Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science

Thermomechanical and Morphological Properties of Loligo vulgaris Squid Sucker Ring Teeth

Climate change is accelerating the increase of temperatures across the planet and resulting in the warming of oceans. Ocean warming threatens the survival of many aquatic species, including squids, and has introduced physiological, behavioral, and developmental changes, as well as physical changes in their biological materials composition, structure, and properties. Here, we characterize and analyze how the structure, morphology, and mechanical properties of European common squid Loligo vulgaris sucker ring teeth (SRT) are affected by temperature. SRT are predatory teethed structures located inside the suction cups of squids that are used to capture prey and are composed of semicrystalline structural proteins with a high modulus (GPa-range). We observed here that this biological material reversibly softens with temperature, undergoing a glass transition at ∼35°C, to a MPa-range modulus. We analyzed the SRT protein nanostructures as a function of temperature, as well as microscale and macroscale morphological changes, to understand their impact in the material properties. The results suggested that even small deviations from their habitat temperatures can result in significant softening of the material (up to 40% in modulus loss). Temperature changes following recent global climate trends and predictions might affect environmental adaptation in squid species and pose emerging survival challenges to adapt to increasing ocean temperatures.

Accelerated Engineering of ELP-Based Materials through Hybrid Biomimetic-De Novo Predictive Molecular Design

Efforts to engineer high-performance protein-based materials inspired by nature have mostly focused on altering naturally occurring sequences to confer the desired functionalities, whereas de novo design lags significantly behind and calls for unconventional innovative approaches. Here, using partially disordered elastin-like polypeptides (ELPs) as initial building blocks this work shows that de novo engineering of protein materials can be accelerated through hybrid biomimetic design, which this work achieves by integrating computational modeling, deep neural network, and recombinant DNA technology. This generalizable approach involves incorporating a series of de novo-designed sequences with α-helical conformation and genetically encoding them into biologically inspired intrinsically disordered repeating motifs. The new ELP variants maintain structural conformation and showed tunable supramolecular self-assembly out of thermal equilibrium with phase behavior in vitro. This work illustrates the effective translation of the predicted molecular designs in structural and functional materials. The proposed methodology can be applied to a broad range of partially disordered biomacromolecules and potentially pave the way toward the discovery of novel structural proteins.

Alternative strategies for the recombinant synthesis, DOPA modification and analysis of mussel foot proteins - A case study for Mefp-3 from Mytilus edulis

Mussel foot proteins (Mfps) possess unique binding properties to various surfaces due to the presence of L-3,4-dihydroxyphenylalanine (DOPA). Mytilus edulis foot protein-3 (Mefp-3) is one of several proteins in the byssal adhesive plaque. Its localization at the plaque-substrate interface approved that Mefp-3 plays a key role in adhesion. Therefore, the protein is suitable for the development of innovative bio-based binders. However, recombinant Mfp-3s are mainly purified from inclusion bodies under denaturing conditions. Here, we describe a robust and reproducible protocol for obtaining soluble and tag-free Mefp-3 using the SUMO-fusion technology. Additionally, a microbial tyrosinase from Verrucomicrobium spinosum was used for the in vitro hydroxylation of peptide-bound tyrosines in Mefp-3 for the first time. The highly hydroxylated Mefp-3, confirmed by MALDI-TOF-MS, exhibited excellent adhesive properties comparable to a commercial glue. These results demonstrate a concerted and simplified high yield production process for recombinant soluble and tag-free Mfp3-based proteins with on demand DOPA modification.

Bridging Nature and Engineering: Protein-Derived Materials for Bio-Inspired Applications

The sophisticated, elegant protein-polymers designed by nature can serve as inspiration to redesign and biomanufacture protein-based materials using synthetic biology. Historically, petro-based polymeric materials have dominated industrial activities, consequently transforming our way of living. While this benefits humans, the fabrication and disposal of these materials causes environmental sustainability challenges. Fortunately, protein-based biopolymers can compete with and potentially surpass the performance of petro-based polymers because they can be biologically produced and degraded in an environmentally friendly fashion. This paper reviews four groups of protein-based polymers, including fibrous proteins (collagen, silk fibroin, fibrillin, and keratin), elastomeric proteins (elastin, resilin, and wheat glutenin), adhesive/matrix proteins (spongin and conchiolin), and cyanophycin. We discuss the connection between protein sequence, structure, function, and biomimetic applications. Protein engineering techniques, such as directed evolution and rational design, can be used to improve the functionality of natural protein-based materials. For example, the inclusion of specific protein domains, particularly those observed in structural proteins, such as silk and collagen, enables the creation of novel biomimetic materials with exceptional mechanical properties and adaptability. This review also discusses recent advancements in the production and application of new protein-based materials through the approach of synthetic biology combined biomimetics, providing insight for future research and development of cutting-edge bio-inspired products. Protein-based polymers that utilize nature's designs as a base, then modified by advancements at the intersection of biology and engineering, may provide mankind with more sustainable products.

Deciphering protein-mediated underwater adhesion in an invasive biofouling ascidian: Discovery, validation, and functional mechanism of an interfacial protein

Discovering macromolecules and understanding the associated mechanisms involved in underwater adhesion are essential for both studying the fundamental ecology of benthos in aquatic ecosystems and developing biomimetic adhesive materials in industries. Here, we employed quantitative proteomics to assess protein expression variations during the development of the distinct adhesive structure - stolon in the model fouling ascidian, Ciona robusta. We found 16 adhesive protein candidates with increased expression in the stolon, with ascidian adhesive protein 1 (AAP1) being particularly rich in adhesion-related signal peptides, amino acids, and functional domains. Western blot and immunolocalization analyses confirmed the prominent AAP1 signals in the mantle, tunic, stolon, and adhesive footprints, indicating the interfacial role of this protein. Surface coating and atomic force microscopy experiments verified AAP1's adhesion to diverse materials, likely through the specific electrostatic and hydrophobic amino acid interactions with various substrates. In addition, molecular docking calculations indicated the AAP1's potential for cross-linking via hydrogen bonds and salt bridges among Von Willebrand factor type A domains, enhancing its adhesion capability. Altogether, the newly discovered interfacial protein responsible for permanent underwater adhesion, along with the elucidated adhesion mechanisms, are expected to contribute to the development of biomimetic adhesive materials and anti-fouling strategies. STATEMENT OF SIGNIFICANCE: Discovering macromolecules and studying their associated mechanisms involved in underwater adhesion are essential for understanding the fundamental ecology of benthos in aquatic ecosystems and developing innovative bionic adhesive materials in various industries. Using multidisciplinary analytical methods, we identified an interfacial protein - Ascidian Adhesive Protein 1 (AAP1) from the model marine fouling ascidian, Ciona robusta. The interfacial functions of AAP1 are achieved by electrostatic and hydrophobic interactions, and the Von Willebrand factor type A domain-based cross-linking likely enhances AAP1's interfacial adhesion. The identification and validation of the interfacial functions of AAP1, combined with the elucidation of adhesion mechanisms, present a promising target for the development of biomimetic adhesive materials and the formulation of effective anti-fouling strategies.

