Protein diffusion in lower-dimensional spaces is used for various cellular functions. For example, sliding on DNA is essential for proteins searching for their target sites, and protein diffusion on microtubules is important for proper cell division and neuronal development. On the one hand, these linear diffusion processes are mediated by long-range electrostatic interactions between positively charged proteins and negatively charged biopolymers and have similar characteristic diffusion coefficients. On the other hand, DNA and microtubules have different structural properties. Here, using computational approaches, we studied the mechanism of protein diffusion along DNA and microtubules by exploring the diffusion of both protein types on both biopolymers. We found that DNA-binding and microtubule-binding proteins can diffuse on each other's substrates; however, the adopted diffusion mechanism depends on the molecular properties of the diffusing proteins and the biopolymers. On the protein side, only DNA-binding proteins can perform rotation-coupled diffusion along DNA, with this being due to their higher net charge and its spatial organization at the DNA recognition helix. By contrast, the lower net charge on microtubule-binding proteins enables them to diffuse more quickly than DNA-binding proteins on both biopolymers. On the biopolymer side, microtubules possess intrinsically disordered, negatively charged C-terminal tails that interact with microtubule-binding proteins, thus supporting their diffusion. Thus, although both DNA-binding and microtubule-binding proteins can diffuse on the negatively charged biopolymers, the unique molecular features of the biopolymers and of their natural substrates are essential for function.

Few therapeutic options exist for treatment of IC/BPS. A novel high MW GAG biopolymer ("SuperGAG") was synthesized by controlled oligomerization of CS, purified by TFF and characterized by SEC-MALLS and 1H-NMR spectroscopy. The modified GAG biopolymer was tested in an OVX female rat model in which bladder permeability was induced by a 10-minute intravesicular treatment with dilute (1 mg/ml) protamine sulfate and measured by classical Ussing Chamber TEER measurements following treatment with SuperGAG, chondroitin sulfate, or saline. The effect on abrogating the abdominal pain response was assessed using von Frey filaments. The SuperGAG biopolymer was then investigated in a second, genetically modified mouse model (URO-MCP1) that increasingly is accepted as a model for IC/BPS. Permeability was induced with a brief exposure to a sub-noxious dose of LPS and was quantified using contrast-enhanced MRI (CE-MRI). The SuperGAG biopolymer restored impermeability to normal levels in the OVX rat model as measured by TEER in the Ussing chamber and reduced the abdominal pain response arising from induced permeability. Evaluation in the URO-MCP1 mouse model also showed restoration of bladder impermeability and showed the utility of CE-MRI imaging for evaluating the efficacy of agents to restore bladder impermeability. We conclude novel high MW SuperGAG biopolymers are effective in restoring urothelial impermeability and reducing pain produced by loss of the GAG layer on the urothelium. SuperGAG biopolymers could offer a novel and effective new therapy for IC/BPS, particularly if combined with MRI to assess the efficacy of the therapy.

The LassoProt server, http://lassoprot.cent.uw.edu.pl/, enables analysis of biopolymers with entangled configurations called lassos. The server offers various ways of visualizing lasso configurations, as well as their time trajectories, with all the results and plots downloadable. Broad spectrum of applications makes LassoProt a useful tool for biologists, biophysicists, chemists, polymer physicists and mathematicians. The server and our methods have been validated on the whole PDB, and the results constitute the database of proteins with complex lassos, supported with basic biological data. This database can serve as a source of information about protein geometry and entanglement-function correlations, as a reference set in protein modeling, and for many other purposes.

Given an input Protein Data Bank file (PDB) for a protein or RNA molecule, LocalMove is a web server that determines an on-lattice representation for the input biomolecule. The web server implements a Markov Chain Monte-Carlo algorithm with simulated annealing to compute an approximate fit for either the coarse-grain model or backbone model on either the cubic or face-centered cubic lattice. LocalMove returns a PDB file as output, as well as dynamic movie of 3D images of intermediate conformations during the computation. The LocalMove server is publicly available at http://bioinformatics.bc.edu/clotelab/localmove/.

