Synergistic Integration of Experimental and Simulation Approaches for the de Novo Design of Silk-Based Materials

Structural conversion of the spidroin C-terminal domain during assembly of spider silk fibers

The major ampullate Spidroin 1 (MaSp1) is the main protein of the dragline spider silk. The C-terminal (CT) domain of MaSp1 is crucial for the self-assembly into fibers but the details of how it contributes to the fiber formation remain unsolved. Here we exploit the fact that the CT domain can form silk-like fibers by itself to gain knowledge about this transition. Structural investigations of fibers from recombinantly produced CT domain from E. australis MaSp1 reveal an α-helix to β-sheet transition upon fiber formation and highlight the helix No4 segment as most likely to initiate the structural conversion. This prediction is corroborated by the finding that a peptide corresponding to helix No4 has the ability of pH-induced conversion into β-sheets and self-assembly into nanofibrils. Our results provide structural information about the CT domain in fiber form and clues about its role in triggering the structural conversion of spidroins during fiber assembly.

Custom-designed, mass silk production in genetically engineered silkworms

Genetically engineered silkworms have been widely used to obtain silk with modified characteristics especially by introducing spider silk genes. However, these attempts are still challenging due to limitations in transformation strategies and difficulties in integration of the large DNA fragments. Here, we describe three different transformation strategies in genetically engineered silkworms, including transcription-activator-like effector nuclease (TALEN)-mediated fibroin light chain (FibL) fusion (BmFibL-F), TALEN-mediated FibH replacement (BmFibH-R), and transposon-mediated genetic transformation with the silk gland-specific fibroin heavy chain (FibH) promoter (BmFibH-T). As the result, the yields of exogenous silk proteins, a 160 kDa major ampullate spidroin 2 (MaSp2) from the orb-weaving spider Nephila clavipes and a 226 kDa fibroin heavy chain protein (EvFibH) from the bagworm Eumeta variegate, reach 51.02 and 64.13% in BmFibH-R transformed cocoon shells, respectively. Moreover, the presence of MaSp2 or EvFibH significantly enhances the toughness of genetically engineered silk fibers by ∼86% in BmFibH-T and ∼80% in BmFibH-R silkworms, respectively. Structural analysis reveals a substantial ∼40% increase in fiber crystallinity, primarily attributed to the presence of unique polyalanines in the repetitive sequences of MaSp2 or EvFibH. In addition, RNA-seq analysis reveals that BmFibH-R system only causes minor impact on the expression of endogenous genes. Our study thus provides insights into developing custom-designed silk production using the genetically engineered silkworm as the bioreactor.

Thermodynamic Analysis of Silk Fibroin-Graphite Hybrid Materials and Their Morphology

Silk fibroin (SF) is a β-sheet-rich protein that is responsible for the remarkable tensile strength of silk. In addition to its mechanical properties, SF is biocompatible and biodegradable, making it an attractive candidate for use in biotic/abiotic hybrid materials. A pairing of particular interest is the use of SF with graphene-based nanomaterials (GBNs). The properties of this interface drive the formation of well-ordered nanostructures and can improve the electronic properties of the resulting hybrid. It was previously demonstrated that SF can form lamellar nanostructures in the presence of graphite; however, the equilibrium morphology and associated driving interactions are not fully understood. In this study, we characterize these interactions between SF and SF lamellar with graphite using molecular dynamics (MD) simulations and umbrella sampling (US). We find that SF lamellar nanostructures have strong orientational and spatial preferences on graphite that are driven by the hydrophobic effect, destabilizing solvent-protein interactions and stabilizing protein-protein and protein-graphite interactions. Finally, we show how careful consideration of these underlying interactions can be applied to rationally modify the nanostructure morphology.

Advanced silk materials for musculoskeletal tissue regeneration

Musculoskeletal diseases are the leading causes of chronic pain and physical disability, affecting millions of individuals worldwide. Over the past two decades, significant progress has been made in the field of bone and cartilage tissue engineering to combat the limitations of conventional treatments. Among various materials used in musculoskeletal tissue regeneration, silk biomaterials exhibit unique mechanical robustness, versatility, favorable biocompatibility, and tunable biodegradation rate. As silk is an easy-to-process biopolymer, silks have been reformed into various materials formats using advanced bio-fabrication technology for the design of cell niches. Silk proteins also offer active sites for chemical modifications to facilitate musculoskeletal system regeneration. With the emergence of genetic engineering techniques, silk proteins have been further optimized from the molecular level with other functional motifs to introduce new advantageous biological properties. In this review, we highlight the frontiers in engineering natural and recombinant silk biomaterials, as well as recent progress in the applications of these new silks in the field of bone and cartilage regeneration. The future potentials and challenges of silk biomaterials in musculoskeletal tissue engineering are also discussed. This review brings together perspectives from different fields and provides insight into improved musculoskeletal engineering.