Bioinspired Squid Peptides─A Tale of Curiosity-Driven Research Leading to Unforeseen Biomedical Applications

The molecular design of many peptide-based materials originates from structural proteins identified in living organisms. Prominent examples that have garnered broad interdisciplinary research interest (chemistry, materials science, bioengineering, etc.) include elastin, silk, or mussel adhesive proteins. The critical first steps in this type of research are to identify a convenient model system of interest followed by sequencing the prevailing proteins from which these biological structures are assembled. In our laboratory, the main model systems for many years have been the hard biotools of cephalopods, particularly their parrot-like tough beak and their sucker ring teeth (SRT) embedded within the sucker cuptions that line the interior surfaces of their arms and tentacles. Unlike the majority of biological hard tissues, these structures are devoid of biominerals and consist of protein/polysaccharide biomolecular composites (the beak) or, in the case of SRT, are entirely made of proteins that are assembled by supramolecular interactions.In this Account, we chronicle our journey into the discovery of these intriguing biological materials. We initially focus on their excellent mechanical robustness followed by the identification and sequencing of the structural proteins from which they are built, using the latest "omics" techniques including next-generation sequencing and high-throughput proteomics. A common feature of these proteins is their modular architecture at the molecular level consisting of short peptide repeats. We describe the molecular design of these peptide building blocks, highlighting the consensus motifs identified to play a key role in biofabrication and in regulating the mechanical properties of the macroscopic biological material. Structure/property relationships unveiled through advanced spectroscopic and scattering techniques, including Raman, infrared, circular dichroism, and NMR spectroscopies as well as wide-angle and small-angle X-ray scattering, are also discussed.We then present recent developments in exploiting the discovered molecular designs to engineer peptides and their conjugates for promising biomedical applications. One example includes short peptide hydrogels that self-assemble entirely under aqueous conditions and simultaneously encapsulate large macromolecules during the gelation process. A second example involves peptide coacervate microdroplets produced by liquid-liquid phase separation. These microdroplets are capable of recruiting and delivering large macromolecular therapeutics (genes, mRNA, proteins, peptides, CRISPR/Cas 9 modalities, etc.) into mammalian cells, which introduces exciting prospects in cancer, gene, and immune therapies.This Account also serves as a testament to how curiosity-driven explorations, which may lack an obvious practical goal initially, can lead to discoveries with unexpected and promising translational potential.

A Minispidroin Guides the Molecular Design for Cellular Condensation Mechanisms in S. cerevisiae

Structural engineering of molecules for condensation is an emerging technique within synthetic biology. Liquid-liquid phase separation of biomolecules leading to condensation is a central step in the assembly of biological materials into their functional forms. Intracellular condensates can also function within cells in a regulatory manner to facilitate reaction pathways and to compartmentalize interactions. We need to develop a strong understanding of how to design molecules for condensates and how their in vivo-in vitro properties are related. The spider silk protein NT2RepCT undergoes condensation during its fiber-forming process. Using parallel in vivo and in vitro characterization, in this study, we mapped the effects of intracellular conditions for NT2RepCT and its several structural variants. We found that intracellular conditions may suppress to some extent condensation whereas molecular crowding affects both condensate properties and their formation. Intracellular characterization of protein condensation allowed experiments on pH effects and solubilization to be performed within yeast cells. The growth of intracellular NT2RepCT condensates was restricted, and Ostwald ripening was not observed in yeast cells, in contrast to earlier observations in E. coli. Our results lead the way to using intracellular condensation to screen for properties of molecular assembly. For characterizing different structural variants, intracellular functional characterization can eliminate the need for time-consuming batch purification and in vitro condensation. Therefore, we suggest that the in vivo-in vitro understanding will become useful in, e.g., high-throughput screening for molecular functions and in strategies for designing tunable intracellular condensates.

Biomimetic Silk Architectures Outperform Animal Horns in Strength and Toughness

Structural biomimicry is an intelligent approach for developing lightweight, strong, and tough materials (LSTMs). Current fabrication technologies, such as 3D printing and two-photon lithography often face challenges in constructing complex interlaced structures, such as the sinusoidal crossed herringbone structure that contributes to the ultrahigh strength and fracture toughness of the dactyl club of peacock mantis shrimps. Herein, bioinspired LSTMs with laminated or herringbone structures is reported, by combining textile processing and silk fiber "welding" techniques. The resulting biomimetic silk LSTMs (BS-LSTMs) exhibit a remarkable combination of lightweight with a density of 0.6-0.9 g cm-3 , while also being 1.5 times stronger and 16 times more durable than animal horns. These findings demonstrate that BS-LSTMs are among the toughest natural materials made from silk proteins. Finite element simulations further reveal that the fortification and hardening of BS-LSTMs arise primarily from the hierarchical organization of silk fibers and mechanically transferable meso-interfaces. This study highlights the rational, cost-effective, controllable mesostructure, and transferable strategy of integrating textile processing and fiber "welding" techniques for the fabrication of BS-LSTMs with advantageous structural and mechanical properties. These findings have significant implications for a wide range of applications in biomedicine, mechanical engineering, intelligent textiles, aerospace industries, and beyond.

Silk Fibroin and Sericin Differentially Potentiate the Paracrine and Regenerative Functions of Stem Cells Through Multiomics Analysis

Silk fibroin (SF) and sericin (SS), the two major proteins of silk, are attractive biomaterials with great potential in tissue engineering and regenerative medicine. However, their biochemical interactions with stem cells remain unclear. In this study, multiomics are employed to obtain a global view of the cellular processes and pathways of mesenchymal stem cells (MSCs) triggered by SF and SS to discern cell-biomaterial interactions at an in-depth, high-throughput molecular level. Integrated RNA sequencing and proteomic analysis confirm that SF and SS initiate widespread but distinct cellular responses and potentiate the paracrine functions of MSCs that regulate extracellular matrix deposition, angiogenesis, and immunomodulation through differentially activating the integrin/PI3K/Akt and glycolysis signaling pathways. These paracrine signals of MSCs stimulated by SF and SS effectively improve skin regeneration by regulating the behavior of multiple resident cells (fibroblasts, endothelial cells, and macrophages) in the skin wound microenvironment. Compared to SS, SF exhibits better immunomodulatory effects in vitro and in vivo, indicating its greater potential as a carrier material of MSCs for skin regeneration. This study provides comprehensive and reliable insights into the cellular interactions with SF and SS, enabling the future development of silk-based therapeutics for tissue engineering and stem cell therapy.