Conjugates of the photoactivated rhodamine dyes with biopolymers (proteins, polysaccharides, and nucleic acids) are important tools for microscopic investigation of biological tissue. In this study, a precursor of the photoactivated fluorescent dye (PFD) has been successfully used for staining of numerous mammalian cells lines and for conjugate formation with chitosan ("Chitosan-PFD") and histone H1 ("Histone H1.3-PFD"). The intensive fluorescence has been observed after photoactivation of these conjugates inside cells (A431, HaCaT, HEK239, HBL-100, and MDCK). Developed procedures and obtained data are important for further application of novel precursors of fluorescent dyes ("caged" dyes) for microscopic probing of biological objects. Thus, the synthesized "Chitosan-PFD" and "Histone H1-PFD" have been successfully applied in this study for intracellular transport visualization by fluorescent microscopy.

Poly (Lactic Acid), PLA, and Poly (ε-CaproLactone), PCL, compatibilized with Ethyl Ester l-Lysine Triisocyanate (LTI) can be employed as biomaterials. We mixed PLA with PCL and LTI in a twin extruder and by a melt spinning process obtained threads with an average diameter of about 0.3 mm. In order to study the possible application of these threads, mechanical tensile (with the calorimetric and morphological investigations) and biological tests were performed. The results highlighted these biopolymers as promising materials for sutures since they can be rigid and elastic (especially by increasing the PCL amount in the blend), and they are bioactive, able to inhibit bacterial growth. This paper represents a starting point to optimize the blend composition for biomedical suture application.

Biopolymers are essential building blocks that constitute cells and tissues with well-defined molecular structures and diverse biological functions. Their three-dimensional (3D) complex architectures are used to analyze, control, and mimic various cells and their ensembles. However, the free-form and high-resolution structuring of various biopolymers remain challenging because their structural and rheological control depend critically on their polymeric types at the submicron scale. Here, direct 3D writing of intact biopolymers is demonstrated using a systemic combination of nanoscale confinement, evaporation, and solidification of a biopolymer-containing solution. A femtoliter solution is confined in an ultra-shallow liquid interface between a fine-tuned nanopipette and a chosen substrate surface to achieve directional growth of biopolymer nanowires via solvent-exclusive evaporation and concurrent solution supply. The evaporation-dependent printing is biopolymer type-independent, therefore, the 3D motor-operated precise nanopipette positioning allows in situ printing of nucleic acids, polysaccharides, and proteins with submicron resolution. By controlling concentrations and molecular weights, several different biopolymers are reproducibly patterned with desired size and geometry, and their 3D architectures are biologically active in various solvents with no structural deformation. Notably, protein-based nanowire patterns exhibit pin-point localization of spatiotemporal biofunctions, including target recognition and catalytic peroxidation, indicating their application potential in organ-on-chips and micro-tissue engineering.

A new structure classification scheme for biopolymers is introduced, which is solely based on main-chain dihedral angles. It is shown that by dividing a biopolymer into segments containing two central residues, a local classification can be performed. The method is referred to as DISICL, short for Dihedral-based Segment Identification and Classification. Compared to other popular secondary structure classification programs, DISICL is more detailed as it offers 18 distinct structural classes, which may be simplified into a classification in terms of seven more general classes. It was designed with an eye to analyzing subtle structural changes as observed in molecular dynamics simulations of biomolecular systems. Here, the DISICL algorithm is used to classify two databases of protein structures, jointly containing more than 10 million segments. The data is compared to two alternative approaches in terms of the amount of classified residues, average occurrence and length of structural elements, and pair wise matches of the classifications by the different programs. In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers II: Polynucleotides. J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400542n), the analysis of polynucleotides is described and applied. Overall, DISICL represents a potentially useful tool to analyze biopolymer structures at a high level of detail.

Plants, animals, bacteria, and food waste are subjects of intensive research, as they are biological sources for the production of biopolymers. The topic links to global challenges related to the extended life cycle of products, and circular economy objectives. A severe and well-known threat to the environment, the non-biodegradability of plastics obliges different stakeholders to find legislative and technical solutions for producing valuable polymers which are biodegradable and also exhibit better characteristics for packaging products. Microorganisms are recognized nowadays as exciting sources for the production of biopolymers with applications in the food industry, package production, and several other fields. Ubiquitous organisms, lactic acid bacteria (LAB) are well studied for the production of exopolysaccharides (EPS), but much less as producers of polylactic acid (PLA) and polyhydroxyalkanoates (PHAs). Based on their good biodegradability feature, as well as the possibility to be obtained from cheap biomass, PLA and PHAs polymers currently receive increased attention from both research and industry. The present review aims to provide an overview of LAB strains' characteristics that render them candidates for the biosynthesis of EPS, PLA, and PHAs, respectively. Further, the biopolymers' features are described in correlation with their application in different food industry fields and for food packaging. Having in view that the production costs of the polymers constitute their major drawback, alternative solutions of biosynthesis in economic terms are discussed.