Engineering Natural and Recombinant Silks for Sustainable Biodevices

Silk fibroin (SF) is a structural protein derived from natural silkworm silks. Materials fabricated based on SF usually inherit extraordinary physical and biological properties, including high mechanical strength, toughness, optical transparency, tailorable biodegradability, and biocompatibility. Therefore, SF has attracted interest in the development of sustainable biodevices, especially for emergent bio-electronic technologies. To expand the function of current silk devices, the SF characteristic sequence has been used to synthesize recombinant silk proteins that benefit from SF and other functional peptides, such as stimuli-responsive elastin peptides. In addition to genetic engineering methods, innovated chemistry modification approaches and improved material processing techniques have also been developed for fabricating advanced silk materials with tailored chemical features and nanostructures. Herein, this review summarizes various methods to synthesize functional silk-based materials from different perspectives. This review also highlights the recent advances in the applications of natural and recombinant silks in tissue regeneration, soft robotics, and biosensors, using B. mori SF and silk-elastin-like proteins (SELPs) as examples.

Gelation Methods to Assemble Fibrous Proteins

Gelation is an efficient way to fabricate fibrous protein materials. Briefly, it is an aggregation process where protein molecules assembly from a random structure into an organized structure such as nanofibrillar networks. According to their mechanisms, the fibrous proteins gelation can be classified into physical gelation and chemical gelation. The physical gelation is formed by the conformational transformation of fibroin proteins, which can be triggered by temperature, concentration, pH, or shear force. On the other hand, the chemical gelation is to cross-link fibrous proteins through chemical and/or enzymatic reactions. In this chapter, we summarize the protocols for preparing fibrous protein hydrogels, including both physical and chemical methods. The mechanisms of these gelation methods are also highlighted.

A review on advances in the applications of spider silk in biomedical issues

Spider silk, as one of the hardest natural and biocompatible substances with extraordinary strength and flexibility, have become an ideal option in various areas of science and have made their path onto the biomedical industry. Despite its growing popularity, the difficulties in the extraction of silks from spiders and farming them have made it unaffordable and almost impossible for industrial scale. Biotechnology helped production of spider silks recombinantly in different hosts and obtaining diverse morphologies out of them based on different processing and assembly procedures. Herein, the characteristics of these morphologies and their advantages and disadvantages are summarized. A detailed view about applications of recombinant silks in skin regeneration and cartilage, tendon, bone, teeth, cardiovascular, and neural tissues engineering are brought out, where there is a need for strong scaffolds to support cell growth. Likewise, spider silk proteins have applications as conduit constructs, medical sutures, and 3D printer bioinks. Other characteristics of spider silks, such as low immunogenicity, hydrophobicity, homogeneity, and adjustability, have attracted much attention in drug and gene delivery. Finally, the challenges and obstacles ahead for industrializing the production of spider silk proteins in sufficient quantities in biomedicine, along with solutions to overcome these barriers, are discussed.

Biomedical applications of silkworm (Bombyx Mori) proteins in regenerative medicine (a narrative review)

Silk worm (Bombyx Mori) protein, have been considered as potential materials for a variety of advanced engineering and biomedical applications for decades. Recently, silkworm silk has gained significant importance in research attention mainly because of its remarkable and exceptional mechanical properties. Silk has already been shown to have unique interactions with cells in tissues through bio-recognition units. The natural silk contains fibroin and sericin and has been used in various tissues of the human body (skin, bone, nerve, and so on). Besides, silk also still has anti-cancer, anti-tyrosinase, anti-coagulant, anti-oxidant, anti-bacterial, and anti-diabetic properties. This article is supposed to describe the diverse biomedical capabilities of B. Mori silk as the appropriate biomaterial among the assorted natural and artificial polymers that are presently accessible, and ideal for usage in regenerative medicine fields.

