Heat flows enrich prebiotic building blocks and enhance their reactivity.

The emergence of biopolymer building blocks is a crucial step during the origins of life1-6. However, all known formation pathways rely on rare pure feedstocks and demand successive purification and mixing steps to suppress unwanted side reactions and enable high product yields. Here we show that heat flows through thin, crack-like geo-compartments could have provided a widely available yet selective mechanism that separates more than 50 prebiotically relevant building blocks from complex mixtures of amino acids, nucleobases, nucleotides, polyphosphates and 2-aminoazoles. Using measured thermophoretic properties7,8, we numerically model and experimentally prove the advantageous effect of geological networks of interconnected cracks9,10 that purify the previously mixed compounds, boosting their concentration ratios by up to three orders of magnitude. The importance for prebiotic chemistry is shown by the dimerization of glycine11,12, in which the selective purification of trimetaphosphate (TMP)13,14 increased reaction yields by five orders of magnitude. The observed effect is robust under various crack sizes, pH values, solvents and temperatures. Our results demonstrate how geologically driven non-equilibria could have explored highly parallelized reaction conditions to foster prebiotic chemistry.

Symmetry breaking and chiral amplification in prebiotic ligation reactions.

The single chirality of biological molecules is a signature of life. Yet, rationalizing how single chirality emerged remains a challenging goal1. Research has commonly focused on initial symmetry breaking and subsequent enantioenrichment of monomer building blocks-sugars and amino acids-that compose the genetic polymers RNA and DNA as well as peptides. If these building blocks are only partially enantioenriched, however, stalling of chain growth may occur, whimsically termed in the case of nucleic acids as "the problem of original syn"2. Here, in studying a new prebiotically plausible route to proteinogenic peptides3-5, we discovered that the reaction favours heterochiral ligation (that is, the ligation of L monomers with D monomers). Although this finding seems problematic for the prebiotic emergence of homochiral L-peptides, we demonstrate, paradoxically, that this heterochiral preference provides a mechanism for enantioenrichment in homochiral chains. Symmetry breaking, chiral amplification and chirality transfer processes occur for all reactants and products in multicomponent competitive reactions even when only one of the molecules in the complex mixture exhibits an imbalance in enantiomer concentrations (non-racemic). Solubility considerations rationalize further chemical purification and enhanced chiral amplification. Experimental data and kinetic modelling support this prebiotically plausible mechanism for the emergence of homochiral biological polymers.

De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity.

Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency of de novo protein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in viscoelastic biomaterials exhibiting fluid-like properties under rest and low shear, but solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and show via fluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly in a manner similar to formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology.

Solvent constraints for biopolymer folding and evolution in extraterrestrial environments.

We propose that spontaneous folding and molecular evolution of biopolymers are two universal aspects that must concur for life to happen. These aspects are fundamentally related to the chemical composition of biopolymers and crucially depend on the solvent in which they are embedded. We show that molecular information theory and energy landscape theory allow us to explore the limits that solvents impose on biopolymer existence. We consider 54 solvents, including water, alcohols, hydrocarbons, halogenated solvents, aromatic solvents, and low molecular weight substances made up of elements abundant in the universe, which may potentially take part in alternative biochemistries. We find that along with water, there are many solvents for which the liquid regime is compatible with biopolymer folding and evolution. We present a ranking of the solvents in terms of biopolymer compatibility. Many of these solvents have been found in molecular clouds or may be expected to occur in extrasolar planets.

Engineering tertiary chirality in helical biopolymers.

Tertiary chirality describes the handedness of supramolecular assemblies and relies not only on the primary and secondary structures of the building blocks but also on topological driving forces that have been sparsely characterized. Helical biopolymers, especially DNA, have been extensively investigated as they possess intrinsic chirality that determines the optical, mechanical, and physical properties of the ensuing material. Here, we employ the DNA tensegrity triangle as a model system to locate the tipping points in chirality inversion at the tertiary level by X-ray diffraction. We engineer tensegrity triangle crystals with incremental rotational steps between immobile junctions from 3 to 28 base pairs (bp). We construct a mathematical model that accurately predicts and explains the molecular configurations in both this work and previous studies. Our design framework is extendable to other supramolecular assemblies of helical biopolymers and can be used in the design of chiral nanomaterials, optically active molecules, and mesoporous frameworks, all of which are of interest to physical, biological, and chemical nanoscience.

Ectoine hyperproduction by engineered Halomonas bluephagenesis.