Phenanthriplatin, that is, (SP-4-3)-diamminechlorido(phenanthridine)platinum(II) nitrate, an effective antitumor cationic Pt(II) complex, was loaded on negatively charged dextran sulfate (DS) as a model vector for drug delivery via electrostatic interactions. The free complex and the corresponding conjugate with DS were tested on two standard human tumor cell lines, namely, ovarian A2780 and colon HCT 116, and on several malignant pleural mesothelioma cell lines (namely, epithelioid BR95, mixed/biphasic MG06, sarcomatoid MM98, and sarcomatoid cisplatin-resistant MM98R). The in vitro results suggest that the conjugate releases the active metabolite phenanthriplatin with a biphasic fashion. In these experimental conditions, the conjugate is slightly less active than free phenanthriplatin; but both exhibited antiproliferative potency higher than the reference metallodrug cisplatin and were able to overcome the acquired cisplatin chemoresistance in MM98R cells.

In tissue engineering, the potential of re-growing new tissue has been considered, however, developments towards such clinical and commercial outcomes have been modest. One of the most important elements here is the selection of a biomaterial that serves as a "scaffold" for the regeneration process. Herein, we designed hydrogels composed of two biocompatible natural polymers, namely gelatin with photopolymerizable functionalities and a pectin derivative amenable to direct protein conjugation. Aiming to design biomimetic hydrogels for bone regeneration, this study proposes double-reinforcement by way of inorganic/biopolymer hybrid filling composed of Si-based compounds and cellulose nanofibers. To attain networks with high flexibility and elastic modulus, a double-crosslinking strategy was envisioned-photochemical and enzyme-mediated conjugation reactions. The dual cross-linked procedure will generate intra- and intermolecular interactions between the protein and polysaccharide and might be a resourceful strategy to develop innovative scaffolding materials.

In vitro meat has recently emerged as a new concept in food biotechnology. Methods to produce in vitro meat generally involve the growth of muscle cells that are cultured on scaffolds using bioreactors. Suitable scaffold design and manufacture are critical to downstream culture and meat production. Most current scaffolds are based on mammalian-derived biomaterials, the use of which is counter to the desire to obviate mammal slaughter in artificial meat production. Consequently, most of the knowledge is related to the design and control of scaffold properties based on these mammalian-sourced materials. To address this, four different scaffold materials were formulated using non-mammalian sources, namely, salmon gelatin, alginate, and additives including gelling agents and plasticizers. The scaffolds were produced using a freeze-drying process, and the physical, mechanical, and biological properties of the scaffolds were evaluated. The most promising scaffolds were produced from salmon gelatin, alginate, agarose, and glycerol, which exhibited relatively large pore sizes (~200 μm diameter) and biocompatibility, permitting myoblast cell adhesion (~40%) and growth (~24 h duplication time). The biodegradation profiles of the scaffolds were followed, and were observed to be less than 25% after 4 weeks. The scaffolds enabled suitable myogenic response, with high cell proliferation, viability, and adequate cell distribution throughout. This system composed of non-mammalian edible scaffold material and muscle-cells is promising for the production of in vitro meat.

Biopolymers, such as polynucleotides, polypeptides and polysaccharides, are macromolecules that direct most of the functions in living beings. Studying the mechanical unfolding of biopolymers provides important information about their molecular elasticity and mechanical stability, as well as their energy landscape, which is especially important in proteins, since their three-dimensional structure is essential for their correct activity. In this primer, we present how to study the mechanical properties of proteins with atomic force microscopy and how to obtain information about their stability and energetic landscape. In particular, we discuss the preparation of polyprotein constructs suitable for AFM single molecule force spectroscopy (SMFS), describe the parameters used in our force-extension SMFS experiments and the models and equations employed in the analysis of the data. As a practical example, we show the effect of the temperature on the unfolding force, the distance to the transition state, the unfolding rate at zero force, the height of the transition state barrier, and the spring constant of the protein for a construct containing nine repeats of the I27 domain from the muscle protein titin. HIGHLIGHTS: 1. Atomic force microscopy (AFM) can be used to study the mechanical unfolding of polymers. 2. AFM provides a direct measurement of unfolding (unbinding) forces. 3. Force measurements for different rates provide information about the distance to the transition state and the unfolding rate at zero force.