The antigenicity of silk-based biomaterials: sources, influential factors and applications

Silk is an ancient material with essential roles in numerous biomedical applications, such as tissue regeneration and drug delivery, because of its excellent tunable mechanical properties and diverse physical structures. In addition to the necessary functionalities for biomedical applications, another critical factor for materials applied in biology is the appropriate immune interactions with the body. This review focuses on the immune responses of silk-based materials applied in biomedical applications, specifically antigenicity. The factors affecting the antigenicity of silk-based materials are complicated and are related to the composition and structural characteristics of the materials. At the same time, the composition of silk-based materials varies with its species sources, such as silkworms, spiders, honey bees, or engineered recombinant silk. Additionally, different processing methods are used to fabricate different material formats, such as films, hydrogels, scaffolds, particles, and fibers, resulting in different structural characteristics. Furthermore, the resulting body reactions are also different with different degrees of the immune response. Silk protein typically induces a mild immune response, and immunogenicity can play active roles in osteogenesis, angiogenesis, and protection from inflammation. However, there are some rare reports of severe immune responses caused by silk, which can result in an allergic response or tissue necrosis. The source of allergenicity in silk-based materials is currently under-studied and how to regulate and eliminate the overreaction of the immune system is essential for further applications. Overall, the diverse characteristics of silk-based materials mostly show beneficial bioresponses with mild immunogenicity, and the tunable properties make it applicable in immune-related biomedical applications.

Understanding Plant Biomass via Computational Modeling

Plant biomass, especially wood, has been used for structural materials since ancient times. It is also showing great potential for new structural materials and it is the major feedstock for the emerging biorefineries for building a sustainable society. The plant cell wall is a hierarchical matrix of mainly cellulose, hemicellulose, and lignin. Herein, the structure, properties, and reactions of cellulose, lignin, and wood cell walls, studied using density functional theory (DFT) and molecular dynamics (MD), which are the widely used computational modeling approaches, are reviewed. Computational modeling, which has played a crucial role in understanding the structure and properties of plant biomass and its nanomaterials, may serve a leading role on developing new hierarchical materials from biomass in the future.

Silk Fibroin Enhances Cytocompatibilty and Dimensional Stability of Alginate Hydrogels for Light-Based Three-Dimensional Bioprinting

Three-dimensional (3D) bioprinting is a technology under active study for use in tissue engineering and regenerative medicine. Bioink comprises cells and polymers and is the essential material for 3D bioprinting. The characteristics of the bioink affect its printability, gelation behavior, and cell compatibility. In this study, alginate derivatives were synthesized to induce rapid gelation, and a bioink was prepared by mixing these alginate derivatives with silk fibroin to enhance cell compatibility. A low-concentration (3 wt %) alginate/silk fibroin (Alg/SF) bioink was pregelated by the ionic cross-linking of Alg to increase the viscosity for 3D printing. The rheological and mechanical properties were analyzed using a rheometer and a texture meter, respectively. Analysis of cell viability and proliferation using fibroblasts (NIH-3T3) in the bioinks showed that the Alg/SF bioink has improved cytocompatibility compared to that of conventional Alg bioinks, making it a promising material for tissue engineering.

Stimuli-responsive composite biopolymer actuators with selective spatial deformation behavior

Bioinspired actuators with stimuli-responsive and deformable properties are being pursued in fields such as artificial tissues, medical devices and diagnostics, and intelligent biosensors. These applications require that actuator systems have biocompatibility, controlled deformability, biodegradability, mechanical durability, and stable reversibility. Herein, we report a bionic actuator system consisting of stimuli-responsive genetically engineered silk-elastin-like protein (SELP) hydrogels and wood-derived cellulose nanofibers (CNFs), which respond to temperature and ionic strength underwater by ecofriendly methods. Programmed site-selective actuation can be predicted and folded into three-dimensional (3D) origami-like shapes. The reversible deformation performance of the SELP/CNF actuators was quantified, and complex spatial transformations of multilayer actuators were demonstrated, including a biomimetic flower design with selective petal movements. Such actuators consisting entirely of biocompatible and biodegradable materials will offer an option toward constructing stimuli-responsive systems for in vivo biomedicine soft robotics and bionic research.

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.