Large-Scale, Proteinaceous Nanotube Arrays with Programmable Hydrophobicity, Oleophilicity, and Gas Permeability

Nanotubular structures possess remarkable advantages in a broad range of areas, such as catalysis, sensing, microencapsulation, selective mass transport, filtration, and drug delivery. While the fields of carbon nanotubes and nanotubes made of several noncarbon materials (e.g., metals, oxides, semiconductors) have been progressing rapidly, proteinaceous nanotubes remained largely underexplored. Here, by retrofitting a template wetting approach with multiple silk-based suspensions, we present a rapidly scalable and robust technology for fabricating large arrays (e.g., 20 × 20 cm²) of well-aligned 1D nanostructures made of silk proteins. Benefiting from the polymorphic nature of silk, precise control over the size, density, aspect ratio, and morphology (tubes versus pillars) of silk nanostructures is achieved, which then allows for programmable modulation of the end materials' functions and properties (e.g., hydrophobicity, oleophilicity, and gas permeability). The silk nanotube arrays fabricated present great utility as antifouling coatings against marine algae and in oil extraction from oil-water mixtures.

The Holothuria leucospilota genome elucidates sacrificial organ expulsion and bioadhesive trap enriched with amyloid-patterned proteins

Some tropical sea cucumbers of the family Holothuriidae can efficiently repel or even fatally ensnare predators by sacrificially ejecting a bioadhesive matrix termed the Cuvierian organ (CO), so named by the French zoologist Georges Cuvier who first described it in 1831. Still, the precise mechanisms for how adhesiveness genetically arose in CO and how sea cucumbers perceive and transduce danger signals for CO expulsion during defense have remained unclear. Here, we report the first high-quality, chromosome-level genome assembly of Holothuria leucospilota, an ecologically significant sea cucumber with prototypical CO. The H. leucospilota genome reveals characteristic long-repeat signatures in CO-specific outer-layer proteins, analogous to fibrous proteins of disparate species origins, including spider spidroin and silkworm fibroin. Intriguingly, several CO-specific proteins occur with amyloid-like patterns featuring extensive intramolecular cross-β structures readily stainable by amyloid indicator dyes. Distinct proteins within the CO connective tissue and outer surface cooperate to give the expelled matrix its apparent tenacity and adhesiveness, respectively. Genomic evidence offers further hints that H. leucospilota directly transduces predator-induced mechanical pressure onto the CO surface through mediation by transient receptor potential channels, which culminates in acetylcholine-triggered CO expulsion in part or in entirety. Evolutionarily, innovative events in two distinct regions of the H. leucospilota genome have apparently spurred CO's differentiation from the respiratory tree to a lethal defensive organ against predators.

Protein-Based Biological Materials: Molecular Design and Artificial Production

Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.

Modulation of Mechanical Properties of Short Bioinspired Peptide Materials by Single Amino-Acid Mutations

The occurrence of modular peptide repeats in load-bearing (structural) proteins is common in nature, with distinctive peptide sequences that often remain conserved across different phylogenetic lineages. These highly conserved peptide sequences endow specific mechanical properties to the material, such as toughness or elasticity. Here, using bioinformatic tools and phylogenetic analysis, we have identified the GX8 peptide with the sequence GLYGGYGX (where X can be any residue) in a wide range of organisms. By simple mutation of the X residue, we demonstrate that GX8 can be self-assembled into various supramolecular structures, exhibiting vastly different physicochemical and viscoelastic properties, from liquid-like coacervate microdroplets to hydrogels to stiff solid materials. A combination of spectroscopic, electron microscopy, mechanical, and molecular dynamics studies is employed to obtain insights into molecular scale interactions driving self-assembly of GX8 peptides, underscoring that π-π stacking and hydrophobic interactions are the drivers of peptide self-assembly, whereas the X residue determines the extent of hydrogen bonding that regulates the macroscopic mechanical response. This study highlights the ability of single amino-acid polymorphism to tune the supramolecular assembly and bulk material properties of GX8 peptides, enabling us to cover a broad range of potential biomedical applications such as hydrogels for tissue engineering or coacervates for drug delivery.

Molecular cloning, expression, mRNA secondary structure and immunological characterization of mussel foot proteins (Mfps) (Mollusca: Bivalvia)

The macroscale production of mussel foot proteins (Mfps) in the expression system has not succeeded to date. The principal reasons for this are low levels of expression and yield of Mfps, lack of post-translational modifications (PTMs), and immunological toxic effects on the host system. Identification of post-translational modification sites, suitable expression hosts, and immunological responses through an experimental approach is very costly and time-consuming. However, in the present study, in silico post-translation modification, antigenicity, allergenicity, and the immunological reaction of all available Mfps were characterized. Furthermore, all Mfps were codon optimized in three different expression systems to determine the best expression host. Finally, we performed the in-silico cloning of all codon-optimized Mfps in a suitable host (E. coli K12, pET28a(+) vector) and analyzed the secondary structure of mRNA and its structural stability. Among the 78 Mfps, six fps are considered potential allergenic proteins, six fps are considered non-allergenic proteins, and all other fps are probably allergenic. High antigenicity was observed in bacterial cells as compared to yeast and tumor cells. Nevertheless, the predicted expression of Mfps in a bacterial host is higher than in other expression hosts. Important to note that all Mfps showed significant immunological activity in the human system, and we concluded that these antigenic, allergenic, and immunological properties are directly correlated with their amino acid composition. The study's major goal is to provide a comprehensive understanding of Mfps and aid in the future genetic engineering and expression of Mfps and its diverse applications in different fields.Communicated by Ramaswamy H. Sarma.

Voltage controlled shutter regulates channel size and motion direction of protein aperture as durable nano-electric rectifier-----An opinion in biomimetic nanoaperture

In optical devices such as camera or microscope, an aperture is used to regulate light intensity for imaging. Here we report the discovery and construction of a durable bio-aperture at nanometerscale that can regulate current at the pico-ampere scale. The nano-aperture is made of 12 identical protein subunits that form a 3.6-nm channel with a shutter and "one-way traffic" property. This shutter responds to electrical potential differences across the aperture and can be turned off for double stranded DNA translocation. This voltage enables directional control, and three-step regulation for opening and closing. The nano-aperture was constructed in vitro and purified into homogeneity. The aperture was stable at pH2-12, and a temperature of -85C-60C. When an electrical potential was held, three reproducible discrete steps of current flowing through the channel were recorded. Each step reduced 32% of the channel dimension evident by the reduction of the measured current flowing through the aperture. The current change is due to the change of the resistance of aperture size. The transition between these three distinct steps and the direction of the current was controlled via the polarity of the voltage applied across the aperture. When the C-terminal of the aperture was fused to an antigen, the antibody and antigen interaction resulted in a 32% reduction of the channel size. This phenomenon was used for disease diagnosis since the incubation of the antigen-nano-aperture with a specific cancer antibody resulted in a change of 32% of current. The purified truncated cone-shape aperture automatically self-assembled efficiently into a sheet of the tetragonal array via head-to-tail self-interaction. The nano-aperture discovery with a controllable shutter, discrete-step current regulation, formation of tetragonal sheet, and one-way current traffic provides a nanoscale electrical circuit rectifier for nanodevices and disease diagnosis.

