APOA1 crystal structure. These structures provide a framework for understanding HDL maturation and revise all previous models of nascent HDL.

Driving Chemical Reactions in Plasmonic Nanogaps with Electrohydrodynamic Flow

Nanoparticles from colloidal solution-with controlled composition, size, and shape-serve as excellent building blocks for plasmonic devices and metasurfaces. However, understanding hierarchical driving forces affecting the geometry of oligomers and interparticle gap spacings is still needed to fabricate high-density architectures over large areas. Here, electrohydrodynamic (EHD) flow is used as a long-range driving force to enable carbodiimide cross-linking between nanospheres and produces oligomers exhibiting sub-nanometer gap spacing over mm² areas. Anhydride linkers between nanospheres are observed via surface-enhanced Raman scattering (SERS) spectroscopy. The anhydride linkers are cleavable via nucleophilic substitution and enable placement of nucleophilic molecules in electromagnetic hotspots. Atomistic simulations elucidate that the transient attractive force provided by EHD flow is needed to provide a sufficient residence time for anhydride cross-linking to overcome slow reaction kinetics. This synergistic analysis shows assembly involves an interplay between long-range driving forces increasing nanoparticle-nanoparticle interactions and probability that ligands are in proximity to overcome activation energy barriers associated with short-range chemical reactions. Absorption spectroscopy and electromagnetic full-wave simulations show that variations in nanogap spacing have a greater influence on optical response than variations in close-packed oligomer geometry. The EHD flow-anhydride cross-linking assembly method enables close-packed oligomers with uniform gap spacings that produce uniform SERS enhancement factors. These results demonstrate the efficacy of colloidal driving forces to selectively enable chemical reactions leading to future assembly platforms for large-area nanodevices.

Synthesis and Swelling Behavior of pH-Sensitive Semi-IPN Superabsorbent Hydrogels Based on Poly(acrylic acid) Reinforced with Cellulose Nanocrystals

pH-sensitive poly(acrylic acid) (PAA) hydrogel reinforced with cellulose nanocrystals (CNC) was prepared. Acrylic acid (AA) was subjected to chemical cross-linking using the cross-linking agent MBA (N,N-methylenebisacrylamide) with CNC entrapped in the PAA matrix. The quantity of CNC was varied between 0, 5, 10, 15, 20, and 25 wt %. X-ray diffraction (XRD) data showed an increase in crystallinity with the addition of CNC, while rheology tests demonstrated a significant increase in the storage modulus of the hydrogel with an increase in CNC content. It was found that the hydrogel reached maximum swelling at pH 7. The potential of the resulting hydrogels to act as drug carriers was then evaluated by means of the drug encapsulation efficiency test using theophylline as a model drug. It was observed that 15% CNC/PAA hydrogel showed the potential to be used as drug carrier system.

The toxic alpha-gliadin peptide 31-43 enters cells without a surface membrane receptor

Alpha-gliadin peptide 31-43 is considered to be the main peptide responsible for the innate immune response in celiac disease patients. Recent evidence indicates that peptide 31-43 rapidly enters cells and interacts with the early endocytic vesicular compartment. However, the mechanism of its uptake is not completely understood. Our aim is to characterize, isolate and identify possible cell surface proteins involved in peptide 31-43 internalization by Caco-2 cells. In this study, we used a chemical cross-linker to block peptide 31-43 on cell surface proteins, and pulled-down peptide-proteins complexes using antibodies raised against peptide 31-43. Through this experimental approach, we did not observe any specific complex between cell proteins and peptide 31-43 in Coomassie-stained denaturating gels or by Western blotting. We also found that type 2 transglutaminase was not necessary for peptide 31-43 internalization, even though it had a regulatory role in the process. Finally, we demonstrated that peptide 31-43 did not behave as a classical ligand, indeed the labeled peptide did not displace the unlabeled peptide in a competitive binding assay. On the basis of these findings and of previous evidence demonstrating that peptide 31-43 is able to interact with a membrane-like environment in vitro, we conclude that membrane composition and organization, rather than a specific receptor protein, may have a major role in peptide 31-43 internalization by cells.

Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b559 in Photosystem II

Photosystem II (PSII), a large pigment protein complex, undergoes rapid turnover under natural conditions. During assembly of PSII, oxidative damage to vulnerable assembly intermediate complexes must be prevented. Psb28, the only cytoplasmic extrinsic protein in PSII, protects the RC47 assembly intermediate of PSII and assists its efficient conversion into functional PSII. Its role is particularly important under stress conditions when PSII damage occurs frequently. Psb28 is not found, however, in any PSII crystal structure, and its structural location has remained unknown. In this study, we used chemical cross-linking combined with mass spectrometry to capture the transient interaction of Psb28 with PSII. We detected three cross-links between Psb28 and the α- and β-subunits of cytochrome b₅₅₉, an essential component of the PSII reaction-center complex. These distance restraints enable us to position Psb28 on the cytosolic surface of PSII directly above cytochrome b₅₅₉, in close proximity to the Q_B site. Protein-protein docking results also support Psb28 binding in this region. Determination of the Psb28 binding site and other biochemical evidence allow us to propose a mechanism by which Psb28 exerts its protective effect on the RC47 intermediate. This study also shows that isotope-encoded cross-linking with the "mass tags" selection criteria allows confident identification of more cross-linked peptides in PSII than has been previously reported. This approach thus holds promise to identify other transient protein-protein interactions in membrane protein complexes.