Ectoine, a crucial osmoprotectant for salt adaptation in halophiles, has gained growing interest in cosmetics and medical industries. However, its production remains challenged by stringent fermentation process in model microorganisms and low production level in its native producers. Here, we systematically engineered the native ectoine producer Halomonas bluephagenesis for ectoine production by overexpressing ectABC operon, increasing precursors availability, enhancing product transport system and optimizing its growth medium. The final engineered H. bluephagenesis produced 85 g/L ectoine in 52 h under open unsterile incubation in a 7 L bioreactor in the absence of plasmid, antibiotic or inducer. Furthermore, it was successfully demonstrated the feasibility of decoupling salt concentration with ectoine synthesis and co-production with bioplastic P(3HB-co-4HB) by the engineered H. bluephagenesis. The unsterile fermentation process and significantly increased ectoine titer indicate that H. bluephagenesis as the chassis of Next-Generation Industrial Biotechnology (NGIB), is promising for the biomanufacturing of not only intracellular bioplastic PHA but also small molecular compound such as ectoine.

Application of liquid-based colorimetric method for high throughput screening of bioplastic-degrading strains using esterase assay.

To alleviate environmental problems caused by using conventional plastics, bioplastics have garnered significant interest as alternatives to petroleum-based plastics. Despite possessing better degradability traits compared to traditional plastics, the degradation of bioplastics still demands a longer duration than initially anticipated. This necessitates the utilization of degradation strains or enzymes to enhance degradation efficiency, ensuring timely degradation. In this study, a novel screening method to identify bioplastic degraders faster was suggested to circumvent the time-consuming and laborious characteristics of solid-based plate assays. This liquid-based colorimetric method confirmed the extracellular esterase activity with p-nitrophenyl esters. It eliminated the needs to prepare plastic emulsion plates at the initial screening system, shortening the time for the overall screening process and providing more quantitative data. p-nitrophenyl hexanoate (C6) was considered the best substrate among the various p-nitrophenyl esters as substrates. The screening was performed in liquid-based 96-well plates, resulting in the discovery of a novel strain, Bacillus sp. SH09, with a similarity of 97.4% with Bacillus licheniformis. Furthermore, clear zone assays, degradation investigations, scanning electron microscopy, and gel permeation chromatography were conducted to characterize the biodegradation capabilities of the new strain, the liquid-based approach offered a swift and less labor-intensive option during the initial stages.

Bacterial nanocellulose: A versatile biopolymer production using a cost-effective wooden disc based rotary reactor.

Bacterial nanocellulose (BNC) has various unique qualities, including high mechanical strength, crystallinity, and high water-holding capacity, which makes it appropriate for a wide range of industrial applications. But its lower yield coupled with its high production cost creates a barrier to its usage. In this study, we have demonstrated the better yield of BNC from an indigenous strain Komagataeibacter rhaeticus MCC-0157 using a rotary disc bioreactor (RDB) having a wooden disc. The RDB was optimized based on the type of disc material, distance between the disc, and rotation speed to get the highest yield of 13.0 g/L dry material using Hestrin-Schramm (H-S) medium. Further, the bioreactor was compared for the BNC production using reported medium, which is used for static condition; the RDB showed up to fivefold increase in comparison with the static condition reported. Komagataeibacter rhaeticus MCC-0157 was previously reported to be one of the highest BNC producing stains, with 8.37 g/L of dry yield in static condition in 15 days incubation. The designed RDB demonstrated 13.0 g/L dry yield of BNC in just 5 days. Other characteristics of BNC remain same as compared with static BNC production, although the difference in the crystallinity index was observed in RDB (84.44%) in comparison with static (89.74%). For the first time, wooden disc was used for rotary bioreactor approach, which demonstrated higher yield of BNC in lesser time and can be further used for sustainable production of BNC at the industrial level.

Protein-based microneedles for biomedical applications: A systematic review.