Autonomous Self-Healing Silk Fibroin Injectable Hydrogels Formed via Surfactant-Free Hydrophobic Association

Many natural materials, such as silk, animal bone, nacre, and plant fibers, achieve outstanding strength and toughness through the rupture of sacrificial bonds between chain segments in the organic phase. In this work, we present a bioinspired strategy to fabricate silk fibroin-based hydrophobic-association (HA) hydrogels by incorporating the hydrophobic interaction as a sacrificial bond into the alginate ionic network, which not only enhanced the mechanical extensibility, strength, and toughness of the hydrogels but also enabled self-recovery and self-healing properties via reversible hydrophobic interactions without external stimuli at room temperature. The hydrophobic interaction system consisted of the hydrophobic monomer stearyl methacrylate (C18M) and an amphiphilic regenerated silk fibroin (RSF) solution. The mechanical tests and rheometry indicated that the hydrophobic interaction served as the sacrificial bond that preferentially ruptures prior to the alginate ionic network under an external load, which dissipated enormous amounts of energy and conferred an improved mechanical performance. Moreover, the structure of HA gels could be quickly recovered after injection due to the existence of hydrophobic interactions. In addition, the degradability of the HA gels in a protease XIV solution was strongly dependent upon the C18M component, which significantly promoted the degradation rate of HA gels. The biomimetic mineralization process of HA gels within a simulated body fluid (SBF), mimicking the inorganic composition of human blood plasma, was performed and the calcium phosphate nanoparticles on the hydrogel were observed. Importantly, in vivo experiments illustrated that the HA gels exhibited satisfactory biocompatibility, and the mouse osteoblasts (MC3T3-E1) could attach and spread on the hydrogels. Overall, the self-healing, biocompatibility, and high mechanical properties of the HA gels render them potentially suitable for load-bearing applications in drug delivery or other soft tissue-engineering applications.

Functional protein materials: beyond elastomeric and structural proteins

In the past two decades researchers have shown great interest in mimicking biological structures and their complex structure–property relationships. Herein we highlight examples of hydrogels and bioelectronic materials that illustrate the rational design of material properties and function.

Multiscale Modeling of Silk and Silk-Based Biomaterials-A Review

Silk embodies outstanding material properties and biologically relevant functions achieved through a delicate hierarchical structure. It can be used to create high-performance, multifunctional, and biocompatible materials through mild processes and careful rational material designs. To achieve this goal, computational modeling has proven to be a powerful platform to unravel the causes of the excellent mechanical properties of silk, to predict the properties of the biomaterials derived thereof, and to assist in devising new manufacturing strategies. Fine-scale modeling has been done mainly through all-atom and coarse-grained molecular dynamics simulations, which offer a bottom-up description of silk. In this work, a selection of relevant contributions of computational modeling is reviewed to understand the properties of natural silk, and to the design of silk-based materials, especially combined with experimental methods. Future research directions are also pointed out, including approaches such as 3D printing and machine learning, that may enable a high throughput design and manufacturing of silk-based biomaterials.

Silkworm silk-based materials and devices generated using bio-nanotechnology

Silks are natural fibrous protein polymers that are spun by silkworms and spiders. Among silk variants, there has been increasing interest devoted to the silkworm silk of B. mori, due to its availability in large quantities along with its unique material properties. Silk fibroin can be extracted from the cocoons of the B. mori silkworm and combined synergistically with other biomaterials to form biopolymer composites. With the development of recombinant DNA technology, silks can also be rationally designed and synthesized via genetic control. Silk proteins can be processed in aqueous environments into various material formats including films, sponges, electrospun mats and hydrogels. The versatility and sustainability of silk-based materials provides an impressive toolbox for tailoring materials to meet specific applications via eco-friendly approaches. Historically, silkworm silk has been used by the textile industry for thousands of years due to its excellent physical properties, such as lightweight, high mechanical strength, flexibility, and luster. Recently, due to these properties, along with its biocompatibility, biodegradability and non-immunogenicity, silkworm silk has become a candidate for biomedical utility. Further, the FDA has approved silk medical devices for sutures and as a support structure during reconstructive surgery. With increasing needs for implantable and degradable devices, silkworm silk has attracted interest for electronics, photonics for implantable yet degradable medical devices, along with a broader range of utility in different device applications. This Tutorial review summarizes and highlights recent advances in the use of silk-based materials in bio-nanotechnology, with a focus on the fabrication and functionalization methods for in vitro and in vivo applications in the field of tissue engineering, degradable devices and controlled release systems.