Pleural injuries and the associated "air leak" are the most common complications after pulmonary surgery. Air leaks are the primary reason for prolonged chest tube use and increased hospital length of stay. Pectin, a plant-derived heteropolysaccharide, has been shown to be an air-tight sealant of pulmonary air leaks. Here, we investigate the morphologic and mechanical properties of pectin adhesion to the visceral pleural surface of the lung. After the application of high-methoxyl citrus pectin films to the murine lung, we used scanning electron microscopy to demonstrate intimate binding to the lung surface. To quantitatively assess pectin adhesion to the pleural surface, we used a custom adhesion test with force, distance, and time recordings. These assays demonstrated that pectin-glycocalyceal tensile adhesive strength was greater than nanocellulose fiber films or pressure-sensitive adhesives (p < 0.001). Simultaneous videomicroscopy recordings demonstrated that pectin-glycocalyceal adhesion was also stronger than the submesothelial connective tissue as avulsed surface remnants were visualized on the separated pectin films. Finally, pleural abrasion and hyaluronidase enzyme digestion confirmed that pectin binding was dependent on the pleural glycocalyx (p < 0.001). The results indicate that high methoxyl citrus pectin is a promising sealant for the treatment of pleural lung injuries.

Composites of polyaniline, starch, polypyrrole, chitosan aniline and chitosan pyrrole using peanut waste were prepared and employed for the adsorption of Crystal Violet (CV) dye from aqueous media. The process variables i.e., composite doses, pH, contact time, CV initial concentration and temperature were optimized. Thermodynamic, equilibrium modelling and kinetics models were fitted to the CV adsorption data in order to understand the mechanism and nature of CV adsorption onto native and composite adsorbents. Maximum CV adsorption of 100.6mg/g was achieved (onto chitosan aniline composite) using 150mg/L dye initial concentration, 50°C temperature, 60min contact time, 0.05g adsorbent dose and>7pH. Effect of composites pre-treatments with salts, surfactants and co-metals ions were also studied. The CV adsorption efficiencies of adsorbents were found in following order; chitosan aniline composite>starch composite>chitosan pyrrole composite>polyaniline composite>polypyrrole composite>native peanut biomass. The pseudo-second-order kinetic model and Freundlich isotherm fitted well to the CV equilibrium adsorption data and intraparticle diffusion was the rate limiting step. Composites showed endothermic and energetically stable nature for CV adsorption. Composites also showed good desorption properties, which revealed the recycling ability of prepared composites.

Lactic acid bacteria (LAB) are microorganisms widely used in the fermented food industry worldwide. Certain LAB are able to produce exopolysaccharides (EPS) either attached to the cell wall (capsular EPS) or released to the extracellular environment (EPS). According to their composition, LAB may synthesize heteropolysaccharides or homopolysaccharides. A wide diversity of EPS are produced by LAB concerning their monomer composition, molecular mass, and structure. Although EPS-producing LAB strains have been traditionally applied in the manufacture of dairy products such as fermented milks and yogurts, their use in the elaboration of low-fat cheeses, diverse type of sourdough breads, and certain beverages are some of the novel applications of these polymers. This work aims to collect the most relevant issues of the former reviews concerning the monomer composition, structure, and yields and biosynthetic enzymes of EPS from LAB; to describe the recently characterized EPS and to present the application of both EPS-producing strains and their polymers in the fermented (specifically beverages and cereal-based) food industry.

The novel silane crosslinked (TEOS) hydrogels based on eco-friendly biodegradable chitosan/guargum were prepared by blending with PEG to develop pH sensitive hydrogels (CGP) and achieved its hydrophilicity and target specificity for controlled release of drug. The crosslinker amount was varied to analyze its effect on the hydrogel properties and were characterized using FTIR, SEM, TGA, swelling studies (water, buffer and ionic solution) and in-vitro release of cephradine (CED). FTIR confirmed the presence of characteristic peaks and crosslinking between the components while SEM images showed the formation of clear micro- and macro-pores. The swelling behavior in water showed that compared to the controlled hydrogel, the crosslinked hydrogels revealed more swelling but a decrease in swelling with further increase in the amount of crosslinker was observed. The hydrogels showed low swelling at basic and neutral pH while maximum swelling was observed at acidic pH. This pH response made these hydrogels an ideal candidate for injectable controlled release. The CED was loaded on hydrogels and its release mechanism was studied in PBS, SGF and SIF which revealed that out of all hydrogels (CGP100, CGP150, CGP200 and CGP250), CGP100 has shown CED release of 85% in 130 min in PBS and 82.4% in SIF.