Plastics in the environment as potential threat to life: an overview

Plastics have become inevitable for human beings in their daily life. Million tons of plastic waste is entering in oceans, soil, freshwater, and sediments. Invasion of plastics in different ecosystems is causing severe problems to inhabitants. Wild animals such as seabirds, fishes, crustaceans, and other invertebrates are mostly effected by plastic entanglements and organic pollutants absorbed and carried by plastics/microplastics. Plastics can also be potentially harmful to human beings and other mammals. Keeping in view the possible harms of plastics, some mitigation strategies must be adopted which may include the use of bioplastics and some natural polymers such as squid-ring teeth protein. This review focuses on the possible sources of intrusion and fate of plastics in different ecosystems, their potential deleterious effects on wildlife, and the measures that can be taken to minimize and avoid the plastic use.

Molecular Insights into the Self-Assembly of Block Copolymer Suckerin Polypeptides into Nanoconfined β-Sheets

Suckerin in squid sucker ring teeth is a block-copolymer peptide comprised of two repeating modules-the alanine and histidine-rich M1 and the glycine-rich M2. Suckerin self-assemblies display excellent thermo-plasticity and pH-responsive properties, along with the high biocompatibility, biodegradability, and sustainability. However, the self-assembly mechanism and the detailed role of each module are still elusive, limiting the capability of applying and manipulating such biomaterials. Here, the self-assembly dynamics of the two modules and two minimalist suckerin-mimetic block-copolymers, M1-M2-M1 and M2-M1-M2, in silico is investigated. The simulation results demonstrate that M2 has a stronger self-association but weaker β-sheet propensities than M1. The high self-assembly propensity of M2 allows the minimalist block-copolymer peptides to coalesce with microphase separation, enabling the formation of nanoconfined β-sheets in the matrix formed by M1-M2 contacts. Since these glycine-rich fragments with scatted hydrophobic and aromatic residues are building blocks of many other block-copolymer peptides, the study suggests that these modules function as the "molecular glue" in addition to the flexible linker or spacer to drive the self-assembly and microphase separation. The uncovered molecular insights may help understand the structure and function of suckerin and also aid in the design of functional block-copolymer peptides for nanotechnology and biomedicine applications.

Diffusive Dynamic Modes of Recombinant Squid Ring Teeth Proteins by Neutron Spectroscopy

Stimuli-responsive structural proteins are emerging as promising biocompatible materials for a wide range of biological and nonbiological applications. To understand the physical properties of structural proteins and to replicate their performance in biosynthetic systems, there is a need to understand the molecular mechanisms and relationships that regulate their structure, dynamics, and properties. Here, we study the dynamics of a recombinant squid-inspired protein from Loligo vulgaris (Lv18) by elastic and quasielastic neutron scattering (QENS) to understand the connection between nanostructure, chain dynamics, and mechanical properties. Lv18 is a semicrystalline structural protein, which is plasticized by water above its glass transition temperature at 35 °C. Elastic scans revealed an increased protein chain mobility upon hydration, superimposed dynamic processes, and a decrease in dynamic transition temperatures. Further analysis by QENS revealed that while dry Lv18 protein dynamics are dominated by localized methyl group rotations, hydrated Lv18 dynamics are dominated by the confined diffusion of flexible chains within a β-sheet nanocrystalline network (8 Å of confinement radius). Our findings establish a relationship between the segment block architecture of Lv18, the diffusive motions within the protein structure, and the mechanical properties of recombinant squid proteins, which will advance the molecular design of novel high-performance protein-inspired materials with tailored dynamics and mechanical properties.

Nanolattice-Forming Hybrid Collagens in Protective Shark Egg Cases

Nanoscopic structural control with long-range ordering remains a profound challenge in nanomaterial fabrication. The nanoarchitectured egg cases of elasmobranchs rely on a hierarchically ordered latticework for their protective function─serving as an exemplary system for nanoscale self-assembly. Although the proteinaceous precursors are known to undergo intermediate liquid crystalline phase transitions before being structurally arrested in the final nanolattice architecture, their sequences have so far remained unknown. By leveraging RNA-seq and proteomic techniques, we identified a cohort of nanolattice-forming proteins comprising a collagenous midblock flanked by domains typically associated with innate immunity and network-forming collagens. Structurally homologous proteins were found in the genomes of other egg-case-producing cartilaginous fishes, suggesting a conserved molecular self-assembly strategy. The identity and stabilizing role of cross-links were subsequently elucidated using mass spectrometry and in situ small-angle X-ray scattering. Our findings provide a new design approach for protein-based liquid crystalline elastomers and the self-assembly of nanolattices.

Liquid-Liquid Phase Separation of the Green Mussel Adhesive Protein Pvfp-5 is Regulated by the Post-Translated Dopa Amino Acid

The underwater adhesive prowess of aquatic mussels has been largely attributed to the abundant post-translationally modified amino acid l-3,4-dihydroxyphenylalanine (Dopa) in mussel foot proteins (MFPs) that make up their adhesive threads. More recently, it has been suggested that during thread fabrication, MFPs form intermediate fluidic phases such as liquid crystals or coacervates regulated by a liquid-liquid phase separation (LLPS) process. Here, it is shown that Dopa plays another central role during mussel fiber formation, by enabling LLPS of Pvfp-5β, a main MFP of the green mussel Perna viridis. Using residue-specific substitution of Tyrosine (Tyr) for Dopa during recombinant expression, Dopa-substituted Pvfp-5β is shown to exhibit LLPS under seawater-like conditions, whereas the Tyr-only version forms insoluble aggregates. Combining quantum chemistry calculations and solution NMR, a transient H-bonding network requiring the two hydroxyl groups of Dopa is found to be critical to enable LLPS in Dopa-mutated Pvfp-5β. Overall, the study suggests that Dopa plays an important role in regulating LLPS of MFPs, which may be critical to concentrate the adhesive proteins at the plaque/substrate interface and therefore produce a more robust adhesive. The findings also provide molecular-level lessons to guide biomanufacturing of protein-based materials such as bioadhesives and load-bearing fibers.