Advanced Cell and Tissue Biomanufacturing

This position paper assesses state-of-the-art advanced biomanufacturing and identifies paths forward to advance this emerging field in biotechnology and biomedical engineering, including new research opportunities and translational and corporate activities. The vision for the field is to see advanced biomanufacturing emerge as a discipline in academic and industrial communities as well as a technological opportunity to spur research and industry growth. To navigate this vision, the paths to move forward and to identify major barriers were a focal point of discussions at a National Science Foundation-sponsored workshop focused on the topic. Some of the major needs include but are not limited to the integration of specific scientific and engineering disciplines and guidance from regulatory agencies, infrastructure requirements, and strategies for reliable systems integration. Some of the recommendations, major targets, and opportunities were also outlined, including some "grand challenges" to spur interest and progress in the field based on the participants at the workshop. Many of these recommendations have been expanded, materialized, and adopted by the field. For instance, the formation of an initial collaboration network in the community was established. This report provides suggestions for the opportunities and challenges to help move the field of advanced biomanufacturing forward. The field is in the early stages of effecting science and technology in biomanufacturing with a bright and important future impact evident based on the rapid scientific advances in recent years and industry progress.

De Novo Design of Recombinant Spider Silk Proteins for Material Applications

Spider silks are well known for their superior mechanical properties that are stronger and tougher than steel despite being assembled at close to ambient conditions and using water as the solvent. However, it is a significant challenge to utilize spider silks for practical applications due to their limited sources. Fortunately, genetic engineering techniques offer a promising approach to produce useable amounts of spider silk variants. Starting from these recombinant spider silk proteins, a series of experiments and simulations strategies are developed to improve the recombinant spider silk proteins (RSSP) material design and fabrication with the aim of biomimicking the structure-property-function relationships of spider silks. Accordingly, in this review, the authors first introduce the structure-property-function relationship of spider silks. Then, the recent progress in the genetic synthesis of RSSPs is discussed and their related multiscale self-assembly behaviors is summarized. Finally, the authors outline works utilizing multiscale modeling to assist RSSP material design.

Advanced Materials through Assembly of Nanocelluloses

There is an emerging quest for lightweight materials with excellent mechanical properties and economic production, while still being sustainable and functionalizable. They could form the basis of the future bioeconomy for energy and material efficiency. Cellulose has long been recognized as an abundant polymer. Modified celluloses were, in fact, among the first polymers used in technical applications; however, they were later replaced by petroleum-based synthetic polymers. Currently, there is a resurgence of interest to utilize renewable resources, where cellulose is foreseen to make again a major impact, this time in the development of advanced materials. This is because of its availability and properties, as well as economic and sustainable production. Among cellulose-based structures, cellulose nanofibrils and nanocrystals display nanoscale lateral dimensions and lengths ranging from nanometers to micrometers. Their excellent mechanical properties are, in part, due to their crystalline assembly via hydrogen bonds. Owing to their abundant surface hydroxyl groups, they can be easily modified with nanoparticles, (bio)polymers, inorganics, or nanocarbons to form functional fibers, films, bulk matter, and porous aerogels and foams. Here, some of the recent progress in the development of advanced materials within this rapidly growing field is reviewed.

Materials-by-Design: Computation, Synthesis, and Characterization from Atoms to Structures

In the 50 years that succeeded Richard Feynman's exposition of the idea that there is "plenty of room at the bottom" for manipulating individual atoms for the synthesis and manufacturing processing of materials, the materials-by-design paradigm is being developed gradually through synergistic integration of experimental material synthesis and characterization with predictive computational modeling and optimization. This paper reviews how this paradigm creates the possibility to develop materials according to specific, rational designs from the molecular to the macroscopic scale. We discuss promising techniques in experimental small-scale material synthesis and large-scale fabrication methods to manipulate atomistic or macroscale structures, which can be designed by computational modeling. These include recombinant protein technology to produce peptides and proteins with tailored sequences encoded by recombinant DNA, self-assembly processes induced by conformational transition of proteins, additive manufacturing for designing complex structures, and qualitative and quantitative characterization of materials at different length scales. We describe important material characterization techniques using numerous methods of spectroscopy and microscopy. We detail numerous multi-scale computational modeling techniques that complements these experimental techniques: DFT at the atomistic scale; fully atomistic and coarse-grain molecular dynamics at the molecular to mesoscale; continuum modeling at the macroscale. Additionally, we present case studies that utilize experimental and computational approaches in an integrated manner to broaden our understanding of the properties of two-dimensional materials and materials based on silk and silk-elastin-like proteins.