Microneedles are minimally-invasive devices with the unique capability of bypassing physiological barriers. Hence, they are widely used for different applications from drug/vaccine delivery to diagnosis and cosmetic fields. Recently, natural biopolymers (particularly carbohydrates and proteins) have garnered attention as safe and biocompatible materials with tailorable features for microneedle construction. Several review articles have dealt with carbohydrate-based microneedles. This review aims to highlight the less-noticed role of proteins through a systematic search strategy based on the PRISMA guideline from international databases of PubMed, Science Direct, Scopus, and Google Scholar. Original English articles with the keyword "microneedle(s)" in their titles along with at least one of the keywords "biopolymers, silk, gelatin, collagen, zein, keratin, fish-scale, mussel, and suckerin" were collected and those in which the proteins undertook a structural role were screened. Then, we focused on the structures and applications of protein-based microneedles. Also, the unique features of some protein biopolymers that make them ideal for microneedle construction (e.g., excellent mechanical strength, self-adhesion, and self-assembly), as well as the challenges associated with them were reviewed. Altogether, the proteins identified so far seem not only promising for the fabrication of "better" microneedles in the future but also inspiring for designing biomimetic structural biopolymers with ideal characteristics.

From Soy Waste to Bioplastics: Industrial Proof of Concept.

The global plastic waste problem is pushing for the development of sustainable alternatives, encouraged by stringent regulations combined with increased environmental consciousness. In response, this study presents an industrial-scale proof of concept to produce self-standing, transparent, and flexible bioplastic films, offering a possible solution to plastic pollution and resource valorization. We achieve this by combining amyloid fibrils self-assembled from food waste with methylcellulose and glycerol. Specifically, soy whey and okara, two pivotal protein-rich byproducts of tofu manufacturing, emerge as sustainable and versatile precursors for amyloid fibril formation and bioplastic development. An exhaustive industrial-scale feasibility study involving the transformation of 500 L of soy whey into ∼1 km (27 kg) of bioplastic films underscores the potential of this technology. To extend the practicality of our approach, we further processed a running kilometer of film at the industrial scale into transparent windows for paper-based packaging. The mechanical properties and the water interactions of the novel film are tested and compared with those of commercially used plastic films. By pioneering the large-scale production of biodegradable bioplastics sourced from food byproducts, this work not only simultaneously addresses the dual challenges of plastic pollution and food waste but also practically demonstrates the feasibility of biopolymeric building block valorization for the development of sustainable materials in real-world scenarios.

From Fundamental Amyloid Protein Self-Assembly to Development of Bioplastics.

Proteins can self-assemble into a range of nanostructures as a result of molecular interactions. Amyloid nanofibrils, as one of them, were first discovered with regard to the relevance of neurodegenerative diseases but now have been exploited as building blocks to generate multiscale materials with designed functions for versatile applications. This review interconnects the mechanism of amyloid fibrillation, the current approaches to synthesizing amyloid protein-based materials, and the application in bioplastic development. We focus on the fundamental structures of self-assembled amyloid fibrils and how external factors can affect protein aggregation to optimize the process. Protein self-assembly is essentially the autonomous congregation of smaller protein units into larger, organized structures. Since the properties of the self-assembly can be manipulated by changing intrinsic factors and external conditions, protein self-assembly serves as an excellent building block for bioplastic development. Building on these principles, general processing methods and pathways from raw protein sources to mature state materials are proposed, providing a guide for the development of large-scale production. Additionally, this review discusses the diverse properties of protein-based amyloid nanofibrils and how they can be utilized as bioplastics. The economic feasibility of the protein bioplastics is also compared to conventional plastics in large-scale production scenarios, supporting their potential as sustainable bioplastics for future applications.

Thermoresponsive Injectable Hydrogel To Mimic the Heat- and Strain-Stiffening Behavior of Biopolymers toward Muscle Cell Proliferation.

Injectable hydrogels with nonlinear mechanical attributes to emulate natural biopolymers hold paramount significance in tissue engineering, offering the potential to create scaffolds that seamlessly mimic the biomechanical intricacies of living tissues. Herein, we unveil a synthetic design strategy employing Schiff base chemistry to furnish a peptide-polymer hierarchical contractile injectable hydrogel network. This innovative design demonstrates cross-linking of supramolecular peptide nanostructures such as nanofibers, 1NF, and twisted bundles, 1TB, with a thermosensitive aldehyde-functionalized polymer, PCHO. These networks exhibit interesting nonlinear mechanical stiffening responses to temperature and external stress. Furthermore, the hydrogels transform into a gel state at physiological temperature to exhibit injectable behavior and demonstrate compression load-bearing capabilities. Finally, the hydrogel network exhibits excellent biocompatibility and cell proliferation toward fibroblast, L929, and myoblast, C2C12, to validate their use as potential extracellular matrix mimetic injectable scaffolds.

Proteins for Applied and Functional Materials.

