Structural ensembles reveal intrinsic disorder for the multi-stimuli responsive bio-mimetic protein Rec1-resilin

Modular Bioorthogonal Lipid Nanoparticle Modification Platforms for Cardiac Homing

Lipid nanoparticles (LNPs) are becoming widely adopted as vectors for the delivery of therapeutic payloads but generally lack intrinsic tissue-homing properties. These extracellular vesicle (EV) mimetics can be targeted toward the liver, lung, or spleen via charge modification of their lipid headgroups. Homing to other tissues has only been achieved via covalent surface modification strategies using small-molecule ligands, peptides, or monoclonal antibodies─methods that are challenging to couple with large-scale manufacturing. Herein, we design a novel modular artificial membrane-binding protein (AMBP) platform for the modification of LNPs postformation. The system is composed of two protein modules that can be readily coupled using bioorthogonal chemistry to yield the AMBP. The first is a membrane anchor module comprising a supercharged green fluorescent protein (scGFP) electrostatically conjugated to a dynamic polymer surfactant corona. The second is a functional module containing a cardiac tissue fibronectin homing sequence from the bacterial adhesin CshA. We demonstrate that LNPs modified using the AMBP exhibit a 20-fold increase in uptake by fibronectin-rich C2C12 cells under static conditions and a 10-fold increase under physiologically relevant shear stresses, with no loss of cell viability. Moreover, we show targeted localization of the AMBP-modified LNPs in zebrafish hearts, highlighting their therapeutic potential as a vector for the treatment of cardiac disease and, more generally, as a smart vector.

Balanced Three-Point Water Model OPC3-B for Intrinsically Disordered and Ordered Proteins

Intrinsically disordered proteins (IDPs) play a critical role in many biological processes. Due to the inherent structural flexibility of IDPs, experimental methods present significant challenges for sampling their conformational information at the atomic level. Therefore, molecular dynamics (MD) simulations have emerged as the primary tools for modeling IDPs whose accuracy depend on force field and water model. To enhance the accuracy of physical modeling of IDPs, several force fields have been developed. However, current water models lack precision and underestimate the interaction between water molecules and proteins. Here, we used Monte-Carlo re-weighting method to re-parameterize a three-point water model based on OPC3 for IDPs (named OPC3-B). We benchmarked the performance of OPC3-B compared with nine different water models for 10 IDPs and three ordered proteins. The results indicate that the performance of OPC3-B is better than other water models for both IDPs and ordered proteins. At the same time, OPC3-B possess the power of transferability with other force field to simulate IDPs. This newly developed water model can be used to insight into the research of sequence-disordered-function paradigm for IDPs.

Intrinsically Disordered Synthetic Polymers in Biomedical Applications

In biology and medicine, intrinsically disordered synthetic polymers bio-mimicking intrinsically disordered proteins, which lack stable three-dimensional structures, possess high structural/conformational flexibility. They are prone to self-organization and can be extremely useful in various biomedical applications. Among such applications, intrinsically disordered synthetic polymers can have potential usage in drug delivery, organ transplantation, artificial organ design, and immune compatibility. The designing of new syntheses and characterization mechanisms is currently required to provide the lacking intrinsically disordered synthetic polymers for biomedical applications bio-mimicked using intrinsically disordered proteins. Here, we present our strategies for designing intrinsically disordered synthetic polymers for biomedical applications based on bio-mimicking intrinsically disordered proteins.

Crowder-directed interactions and conformational dynamics in multistimuli-responsive intrinsically disordered protein

The consequences of crowding on the dynamic conformational ensembles of intrinsically disordered proteins (IDPs) remain unresolved because of their ultrafast motion. Here, we report crowder-induced interactions and conformational dynamics of a prototypical multistimuli-responsive IDP, Rec1-resilin. The effects of a range of crowders of varying sizes, forms, topologies, and concentrations were examined using spectroscopic, spectrofluorimetric, and contrast-matching small- and ultrasmall-angle neutron scattering investigation. To achieve sufficient neutron contrast against the crowders, deuterium-labeled Rec1-resilin was biosynthesized successfully. Moreover, the ab initio "shape reconstruction" approach was used to obtain three-dimensional models of the conformational assemblies. The IDP revealed crowder-specific systematic extension and compaction with the level of macromolecular crowding. Last, a robust extension-contraction model has been postulated to capture the fundamental phenomena governing the observed behavior of IDPs. The study provides insights and fresh perspectives for understanding the interactions and structural dynamics of IDPs in crowded states.