Complete Sequences of the Velvet Worm Slime Proteins Reveal that Slime Formation is Enabled by Disulfide Bonds and Intrinsically Disordered Regions

The slime of velvet worms (Onychophora) is a strong and fully biodegradable protein material, which upon ejection undergoes a fast liquid-to-solid transition to ensnare prey. However, the molecular mechanisms of slime self-assembly are still not well understood, notably because the primary structures of slime proteins are yet unknown. Combining transcriptomic and proteomic studies, the authors have obtained the complete primary sequences of slime proteins and identified key features for slime self-assembly. The high molecular weight slime proteins contain cysteine residues at the N- and C-termini that mediate the formation of multi-protein complexes via disulfide bonding. Low complexity domains in the N-termini are also identified and their propensity for liquid-liquid phase separation is established, which may play a central role in slime biofabrication. Using solid-state nuclear magnetic resonance, rigid and flexible domains of the slime proteins are mapped to specific peptide domains. The complete sequencing of major slime proteins is an important step toward sustainable fabrication of polymers inspired by the velvet worm slime.

Comparative proteomics for an in-depth understanding of bioadhesion mechanisms and evolution across metazoans

Bioadhesion is a critical process for many marine and freshwater invertebrate animals. Bioadhesives mainly made of proteins have remarkable adhesive ability underwater. Unraveling the molecular composition of bioadhesives is fundamental to understanding their physiological roles as well as their potential for biotechnology applications and antibiofouling strategies. With the development of high-throughput methods such as proteomics, bioadhesive protein data in diverse taxa are rapidly accumulating, but the common mechanism across species is elusive due to the vast variety of bioadhesives. In this review, bioadhesive proteins from various taxa are reviewed, with the aim of facilitating researchers to appreciate the diversity of bioadhesive proteins (mostly 20-40) across species. By comparing proteomes across species, it was found that glycine-rich, epidermal growth factor, peroxidase, and DOPA together with typical extracellular domains are the most commonly used domains. Additionally, permanent and temporary adhesion show obvious differences in terms of domains or proteins. A basic recipe for bioadhesives composed of six components is proposed: structural elements, extracellular domains, modification enzymes, proteinase inhibitors, cytoskeletal proteins, and others. The extracellular domains are mostly related to interactions with other macromolecules (proteins, carbohydrates, and lipids), suggesting that domain shuffling and macromolecule interaction might be fundamental for bioadhesive evolution.

Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-right Shell Asymmetry in Bivalves

Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems. Across these ancient lineages, colony-founding larvae anchor themselves either by byssus production or by cemented attachment. The latter mode of sessile life is strongly molded by left-right shell asymmetry during larval development of Ostreoida oysters such as Crassostrea hongkongensis. Here, we sequenced the genome of C. hongkongensis in high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry. Importantly, loss of the homeobox gene Antennapedia (Antp) and broad expansion of lineage-specific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves. Comparative transcriptomic analysis shows a conspicuous divergence between left-right asymmetrical C. hongkongensis and symmetrical Pinctada fucata in their expression profiles. Especially, a couple of orthologous transcription factor genes and lineage-specific shell-related gene families including that encoding tyrosinases are elevated, and may cooperatively govern asymmetrical shell formation in Ostreoida oysters.

Omics Technologies for High-Throughput-Screening of Cell-Biomaterial Interactions

Recent research effort in biomaterial development has largely focused on engineering bio-instructive materials to stimulate specific cell signaling. Assessing the biological performance of these materials using time-consuming and trial-and-error traditional...

Evolutionary development of the cephalopod arm armature: a review

The cephalopod arm armature is certainly one of the most important morphological innovations responsible for the evolutionary success of the Cephalopoda. New palaeontological discoveries in the recent past afford to review and reassess origin and homology of suckers, sucker rings, hooks, and cirri. Since a priori character state reconstructions are still ambiguous, we suggest and discuss three different evolutionary scenarios. Each of them is based on the following assumptions: (1) Neocoleoidea uniting extant Decabrachia and Octobrachia is monophyletic (= proostracum-bearing coleoids); (2) extinct Belemnitida and Diplobelida are stem decabrachians; (3) proostracum-less coleoids (Hematitida, Donovaniconida, Aulacoceratida) represent stem-neocoleoids; (4) Ammonoidea and Bactritoidea are stem coleoids. We consider a scenario where belemnoid hooks derived from primitive suckers as well-supported. Regarding belemnoid hooks and suckers as homologues implies that belemnoid, oegopsid, and probably ammonoid arm hooks arose through parallel evolution. Our conclusions challenge the widespread opinion, whereupon belemnoid hooks evolved de novo, and instead support earlier ideas formulated by Sigurd von Boletzky.

Exploration of sea anemone-inspired high-performance biomaterials with enhanced antioxidant activity

Antioxidant biomaterials have attracted much attention in various biomedical fields because of their effective inhibition and elimination of reactive oxygen species (ROS) in pathological tissues. However, the difficulty in ensuring biocompatibility, biodegradability and bioavailability of antioxidant materials has limited their further development. Novel bioavailable antioxidant materials that are derived from natural resources are urgently needed. Here, an integrated multi-omics method was applied to fabricate antioxidant biomaterials. A key cysteine-rich thrombospondin-1 type I repeat-like (TSRL) protein was efficiently discovered from among 1262 adhesive components and then used to create a recombinant protein with a yield of 500 mg L^-1. The biocompatible TSRL protein was able to self-assemble into either a water-resistant coating through Ca²⁺-mediated coordination or redox-responsive hydrogels with tunable physical properties. The TSRL-based hydrogels showed stronger 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging rates than glutathione (GSH) and ascorbic acid (Aa) and protected cells against external oxidative stress significantly more effectively. When topically applied to mice skin, TSRL alleviated epidermal hyperplasia and suppressed the degradation of collagen and elastic fibers caused by ultraviolet radiation B (UVB) irradiation, confirming that it enhanced antioxidant activity in vivo. This is the first study to successfully characterize natural antioxidant biomaterials created from marine invertebrate adhesives, and the findings indicate the excellent prospects of these biomaterials for great applications in tissue regeneration and cosmeceuticals.