Biomedical Applications of Recombinant Silk-Based Materials

Silk is mostly known as a luxurious textile, which originates from silkworms first cultivated in China. A deeper look into the variety of silk reveals that it can be used for much more, in nature and by humanity. For medical purposes, natural silks were recognized early as a potential biomaterial for surgical threads or wound dressings; however, as biomedical engineering advances, the demand for high-performance, naturally derived biomaterials becomes more pressing and stringent. A common problem of natural materials is their large batch-to-batch variation, the quantity available, their potentially high immunogenicity, and their fast biodegradation. Some of these common problems also apply to silk; therefore, recombinant approaches for producing silk proteins have been developed. There are several research groups which study and utilize various recombinantly produced silk proteins, and many of these have also investigated their products for biomedical applications. This review gives a critical overview over of the results for applications of recombinant silk proteins in biomedical engineering.

Nanofibrils in nature and materials engineering

Nanofibrillar materials, such as cellulose, chitin and silk, are highly ordered architectures, formed through the self-assembly of repetitive building blocks into higher-order structures, which are stabilized by non-covalent interactions. This hierarchical building principle endows many biological materials with remarkable mechanical strength, anisotropy, flexibility and optical properties, such as structural colour. These features make nanofibrillar biopolymers interesting candidates for the development of strong, sustainable and biocompatible materials for environmental, energy, optical and biomedical applications. However, recreating their architecture is challenging from an engineering perspective. Rational design approaches, applying a combination of theoretical and experimental protocols, have enabled the design of biopolymer-based materials through mimicking nature's multiscale assembly approach. In this Review, we summarize hierarchical design strategies of cellulose, silk and chitin, focusing on nanoconfinement, fibrillar orientation and alignment in 2D and 3D structures. These multiscale architectures are discussed in the context of mechanical and optical properties, and different fabrication strategies for the manufacturing of biopolymer nanofibril-based materials are investigated. We highlight the contribution of rational material design strategies to the development of mechanically anisotropic and responsive materials and examine the future of the material-by-design paradigm.

Silk Materials Functionalized via Genetic Engineering for Biomedical Applications

The great mechanical properties, biocompatibility and biodegradability of silk-based materials make them applicable to the biomedical field. Genetic engineering enables the construction of synthetic equivalents of natural silks. Knowledge about the relationship between the structure and function of silk proteins enables the design of bioengineered silks that can serve as the foundation of new biomaterials. Furthermore, in order to better address the needs of modern biomedicine, genetic engineering can be used to obtain silk-based materials with new functionalities. Sequences encoding new peptides or domains can be added to the sequences encoding the silk proteins. The expression of one cDNA fragment indicates that each silk molecule is related to a functional fragment. This review summarizes the proposed genetic functionalization of silk-based materials that can be potentially useful for biomedical applications.

Predicting Silk Fiber Mechanical Properties through Multiscale Simulation and Protein Design

Silk is a promising material for biomedical applications, and much research is focused on how application-specific, mechanical properties of silk can be designed synthetically through proper amino acid sequences and processing parameters. This protocol describes an iterative process between research disciplines that combines simulation, genetic synthesis, and fiber analysis to better design silk fibers with specific mechanical properties. Computational methods are used to assess the protein polymer structure as it forms an interconnected fiber network through shearing and how this process affects fiber mechanical properties. Model outcomes are validated experimentally with the genetic design of protein polymers that match the simulation structures, fiber fabrication from these polymers, and mechanical testing of these fibers. Through iterative feedback between computation, genetic synthesis, and fiber mechanical testing, this protocol will enable a priori prediction capability of recombinant material mechanical properties via insights from the resulting molecular architecture of the fiber network based entirely on the initial protein monomer composition. This style of protocol may be applied to other fields where a research team seeks to design a biomaterial with biomedical application-specific properties. This protocol highlights when and how the three research groups (simulation, synthesis, and engineering) should be interacting to arrive at the most effective method for predictive design of their material.