Shifting from a petroleum-based plastic society to a newer one built on circular economy principles requires maximizing the use of renewable resources and resolving the challenges that come with their use. Biopolymers have taken an important role in the design of biobased materials with functional properties, especially those derived from biomass available at a large scale. A number of recent studies have shown how proteins have a new dimension in developing functional materials, taking a step forward from their traditional use in food and biomedicine. Correlating the amino acidic profile of proteins at the nanoscale with their thermomechanical properties at the macroscale enables us to translate these precision polymers into a versatile design of materials, targeting large-scale applications such as foams and food packaging. Moreover, the advances in understanding proteins from a bottom-up perspective reached promising achievements for their use in applications that were not foreseen before, including biosensors, optoelectronics, and semiconductors.

Nanoencapsulation of a Far-Red Absorbing Phthalocyanine into Poly(benzylmalate) Biopolymers and Modulation of Their Photodynamic Efficiency.

Two different poly(benzylmalate) biopolymers, a hydrophobic non-PEGylated (PMLABe73) and an amphiphilic PEGylated derivative (PEG42-b-PMLABe73), have been used to encapsulate a phthalocyanine chosen for its substitution pattern that is highly suitable for photodynamic therapy. Different phthalocyanine/(co)polymers ratios have been used for the nanoprecipitation. A set of six nanoparticles has been obtained. If the amphiphilic PEGylated copolymer proved to be slightly more efficient for the encapsulation and to lower the aggregation of the phthalocyanine inside the nanoparticles, it is, however, the hydrophobic PMLABe73-based nanoparticles that exhibited the best photodynamic efficiency.

Ag Nanoparticle Incorporated Guar Gum-Sodium Alginate-I-Carrageenan Tribiopolymer Blended Cloth Waste Lint Extracted Cellulose Nanocrystal Antimicrobial Composite Film.

A biopolymer-based formulation for robust and active food packaging material was developed. This material consisted of a blend of three biopolymers (guar gum-sodium alginate-i-carrageenan) reinforced by cellulose nanocrystals (CNC) alongside the integration of silver nanoparticles (AgNPs) with varying sizes. The CNC utilized in this process was derived from cloth waste lint (CWL) generated from a household cloth dryer machine. This CNC synthesis underwent a series of solvent treatments to yield the CNC used in the composite. CNC and AgNPs were incorporated into the tribiopolymeric blend matrix to construct a nanocomposite film that showed excellent tensile strength (∼90 MPa). The nanocomposite film also exhibited antimicrobial activity against Escherichia coli ATCC 25922 and Bacillus cereus MTCC 1272. In this report, it was demonstrated that the zone of inhibition against E. coli and B. cereus depends on the variation of size and amount of AgNPs inside the polymeric matrix. The practical applicability of such a film was also demonstrated by applying it to sliced bread and the enhancement of the shelf life of the raped bread was compared with a control. Thus, the guar gum-sodium alginate-i-carrageenan tribiopolymer blend with a cloth waste lint extracted cellulose nanocrystal composite film is antimicrobial, hence, an excellent candidate as an active packaging film.

Simple and complex coacervation in systems involving plant proteins.

Plant-based foods are gaining popularity as alternatives to meat and dairy products due to sustainability and health concerns. As a consequence, there is a renewed interest in the phase behaviour of plant proteins and of mixtures of plant proteins and polysaccharides, in particular in the cases where coacervation is found to occur, i.e., liquid-liquid phase separation (LLPS) into two phases, one of which is rich in biopolymers and one of which is poor in biopolymer. Here we review recent research into both simple and complex coacervation in systems involving plant proteins, and their applications in food- as well as other technologies, such as microencapsulation, microgel production, adhesives, biopolymer films, and more.

Effect of local active fluctuations on structure and dynamics of flexible biopolymers.

Active fluctuations play a significant role in the structure and dynamics of biopolymers (e.g. chromatin and cytoskeletal proteins) that are instrumental in the functioning of living cells. For a large range of experimentally accessible length and time scales, these polymers can be represented as flexible chains that are subjected to spatially and temporally varying fluctuating forces. In this work, we introduce a mathematical framework that correlates the spatial and temporal patterns of the fluctuations to different observables that describe the dynamics and conformations of the polymer. We demonstrate the power of this approach by analyzing the case of a point fluctuation on the polymer with an exponential decay of correlation in time with a finite time constant. Specifically, we identify the length and time scale over which the behavior of the polymer exhibits a significant departure from the behavior of a Rouse chain and the range of impact of the fluctuation along the chain. Furthermore, we show that the conformation of the polymer retains the memory of the active fluctuation from earlier times. Altogether, this work sets the basis for understanding and interpreting the role of spatio-temporal patterns of fluctuations in the dynamics, conformation, and functionality of biopolymers in living cells.