A buried glutamate in the cross-β core renders β-endorphin fibrils reversible

Functional amyloids are abundant in living organisms from prokaryotes to eukaryotes playing diverse biological roles. In contrast to the irreversible aggregation of most known pathological amyloids, we postulate that naturally-occurring functional amyloids are reversible under evolutionary pressure to be able to modulate the fibrillization process, reuse the composite peptides, or perform their biological functions. β-Endorphin, an endogenous opioid peptide hormone, forms such kinds of reversible amyloid fibrils in secretory granules for efficient storage and returns to the functional state of monomers upon release into the blood. The environmental change between low pH in secretory granules and neutral pH in extracellular spaces is believed to drive the reversible fibrillization of β-endorphin. Here, we investigate the critical role of a buried glutamate, Glu8, in the pH-responsive disassembly of β-endorphin fibrils using all-atom molecular dynamics simulations along with structure-based pKa prediction. The fibril was stable at pH 5.5 or lower with all the buried Glu8 residues protonated and neutrally charged. After switching to neutral pH, the Glu8 residues of peptides at the outer layers of the ordered fibrils became deprotonated due to partial solvent exposure, causing sheet-to-coil conformational changes and subsequent exposure of adjacent Glu8 residues in the inner chains. Via iterative deprotonation of Glu8 and induced structural disruption, all Glu8 residues would be progressively deprotonated. Electrostatic repulsion between deprotonated Glu8 residues along with their high solvation tendency disrupted the hydrogen bonding between the β1 strands and increased the solvent exposure of those otherwise buried residues in the cross-β core. Overall, our computational study reveals that the strategic positioning of ionizable residues into the cross-β core is a potential approach for designing reversible amyloid fibrils as pH-responsive smart bio-nanomaterials.

Integrated transcriptomics and proteomics revealed the distinct toxicological effects of multi-metal contamination on oysters

The Pearl River Estuary (PRE) is the largest estuary in southern China and under high metal stress. In the present study, we employed an integrated method of transcriptomics and proteomics to investigate the ecotoxicological effects of trace metals on the Hong Kong oyster Crassostrea hongkongensis. Three oyster populations with distinct spatial distributions of metals were sampled, including the Control (Station QA, the lowest metal levels), the High Cd (Station JZ, the highest Cd), and the High Zn-Cu-Cr-Ni (Station LFS, with the highest levels of zinc, copper, chromium, and nickel). Dominant metals in oysters were differentiated by principal component analysis (PCA), and theirgene and protein profiles were studied using RNA-seq and iTRAQ techniques. Of the 2250 proteins identified at both protein and RNA levels, 70 proteins exhibited differential expressions in response to metal stress in oysters from the two contaminated stations. There were 8 proteins altered at both stations, with the potential effects on mitochondria and endoplasmic reticulum by Ag. The genotoxicity, including impaired DNA replication and transcription, was specifically observed in the High Cd oysters with the dominating influence of Cd. The structural components (cytoskeleton and chromosome-associated proteins) were impaired by the over-accumulated Cu, Zn, Cr, and Ni at Station LFS. However, enhanced tRNA biogenesis and exosome activity might help the oysters to alleviate the toxicities resulting from their exposure to these metals. Our study provided comprehensive information on the molecular changes in oysters at both protein and RNA levels in responding to multi-levels of trace metal stress.

Application of Thermoresponsive Intrinsically Disordered Protein Polymers in Nanostructured and Microstructured Materials

Modulation of inter- and intramolecular interactions between bioinspired designer molecules can be harnessed for developing functional structures that mimic the complex hierarchical organization of multicomponent assemblies observed in nature. Furthermore, such multistimuli-responsive molecules offer orthogonal tunability for generating versatile multifunctional platforms via independent biochemical and biophysical cues. In this review, the remarkable physicochemical and mechanical properties of genetically engineered protein polymers derived from intrinsically disordered proteins, specifically elastin and resilin, are discussed. This review highlights emerging technologies which use them as building blocks in the fabrication of highly programmable structured biomaterials for applications in delivery of biotherapeutic cargo and regenerative medicine.

Protein-mediated bioadhesion in marine organisms: A review

Protein-mediated bioadhesion is one of the crucial physiological processes in marine organisms, by which they can firmly adhere to underwater substrates. Most marine adhesive organisms are biofoulers, causing negative effects on marine ecosystems and huge economic losses to aquaculture and maritime industries. Furthermore, adhesive proteins in these organisms are promising bionic candidates for high-performance artificial materials with great application value. In-depth understanding of the bioadhesion in marine ecosystems is of dual significance for resolving biofouling issue and developing marine bionic products. Here, we review the research progress of protein-mediated bioadhesion in marine organisms. The adhesion processes such as protein biosynthesis and secretion are similar among organisms, but the detailed features such as compositions, structures, and molecular functions of adhesive proteins are distinct. Hydroxylation, glycosylation, and phosphorylation are important post-translational modifications during the processes of adhesion. The contents of some amino acids such as glycine, tyrosine and cysteine involved in underwater adhesion are significantly higher, which is a sequence feature of barnacle cement and mussel foot proteins. The amyloid structures and conserved domains/motifs such as EGF and vWFA distributed in adhesive proteins are involved in the underwater adhesion. In addition, the oxidative cross-linking also plays an important role in marine bioadhesion. Overall, the unique and common features identified for the protein-mediated bioadhesion in diverse marine organisms here provide background information and essential reference for characterizing marine adhesive proteins and associated functional domains, formulating antifouling strategies, and developing novel biomimetic adhesives.

Nanocapsules Produced by Nanoprecipitation of Designed Suckerin-Silk Fusion Proteins

Herein, we report on the precise design of a modular fusion protein amenable to the construction of nanocapsules by nanoprecipitation. The central squid suckerin-derived peptide block provides structural stability, whereas both termini from spider silk fibroins make the protein highly soluble at physiological pH, a critical requirement for the nanoprecipitation process. With this design, nanocapsules consisting of fusion protein shells and oily cores with sizes in the range of 190-250 nm are built in a straightforward manner.

High-Throughput Methods in the Discovery and Study of Biomaterials and Materiobiology

The complex interaction of cells with biomaterials (i.e., materiobiology) plays an increasingly pivotal role in the development of novel implants, biomedical devices, and tissue engineering scaffolds to treat diseases, aid in the restoration of bodily functions, construct healthy tissues, or regenerate diseased ones. However, the conventional approaches are incapable of screening the huge amount of potential material parameter combinations to identify the optimal cell responses and involve a combination of serendipity and many series of trial-and-error experiments. For advanced tissue engineering and regenerative medicine, highly efficient and complex bioanalysis platforms are expected to explore the complex interaction of cells with biomaterials using combinatorial approaches that offer desired complex microenvironments during healing, development, and homeostasis. In this review, we first introduce materiobiology and its high-throughput screening (HTS). Then we present an in-depth of the recent progress of 2D/3D HTS platforms (i.e., gradient and microarray) in the principle, preparation, screening for materiobiology, and combination with other advanced technologies. The Compendium for Biomaterial Transcriptomics and high content imaging, computational simulations, and their translation toward commercial and clinical uses are highlighted. In the final section, current challenges and future perspectives are discussed. High-throughput experimentation within the field of materiobiology enables the elucidation of the relationships between biomaterial properties and biological behavior and thereby serves as a potential tool for accelerating the development of high-performance biomaterials.