The use of biologics in the treatment of numerous diseases has increased steadily over the past decade due to their high specificities, low toxicity, and limited side effects. Despite this success, peptide- and protein-based drugs are limited by short half-lives and immunogenicity. To address these challenges, we use a genomically recoded organism to produce genetically encoded elastin-like polypeptide-protein fusions containing multiple instances of para-azidophenylalanine (pAzF). Precise lipidation of these pAzF residues generated a set of sequence-defined synthetic biopolymers with programmable binding affinity to albumin without ablating the activity of model fusion proteins, and with tunable blood serum half-lives spanning 5 to 94% of albumin's half-life in a mouse model. Our findings present a proof of concept for the use of genetically encoded bioorthogonal conjugation sites for multisite lipidation to tune protein stability in mouse serum. This work establishes a programmable approach to extend and tune the half-life of protein or peptide therapeutics and a technical foundation to produce functionalized biopolymers endowed with programmable chemical and biophysical properties with broad applications in medicine, materials science, and biotechnology.

Biological electron transfer (ET) across proteins is ubiquitous, such as the notable photosynthesis example, where light-induced charge separation takes place within the reaction center, followed by sequential ET via intramolecular cofactors within the protein. Far from biology, carbon dots (C-Dots) with their unique optoelectronic properties can be considered as game-changers for next-generation advanced technologies. Here, we use C-Dots for making heterostructure (HS) configurations by conjugating them to a natural ET mediator, the hemin molecule, thus making an electron donor-acceptor system. We show by transient absorption and emission spectroscopy that the rapid intramolecular charge separation happens following light excitation, which can be ascribed to an ultrafast electron and hole transfer (HT) from the C-Dot donor to the hemin acceptor. Upon integrating the HS into a protein matrix, we show that this HT within the HS configuration is 3.3 times faster compared to the same process in solution, indicating the active role of the protein in supporting the rapid light-induced long-range intermolecular charge separation. We further use impedance, electrochemical, and transient photocurrent measurements to show that the light-induced transient charge separation results in an enhanced ET and HT efficiency across the protein biopolymer. The charge conduction across our protein biopolymers, reaching nearly 0.01 S cm-1, along with the simplicity and low-cost of their formation promotes their use in a variety of optoelectronic devices, such as artificial photosynthesis, photo-responsive protonic-electronic transistors, and photodetectors.

It is presumed that structural and functional alterations of biopolymers, which occur during grinding, are caused by a mechanical modification of polymers. As a result, thermally induced changes of flours are neglected. In this study, the impact of thermo-mechanical stress (TMS), as occurring during general grinding procedures, was further differentiated into thermal stress (TS) and mechanical stress (MS). For TS, native wheat flour, as well as the purified polymers of wheat-starch and gluten-were heated without water addition up to 110 ∘ C. Isolated MS was applied in a temperature-controlled ultra-centrifugal grinder (UCG), whereby thermal and mechanical treatment (TMS) was simultaneously performed in a non-cooled UCG. TS starch (110 ∘ C) and reference starch did not show differences in starch modification degree (2.53 ± 0.24 g/100 g and 2.73 ± 0.15 g/100 g, AACC 76-31), gelatinization onset (52.44 ± 0.14 ∘ C and 52.73 ± 0.27 ∘ C, differential scanning calorimetry (DSC)) and hydration properties (68.9 ± 0.8% dm and 75.8 ± 3.0%, AACC 56-11), respectively. However, TS led to an elevated gelatinization onset and a rise of water absorption of flours (Z-kneader) affecting the processing of cereal-based dough. No differences were visible between MS and TMS up to 18,000 rpm regarding hydration properties (65.0 ± 2.0% dm and 66.5 ± 0.3% dm, respectively). Consequently, mechanical forces are the main factor controlling the structural modification and functional properties of flours during grinding.