Emerging bioadhesives: from traditional bioactive and bioinert to a new biomimetic protein-based approach

Bioadhesives have reached significant milestones over the past two decades. Research has shown not only to produce adhesives capable of adhering to dry tissue but recently wet tissue as well. However, most bioadhesives developed have exhibited high adhesion strength yet lack other properties required for versatility in application, such as elasticity, biocompatibility and biodegradability. Adapting from limitations met from early bioadhesives and meeting the current demand allows novel bioadhesives to reach new milestones for the future. In this review, we overview the progression and variations of bioadhesives, current trends, characterisation techniques and conclude with future perspectives for bioadhesives for tissue engineering applications.

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.

Switchable Self-Assembly of Elastin- and Resilin-Based Block Copolypeptides with Converse Phase Transition Behaviors

Self-assembly of thermally responsive polypeptides into unique nanostructures offers intriguing attributes including dynamic physical dimensions, biocompatibility, and biodegradability for the smart bio-nanomaterials. As elastin-based polypeptide (EBP) fusion proteins with lower critical solution temperature (LCST) are studied as drug delivery systems, EBP block copolypeptides with the resilin-based polypeptide (RBP) displaying an upper critical solution temperature (UCST) have been of great interest. In this study, we report thermally triggered, dynamic self-assembly of EBP- and RBP-based diblock copolypeptides into switched nanostructures with reversibility under physiological conditions. Molecular DNA clones encoding for the EBP-RBP diblocks at different block length ratios were biosynthesized via recursive directional ligation and overexpressed, followed by nonchromatographic purification by inverse transition cycling. Genetically engineered diblock copolypeptides composed of the EBP with an LCST and the RBP with a UCST showed converse phase transition behaviors with both a distinct LCST and a distinct UCST (LCST < UCST). As temperature increased, three phases of these EBP-RBP diblocks were observed: (1) self-assembled micelles or vesicles below both LCST and UCST, (2) whole aggregates above LCST and below UCST, and (3) reversed micelles above both LCST and UCST. In conclusion, these stimuli-triggered, dynamic protein-based nanostructures are promising for advanced drug delivery systems, regenerative medicine, and biomedical nanotechnology.

Resilin-mimetics as a smart biomaterial platform for biomedical applications

Intrinsically disordered proteins have dramatically changed the structure-function paradigm of proteins in the 21st century. Resilin is a native elastic insect protein, which features intrinsically disordered structure, unusual multi-stimuli responsiveness and outstanding resilience. Advances in computational techniques, polypeptide synthesis methods and modular protein engineering routines have led to the development of novel resilin-like polypeptides (RLPs) including modular RLPs, expanding their applications in tissue engineering, drug delivery, bioimaging, biosensors, catalysis and bioelectronics. However, how the responsive behaviour of RLPs is encoded in the amino acid sequence level remains elusive. This review summarises the milestones of RLPs, and discusses the development of modular RLP-based biomaterials, their current applications, challenges and future perspectives. A perspective of future research is that sequence and responsiveness profiling of RLPs can provide a new platform for the design and development of new modular RLP-based biomaterials with programmable structure, properties and functions.

Recent trends in protein and peptide-based biomaterials for advanced drug delivery

Engineering protein and peptide-based materials for drug delivery applications has gained momentum due to their biochemical and biophysical properties over synthetic materials, including biocompatibility, ease of synthesis and purification, tunability, scalability, and lack of toxicity. These biomolecules have been used to develop a host of drug delivery platforms, such as peptide- and protein-drug conjugates, injectable particles, and drug depots to deliver small molecule drugs, therapeutic proteins, and nucleic acids. In this review, we discuss progress in engineering the architecture and biological functions of peptide-based biomaterials -naturally derived, chemically synthesized and recombinant- with a focus on the molecular features that modulate their structure-function relationships for drug delivery.