Genomics and Transcriptomics of the green mussel explain the durability of its byssus

Mussels, which occupy important positions in marine ecosystems, attach tightly to underwater substrates using a proteinaceous holdfast known as the byssus, which is tough, durable, and resistant to enzymatic degradation. Although various byssal proteins have been identified, the mechanisms by which it achieves such durability are unknown. Here we report comprehensive identification of genes involved in byssus formation through whole-genome and foot-specific transcriptomic analyses of the green mussel, Perna viridis. Interestingly, proteins encoded by highly expressed genes include proteinase inhibitors and defense proteins, including lysozyme and lectins, in addition to structural proteins and protein modification enzymes that probably catalyze polymerization and insolubilization. This assemblage of structural and protective molecules constitutes a multi-pronged strategy to render the byssus highly resistant to environmental insults.

Identification of novel adhesive proteins in pearl oyster by proteomic and bioinformatic analysis

Byssuses, which are proteinaceous fibers secreted by mollusks, are remarkable underwater adhesives. Although mussel adhesives are well known, much less is known about the byssal proteins of pearl oysters especially in the adhesive regions. In this study, adhesive proteins from the pearl oyster Pinctada fucata were studied in depth by transcriptomics and proteomics approaches. In total, 16 novel proteins were identified including a von Willebrand factor type A domain-containing protein, a thrombospondin-1-like protein, tyrosinase, mucin-like proteins, protease inhibitors, and Pinctada unannotated foot protein 3 (PUF3) to PUF6. Interestingly, PUF3-6 are enriched with glycine, serine, and PXG (X = F/Y/W/K/L) motifs and are highly expressed in the foot. The identification of byssal proteins of the pearl oyster is a key step for understanding byssus formation and may inspire the synthesis of novel adhesives for underwater use and the development of anti-biofouling strategies.

Omics-based molecular analyses of adhesion by aquatic invertebrates

Many aquatic invertebrates are associated with surfaces, using adhesives to attach to the substratum for locomotion, prey capture, reproduction, building or defence. Their intriguing and sophisticated biological glues have been the focus of study for decades. In all but a couple of specific taxa, however, the precise mechanisms by which the bioadhesives stick to surfaces underwater and (in many cases) harden have proved to be elusive. Since the bulk components are known to be based on proteins in most organisms, the opportunities provided by advancing 'omics technologies have revolutionised bioadhesion research. Time-consuming isolation and analysis of single molecules has been either replaced or augmented by the generation of massive data sets that describe the organism's translated genes and proteins. While these new approaches have provided resources and opportunities that have enabled physiological insights and taxonomic comparisons that were not previously possible, they do not provide the complete picture and continued multi-disciplinarity is essential. This review covers the various ways in which 'omics have contributed to our understanding of adhesion by aquatic invertebrates, with new data to illustrate key points. The associated challenges are highlighted and priorities are suggested for future research.

Characterizing and Controlling Nanoscale Self-Assembly of Suckerin-12

Structural proteins such as "suckerins" present promising avenues for fabricating functional materials. Suckerins are a family of naturally occurring block copolymer-type proteins that comprise the sucker ring teeth of cephalopods and are known to self-assemble into supramolecular networks of nanoconfined β-sheets. Here, we report the characterization and controllable, nanoscale self-assembly of suckerin-12 (S12). We characterize the impacts of salt, pH, and protein concentration on S12 solubility, secondary structure, and self-assembly. In doing so, we identify conditions for fabricating ∼100 nm nanoassemblies (NAs) with narrow size distributions. Finally, by installing a noncanonical amino acid (ncAA) into S12, we demonstrate the assembly of NAs that are covalently conjugated with a hydrophobic fluorophore and the ability to change self-assembly and β-sheet content by PEGylation. This work presents new insights into the biochemistry of suckerin-12 and demonstrates how ncAAs can be used to expedite and fine-tune the design of protein materials.

Biosynthetic self-healing materials for soft machines

Self-healing materials are indispensable for soft actuators and robots that operate in dynamic and real-world environments, as these machines are vulnerable to mechanical damage. However, current self-healing materials have shortcomings that limit their practical application, such as low healing strength (below a megapascal) and long healing times (hours). Here, we introduce high-strength synthetic proteins that self-heal micro- and macro-scale mechanical damage within a second by local heating. These materials are optimized systematically to improve their hydrogen-bonded nanostructure and network morphology, with programmable healing properties (2-23 MPa strength after 1 s of healing) that surpass by several orders of magnitude those of other natural and synthetic soft materials. Such healing performance creates new opportunities for bioinspired materials design, and addresses current limitations in self-healing materials for soft robotics and personal protective equipment.

Marine Structural Protein Stability Induced by Hofmeister Salt Annealing and Enzymatic Cross-Linking

The Humboldt squid is one of the fiercest marine predators thanks in part to its sucker ring teeth that are biopolymer blends of a protein isoform family called suckerin with compression strength that rivals silkworm silk. Here, we focus on the popular suckerin-12 isoform to understand what makes the secondary structure of this biopolymer different in water and the potential role of diverse physical and chemical cross-linkings. By choosing a salt post-treatment, in accordance with the Hofmeister series, we achieved film stability with salt annealing that is comparable to chemical cross-links. By correlating the film morphology with the protein secondary structure changes, suckerin-12 films were shown to contract upon treatment with kosmotropic salts and exhibited increased stability in water. These changes are related to the rearrangement of suckerin-12 secondary structure from random coils and helices to β-sheets. Overall, understanding secondary structure changes caused by aqueous and ionic environments can be instructive for the tuning of the suckerin film sclerotization, its conversion to a tough biological material, and to ultimately produce the natural squid sucker ring teeth.

Structure and sequence features of mussel adhesive protein lead to its salt-tolerant adhesion ability

Mussels can strongly adhere to hydrophilic minerals in sea habitats by secreting adhesive proteins. The adhesion ability of these proteins is often attributed to the presence of Dopa derived from posttranslational modification of Tyr, whereas the contribution of structural feature is overlooked. It remains largely unknown how adhesive proteins overcome the surface-bound water layer to establish underwater adhesion. Here, we use molecular dynamics simulations to probe the conformations of adhesive protein Pvfp-5β and its salt-tolerant underwater adhesion on superhydrophilic mica. Dopa and positively charged basic residues form pairs, in this intrinsically disordered protein, and these residue pairs can lead to firm surface binding. Our simulations further suggest that the unmodified Tyr shows similar functions on surface adhesion by forming pairing structure with a positively charged residue. We confirm the presence of these residue pairs and verify the strong binding ability of unmodified proteins using nuclear magnetic resonance spectroscopy and lap shear tests.