Physicochemical characterization of polyhydroxybutyrate (PHB) produced by the rare halophile Brachybacterium paraconglomeratum MTCC 13074.

BACKGROUND: Polyhydroxybutyrate is a biopolymer produced by bacteria and archaea under nitrogen-limiting conditions. PHB is an essential polymer in the bioplastic sector because of its biodegradability, eco-friendliness, and adaptability. The characterization of PHB is a multifaceted process for studying the structure and its properties. This entire aspect can assure the long-term viability and performance attributes of the PHB. The characteristics of PHB extracted from the halophile Brachybacterium paraconglomeratum were investigated with the objective of making films for application in healthcare. RESULTS: This was the first characterization study on PHB produced by a rare halophile, Brachybacterium paraconglomeratum (MTCC 13074). In this study, the strain produced 2.72 g/l of PHB for.5.1 g/l of biomass under optimal conditions. Methods are described for the determination of the physicochemical properties of PHB. The prominent functional groups CH3 and C = O were observed by FT-IR and the actual chemical structure of the PHB was deduced by NMR. GCMS detects the confirmation of four methyl ester derivatives of the extracted PHB in the sample. Mass spectrometry revealed the molecular weight of methyl 3-hydroxybutyric acid (3HB) present in the extract. The air-dried PHB films were exposed to TGA, DSC and a universal testing machine to determine the thermal profile and mechanical stability. Additionally, the essential property of biopolymers like viscosity was also assessed for the extracted PHB. CONCLUSIONS: The current study demonstrated the consistency and quality of B. paraconglomeratum PHB. Therefore, Brachybacterium sps are also a considerable source of PHB with desired characteristics for industrial production.

DeltaGzip: Computing Biopolymer-Ligand Binding Affinity via Kolmogorov Complexity and Lossless Compression.

The design of biosequences for biosensing and therapeutics is a challenging multistep search and optimization task. In principle, computational modeling may speed up the design process by virtual screening of sequences based on their binding affinities to target molecules. However, in practice, existing machine-learned models trained to predict binding affinities lack the flexibility with respect to reaction conditions, and molecular dynamics simulations that can incorporate reaction conditions suffer from high computational costs. Here, we describe a computational approach called DeltaGzip that evaluates the free energy of binding in biopolymer-ligand complexes from ultrashort equilibrium molecular dynamics simulations. The entropy of binding is evaluated using the Kolmogorov complexity definition of entropy and approximated using a lossless compression algorithm, Gzip. We benchmark the method on a well-studied data set of protein-ligand complexes comparing the predictions of DeltaGzip to the free energies of binding obtained using Jarzynski equality and experimental measurements.

Parameterization of General Organic Polymers within the Open Force Field Framework.

Polymer and chemically modified biopolymer systems present unique challenges to traditional molecular simulation preparation workflows. First, typical polymer and biomolecular input formats, such as Protein Data Bank (PDB) files, lack adequate chemical information needed for the parameterization of new chemistries. Second, polymers are typically too large for accurate partial charge generation methods. In this work, we employ direct chemical perception through the Open Force Field toolkit to create a flexible polymer simulation workflow for organic polymers, encompassing everything from biopolymers to soft materials. We propose and test a new input specification for monomer information that can, along with a 3D conformational geometry, parametrize and simulate most soft-material systems within the same workflow used for smaller ligands. The monomer format encompasses a subset of the SMIRKS substructure query language to uniquely identify chemical information and repeating charges in underspecified systems through matching atomic connectivity. This workflow is combined with several different approaches for automatic partial-charge generation for larger systems. As an initial proof of concept, a variety of diverse polymeric systems were parametrized with the Open Force Field toolkit, including functionalized proteins, DNA, homopolymers, cross-linked systems, and sugars. Additionally, shape properties and radial distribution functions were computed from molecular dynamics simulations of poly(ethylene glycol), polyacrylamide, and poly(N-isopropylacrylamide) homopolymers in aqueous solution and compared to previous simulation results in order to demonstrate a start-to-finish workflow for simulation and property prediction. We expect that these tools will greatly expedite the day-to-day computational research of soft-matter simulations and create a robust atomic-scale polymer specification in conjunction with existing polymer structural notations.