A Sustainable Biomineralization Approach for the Synthesis of Highly Fluorescent Ultra-Small Pt Nanoclusters

Herein we report the first example of a facile biomineralization process to produce ultra-small-sized highly fluorescent aqueous dispersions of platinum noble metal quantum clusters (Pt-NMQCs) using a multi-stimulus responsive, biomimetic intrinsically disordered protein (IDP), Rec1-resilin. We demonstrate that Rec1-resilin acts concurrently as the host, reducing agent, and stabilizer of the blue-green fluorescent Pt-NMQCs once they are being formed. The photophysical properties, quantum yield, and fluorescence lifetime measurements of the synthesized Pt-NMQCs were examined using UV-Vis and fluorescence spectroscopy. The oxidation state of the Pt-NMQCs was quantitatively analyzed using X-ray photoelectron spectroscopy. Both a small angle X-ray scattering technique and a modeling approach have been attempted to present a detailed understanding of the structure and conformational dynamics of Rec1-resilin as an IDP during the formation of the Pt-NMQCs. It has been demonstrated that the green fluorescent Pt-NMQCs exhibit a high quantum yield of ~7.0% and a lifetime of ~9.5 ns in aqueous media. The change in photoluminescence properties due to the inter-dot interactions between proximal dots and aggregation of the Pt-NMQCs by evaporation was also measured spectroscopically and discussed.

Trends in the design and use of elastin-like recombinamers as biomaterials

Elastin-like recombinamers (ELRs), which derive from one of the repetitive domains found in natural elastin, have been intensively studied in the last few years from several points of view. In this mini review, we discuss all the recent works related to the investigation of ELRs, starting with those that define these polypeptides as model intrinsically disordered proteins or regions (IDPs or IDRs) and its relevance for some biomedical applications. Furthermore, we summarize the current knowledge on the development of drug, vaccine and gene delivery systems based on ELRs, while also emphasizing the use of ELR-based hydrogels in tissue engineering and regenerative medicine (TERM). Finally, we show different studies that explore applications in other fields, and several examples that describe biomaterial blends in which ELRs have a key role. This review aims to give an overview of the recent advances regarding ELRs and to encourage further investigation of their properties and applications.

Evolution of the Interfacial Structure of a Catalyst Ink with the Quality of the Dispersing Solvent: A Contrast Variation Small-Angle and Ultrasmall-Angle Neutron Scattering Investigation

The electrocatalyst layer (ECL) of the proton-exchange membrane fuel cell (PEMFC) is commonly fabricated from colloidal catalyst ink containing carbon-supported catalyst nanoparticles (NPs), ionomer stabilizer, and dispersion medium (DM). The structure, stability, and aggregate size distribution of fuel cell catalyst ink are critically dependent on the quality of DM. However, understanding of the influence of the quality of DM on the hierarchical structure of the ECL is lacking. This work presents a systematic investigation of the effects of reducing alcohol content in isopropyl alcohol/water (IPA/H₂O) binary mixtures as DM on the structural evolution of water-rich (green) catalyst ink using contrast-variation small-angle and ultrasmall-angle neutron scattering techniques. Both qualitative and quantitative information are extracted from the data to obtain information about the size, structure, and organization of the catalyst ink using different model functions fit to the experimental data. The catalyst ink prepared using 70% IPA (commonly employed in industry and extensively reported in the literature) is shown to consist of randomly distributed globular carbon aggregates (mean radius of gyration of ∼178.9 nm) stabilized by an ionomer mass fractal shell (thickness of ∼13.0 nm), which is dispersed in the matrix of rodlike (∼1.3 nm radius and ∼35.0 nm length) negatively surface-charged ionomer NPs. These well characterized baseline data are then compared and contrasted with DM formulations of lower IPA content. A sequential reduction in IPA content of DM shows a progressive increase in the ionomer NP radius and electrostatic repulsion, concomitantly with the decrease in the carbon aggregate size and ionomer shell thickness of the catalyst ink. Therefore, the changes in the interfacial structure via adjustments of the DM composition can be used as a controlling parameter to tailor the hierarchical structure of the colloidal fuel cell catalyst ink and to further optimize the performance of the ECL.