Sea anemones (Exaiptasia pallida) use a secreted adhesive and complex pedal disc morphology for surface attachment

Background

The mechanism by which sea anemones attach to surfaces underwater remains elusive, which is surprising given their ubiquitous distribution in the world’s oceans and tractability for experimental biology. Their adhesion is mechanically interesting, bridging the interface between very hard and soft materials. The Cnidaria are thought to have evolved adhesion to surfaces at least 505 Ma ago implying that, among the Metazoa, only Porifera developed this capability earlier. The purpose of this study was primarily to address an existing hypothesis, that spirocysts (a sticky class of cnidocyst) facilitate adhesion to surfaces, as observed during prey capture.

Results

We demonstrated conclusively that spirocysts were not involved in the pedal disc adhesion of Exaiptasia pallida. Second, we applied a variety of imaging methods to develop an understanding of the true adhesion mechanism. Morphological studies using scanning electron microscopy identified a meshwork of adhesive material, unique to the pedal disc. Serial block-face SEM highlighted four classes of cells that could secrete the adhesive from the pedal disc ectoderm. A variety of histochemical techniques identified proteins, glycans and quinones in the cell contents and secreted adhesive, with variation in contents of specific cell-types in different areas of the body.

Conclusions

Spirocysts are not used by Exaiptasia pallida for adhesion to surfaces. Instead, a structurally and compositionally complex secreted glue was observed, firmly attaching the animals underwater. The results of this study provide a basis for further investigations of adhesion in Cnidaria, and establish E. pallida as a new model organism for bioadhesion research.

Light, Strong, and Ductile Architectures Achieved by Silk Fiber "Welding" Processing

Light, strong, and ductile materials (LSDMs) are desired in many emerging fields, such as biomedicine, aerospace industries, and structural engineering materials. However, producing such materials remains a significant challenge because their structures cannot confer the desired mechanical properties. In this study, we developed a silk fiber "welding" strategy to construct bioinspired LSDMs. The key to the welding process is to etch the surface of silk fiber through a partial dissolution process. The dissolved silk proteins further serve as welding materials or glues to bond the silk fibers together. Remarkably, these silk-LSDMs are not only lightweight (with the densities of around 0.28 g cm^-3) but also strong and tough. Their compression strength reaches up to 13.8 ± 3.4 MPa, which is higher than those of most natural and engineered porous materials. These favorable structural and mechanical characteristics, together with outstanding biocompatibility of silk proteins, render these silk-LSDMs applicable in regenerated engineered tissues and water treatment materials.

Synthetic biology for protein-based materials

Recombinant protein polymers that mimic the structures and functions of natural proteins and those tailor-designed with new properties provide a family of uniquely tunable and functional materials. However, the diversity of genetically engineered protein polymers is still limited. As a powerful engine for the creation of new biological devices and systems, synthetic biology is promising to tackle the challenges that exist in conventional studies on protein polymers. Here we review the advances in design and biosynthesis of advanced protein materials by synthetic biology approaches. In particular, we highlight their roles in expanding the variety of designer protein polymers and creating programmable materials with live cells.

The evo-devo of molluscs: Insights from a genomic perspective

Molluscs represent one of ancient and evolutionarily most successful groups of marine invertebrates, with a tremendous diversity of morphology, behavior, and lifestyle. Molluscs are excellent subjects for evo-devo studies; however, understanding of the evo-devo of molluscs has been largely hampered by incomplete fossil records and limited molecular data. Recent advancement of genomics and other technologies has greatly fueled the molluscan "evo-devo" field, and decoding of several molluscan genomes provides unprecedented insights into molluscan biology and evolution. Here, we review the recent progress of molluscan genome sequencing as well as novel insights gained from their genomes, by emphasizing how molluscan genomics enhances our understanding of the evo-devo of molluscs.

Thermo- and pH-responsive fibrillization of squid suckerin A1H1 peptide

Stimuli-responsive smart materials have attracted considerable attention with numerous applications in nanotechnology, sensing, and biomedicine. Suckerin family proteins found in squid ring teeth represent such a class of peptide-based smart materials with their self-assemblies featuring excellent thermo-plasticity and pH-dependence. Similar to block copolymers, suckerin proteins are comprised of two repeating sequence motifs, where M1 motifs are abundant in alanine and histidine residues and M2 are rich in glycine. Experimental studies of suckerin assemblies suggested that M1 regions mainly formed nano-confined β-sheets within an amorphous matrix made of M2 modules stabilizing these β-rich nano-assemblies. The histidine-containing M1 modules are believed to govern the pH- and temperature-sensitive properties of suckerin assemblies. To better understand the stimuli-responsive properties of suckerin assemblies at the molecular level, we systematically studied the self-assembly dynamics of A1H1 peptides - a representative M1 sequence - at different temperatures and pH conditions with atomistic discrete molecular dynamic simulations. Our simulations with twenty A1H1 peptides demonstrated that below the transition temperature Tagg, they could readily self-assemble from isolated monomers into well-defined β-sheet nanostructures by both primary and secondary nucleation of β-sheets and subsequent aggregation growth via elongation and coagulation. Interestingly, the dissociation of pre-formed A1H1 β-sheet nanostructures featured a melting temperature Tm higher than Tagg, exhibiting the thermal hysteresis that is characteristic of first-order phase transitions with high energy barriers. In acidic environments where all histidine residues were protonated, the stability of the A1H1 β-sheet nano-assemblies was reduced and the β-rich assemblies easily dissociated into unstructured monomers at significantly lower temperatures than in the neutral solution. The computationally derived molecular mechanisms for pH- and temperature-dependent A1H1 self-assembly will help to understand the supramolecular assembly structures and functions of the large suckerin family and aid in the future design of peptide-based stimuli-responsive smart materials.

Computational modelling of wet adhesive mussel foot proteins (Bivalvia): Insights into the evolutionary convolution in diverse perspectives

Underwater adhesion in mussels (Bivalvia) is an extreme adaptation to achieve robust and firm wet adhesion in the freshwater/brackish/ocean, which biochemically shaped through millions of years. The protein-based adhesion has huge prospective in various fields like industry, medical, etc. Currently, no comprehensive records related to the systematic documentation of structural and functional properties of Mussel foot proteins (Mfps). In this study, we identified the nine species of bivalves in which the complete sequence of at least one adhesive protein is known. The insilico characterization revealed the specific physio-chemical structural and functional characters of each Mfps. The evolutionary analyses of selected bivalves are mainly based on Mfps, Mitogenome, and TimeTree. The outcome of the works has great applications for designing biomimetic materials in future.