Tough Photocrosslinked Silk Fibroin/Graphene Oxide Nanocomposite Hydrogels

The development of protein-based hydrogels for tissue engineering applications is often limited by their mechanical properties. Herein, we present the facile fabrication of tough regenerated silk fibroin (RSF)/graphene oxide (GO) nanocomposite hydrogels by a photochemical cross-linking method. The RSF/GO composite hydrogels demonstrated soft and adhesive properties during initial stages of photocrosslinking (<2 min), which is not observed for the pristine RSF hydrogel, and rendered a tough and nonadhesive hydrogel upon complete cross-linking (10 min). The composite hydrogels exhibited superior tensile mechanical properties, increased β-sheet content, and decreased chain mobility compared to that of the pristine RSF hydrogels. The composite hydrogels demonstrated Young's modulus as high as ∼8 MPa, which is significantly higher than native cartilage (∼1.5 MPa), and tensile toughness as high as ∼2.4 MJ/m³, which is greater than that of electroactive polymer muscles and at par with RSF/GO composite membranes fabricated by layer-by-layer assembly. Small-angle scattering study reveals the hierarchical structure of photocrosslinked RSF hydrogels to comprise randomly distributed water-poor (hydrophobic) and water-rich (hydrophilic) regions at the nanoscale, whereas water pores and channels exhibiting fractal-like characteristics at the microscale. The size of hydrophobic domain (containing β-sheets) was observed to increase slightly with GO incorporation and/or alcohol post-treatment, whereas the size of the hydrophilic domain (intersheet distance containing random coils) was observed to increase significantly, which influences/affects water uptake capacity, cross-link density, and mechanical properties of hydrogels. The presented results have implications for both fundamental understanding of the structure-property relationship of RSF-based hydrogels and their technological applications.

Coacervation of resilin fusion proteins containing terminal functionalities

Liquid-liquid phase transition known as coacervation of resilin-like-peptide fusion proteins containing different terminal domains were investigated. Two different modular proteins were designed and produced and their behavior were compared to a resilin-like-peptide without terminal domains. The size of the particle-like coacervates was modulated by the protein concentration, pH and temperature. The morphology and three-dimensional (3D) structural details of the coacervate particles were investigated by cryogenic transmission electron microscopy (cryo-TEM) and tomography (cryo-ET) reconstruction. Selective adhesion of the coacervates on cellulose and graphene surfaces was demonstrated.

Convergence of Artificial Protein Polymers and Intrinsically Disordered Proteins

A flurry of research in recent years has revealed the molecular origins of many membraneless organelles to be the liquid phase separation of intrinsically disordered proteins (IDPs). Consequently, protein disorder has emerged as an important driver of intracellular compartmentalization by providing specialized microenvironments chemically distinct from the surrounding medium. Though the importance of protein disorder and its relationship to intracellular phase behavior are clear, a detailed understanding of how such phase behavior can be predicted and controlled remains elusive. While research in IDPs has largely focused on the implications of structural disorder on cellular function and disease, another field, that of artificial protein polymers, has focused on the de novo design of protein polymers with controllable material properties. A subset of these polymers, specifically those derived from structural proteins such as elastin and resilin, are also disordered sequences that undergo liquid-liquid phase separation. This phase separation has been used in a variety of biomedical applications, and researchers studying these polymers have developed methods to precisely characterize and tune their phase behavior. Despite their disparate origins, both fields are complementary as they study the phase behavior of intrinsically disordered polypeptides. This Perspective hopes to stimulate collaborative efforts by highlighting the similarities between these two fields and by providing examples of how such collaboration could be mutually beneficial.

Order, Disorder, and Temperature-Driven Compaction in a Designed Elastin Protein

Artificial minielastin constructs have been designed that replicate the structure and function of natural elastins in a simpler context, allowing the NMR observation of structure and dynamics of elastin-like proteins with complete residue-specific resolution. We find that the alanine-rich cross-linking domains of elastin have a partially helical structure, but only when capped by proline-rich hydrophobic domains. We also find that the hydrophobic domains, composed of prominent 6-residue repeats VPGVGG and APGVGV found in natural elastins, appear random coil by both NMR chemical shift analysis and circular dichroism. However, these elastin hydrophobic domains exhibit structural bias for a dynamically disordered conformation that is neither helical nor β sheet with a degree of nonrandom structural bias which is dependent on residue type and position in the sequence. Another nonrandom-coil aspect of hydrophobic domain structure lies in the fact that, in contrast to other intrinsically disordered proteins, these hydrophobic domains retain a relatively condensed conformation whether attached to cross-linking domains or not. Importantly, these domains and the proteins containing them constrict with increasing temperature by up to 30% in volume without becoming more ordered. This property is often observed in nonbiological polymers and suggests that temperature-driven constriction is a new type of protein structural change that is linked to elastin's biological functions of coacervation-driven assembly and elastic recoil.

How Do We Study the Dynamic Structure of Unstructured Proteins: A Case Study on Nopp140 as an Example of a Large, Intrinsically Disordered Protein

Intrinsically disordered proteins (IDPs) represent approximately 30% of the human genome and play key roles in cell proliferation and cellular signaling by modulating the function of target proteins via protein-protein interactions. In addition, IDPs are involved in various human disorders, such as cancer, neurodegenerative diseases, and amyloidosis. To understand the underlying molecular mechanism of IDPs, it is important to study their structural features during their interactions with target proteins. However, conventional biochemical and biophysical methods for analyzing proteins, such as X-ray crystallography, have difficulty in characterizing the features of IDPs because they lack an ordered three-dimensional structure. Here, we present biochemical and biophysical studies on nucleolar phosphoprotein 140 (Nopp140), which mostly consists of disordered regions, during its interaction with casein kinase 2 (CK2), which plays a central role in cell growth. Surface plasmon resonance and electron paramagnetic resonance studies were performed to characterize the interaction between Nopp140 and CK2. A single-molecule fluorescence resonance energy transfer study revealed conformational change in Nopp140 during its interaction with CK2. These studies on Nopp140 can provide a good model system for understanding the molecular function of IDPs.

Elastic and pH-Responsive Hybrid Interfaces Created with Engineered Resilin and Nanocellulose

We investigated how a genetically engineered resilin fusion protein modifies cellulose surfaces. We characterized the pH-responsive behavior of a resilin-like polypeptide (RLP) having terminal cellulose binding modules (CBM) and showed its binding to cellulose nanofibrils (CNF). Characterization of the resilin fusion protein at different pHs revealed substantial conformational changes of the protein, which were observed as swelling and contraction of the protein layer bound to the nanocellulose surface. In addition, we showed that employment of the modified resilin in cellulose hydrogel and nanopaper increased their modulus of stiffness through a cross-linking effect.

Phase Behavior and Self-Assembly of Perfectly Sequence-Defined and Monodisperse Multiblock Copolypeptides

This paper investigates how the properties of multiblock copolypeptides can be tuned by their block architecture, defined by the size and distribution of blocks along the polymer chain. These parameters were explored by the precise, genetically encoded synthesis of recombinant elastin-like polypeptides (ELPs). A family of ELPs was synthesized in which the composition and length were conserved while the block length and distribution were varied, thus creating 11 ELPs with unique block architectures. To our knowledge, these polymers are unprecedented in their intricately and precisely varied architectures. ELPs exhibit lower critical solution temperature (LCST) behavior and micellar self-assembly, both of which impart easily measured physicochemical properties to the copolymers, providing insight into polymer hydrophobicity and self-assembly into higher order structures, as a function of solution temperature. Even subtle variation in block architecture changed the LCST phase behavior and morphology of these ELPs, measured by their temperature-triggered phase transition and nanoscale self-assembly. Size and morphology of polypeptide micelles could be tuned solely by controlling the block architecture, thus demonstrating that when sequence can be precisely controlled, nanoscale self-assembly of polypeptides can be modulated by block architecture.

Effects of Crowding and Environment on the Evolution of Conformational Ensembles of the Multi-Stimuli-Responsive Intrinsically Disordered Protein, Rec1-Resilin: A Small-Angle Scattering Investigation

In this study, we explore the overall structural ensembles and transitions of a biomimetic, multi-stimuli-responsive, intrinsically disordered protein (IDP), Rec1-resilin. The structural transition of Rec1-resilin with change in molecular crowding and environment is evaluated using small-angle neutron scattering and small-angle X-ray scattering. The quantitative analyses of the experimental scattering data using a combination of computational models allowed comprehensive description of the structural evolution, organization, and conformational ensembles of Rec1-resilin in response to the changes in concentration, pH, and temperature. Rec1-resilin in uncrowded solutions demonstrates the equilibrium intrinsic structure quality of an IDP with radius of gyration Rg ∼ 5 nm, and a scattering function for the triaxial ellipsoidal model best fit the experimental dataset. On crowding (increase in concentration >10 wt %), Rec1-resilin molecules exert intermolecular repulsive force of interaction, the Rg value reduces with a progressive increase in concentration, and molecular chains transform from a Gaussian coil to a fully swollen coil. It is also revealed that the structural organization of Rec1-resilin dynamically transforms from a rod (pH 2) to coil (pH 4.8) and to globular (pH 12) as a function of pH. The findings further support the temperature-triggered dual-phase-transition behavior of Rec1-resilin, exhibiting rod-shaped structural organization below the upper critical solution temperature (∼4 °C) and a large but compact structure above the lower critical solution temperature (∼75 °C). This work attempted to correlate unusual responsiveness of Rec1-resilin to the evolution of conformational ensembles.

Tick receptor for outer surface protein A from Ixodes ricinus - the first intrinsically disordered protein involved in vector-microbe recognition

The tick receptor for outer surface protein A (TROSPA) is the only identified factor involved in tick gut colonization by various Borrelia species. TROSPA is localized in the gut epithelium and can recognize and bind the outer surface bacterial protein OspA via an unknown mechanism. Based on earlier reports and our latest observations, we considered that TROSPA would be the first identified intrinsically disordered protein (IDP) involved in the interaction between a vector and a pathogenic microbe. To verify this hypothesis, we performed structural studies of a TROSPA mutant from Ixodes ricinus using both computational and experimental approaches. Irrespective of the method used, we observed that the secondary structure content of the TROSPA polypeptide chain is low. In addition, the collected SAXS data indicated that this protein is highly extended and exists in solution as a set of numerous conformers. These features are all commonly considered hallmarks of IDPs. Taking advantage of our SAXS data, we created structural models of TROSPA and proposed a putative mechanism for the TROSPA-OspA interaction. The disordered nature of TROSPA may explain the ability of a wide spectrum of Borrelia species to colonize the tick gut.

Tunable Thermoresponsiveness of Resilin via Coassembly with Rigid Biopolymers

The ability to tune the thermoresponsiveness of recombinant resilin protein, Rec1-resilin, through a facile coassembly system was investigated in this study. The effects of change in conformation and morphology with time and the responsive behavior of Rec1-resilin in solution were studied in response to the addition of a rigid model polypeptide (poly-l-proline) or a hydrophobic rigid protein (Bombyx mori silk fibroin). It was observed that by inducing more ordered conformations and increasing the hydrophobicity the lower critical solution temperature (LCST) of the system was tuned to lower values. Time and temperature were found to be critical parameters in controlling the coassembly behavior of Rec1-resilin in both the model polypeptide and more complex protein systems. Such unique properties are useful for a wide range of applications, including drug delivery and soft tissue engineering applications.

A multi-responsive intrinsically disordered protein (IDP)-directed green synthesis of fluorescent gold nanoclusters

Herein we demonstrate the green synthesis of fluorescent gold nanoclusters (AuNCs) using a multi-responsive intrinsically disordered protein (IDP) polymer, Rec1-resilin, as a multi-functional template.