Design and application of stimulus-responsive peptide systems

Bibliometric analysis of stem cells for spinal cord injury: current status and emerging frontiers

Background: This study aimed to conduct a bibliometric analysis of the literature on stem cell therapy for spinal cord injury to visualize the research status, identify hotspots, and explore the development trends in this field. Methods: We searched the Web of Science Core Collection database using relevant keywords ("stem cells" and "spinal cord injury") and retrieved the published literature between 2000 and 2022. Data such as journal title, author information, institutional affiliation, country, and keywords were extracted. Afterwards, we performed bibliometric analysis of the retrieved data using Bibliometrix, VOSviewer, and CiteSpace. Results: A total of 5375 articles related to stem cell therapy for spinal cord injury were retrieved, and both the annual publication volume and the cumulative publication volume showed an upward trend. neural regeneration research was the journal with the most publications and the fastest cumulative publication growth (162 articles), Okano Hideyuki was the author with the highest number of publications and citations (114 articles), Sun Yat-sen University was the institution with the highest number of publications (420 articles), and China was the country with the highest number of publications (5357 articles). However, different authors, institutions, and countries need to enhance their cooperation in order to promote the generation of significant academic achievements. Current research in this field has focused on stem cell transplantation, neural regeneration, motor function recovery, exosomes, and tissue engineering. Meanwhile, future research directions are primarily concerned with the molecular mechanisms, safety, clinical trials, exosomes, scaffolds, hydrogels, and inflammatory responses of stem cell therapy for spinal cord injuries. Conclusion: In summary, this study provided a comprehensive analysis of the current research status and frontiers of stem cell therapy for spinal cord injury. The findings provide a foundation for future research and clinical translation efforts of stem cell therapy in this field.

Microfluidic-driven ultrafast self-assembly of a dipeptide into stimuli-responsive 0D, 1D, and 2D nanostructures and as hydrolase mimic

Numerous peptides have been utilized to explore the efficacy of their self-assembly to produce nanostructures to mimic the self-organization capability of biomolecules in nature. Self-assembled nanostructures have significant applicability for a range of diverse applications. While the ability to create self-assembled functional materials has greatly improved, the self-assembly process, which results in ordered 0D, 1D, and 2D nanostructures, is still time-consuming. Moreover, in situ structural transformation from one self-assembled structure to another with different dimensions presents an additional challenge. Therefore, in this report, we demonstrate self-assembly in an ultrafast fashion to access four different nanostructures, namely, twisted bundle (TB), nanoparticle (NP), nanofiber (NF), and nanosheet (NS), from a simple dipeptide with the aid of simple microfluidic reactors by applying different stimuli. Additionally, an integrated microfluidic system enabled rapid structural switchover between two types in an ultrashort period of time. It is interesting to note that the formation of the twisted bundle (TB) morphology enabled the formation of an extended entangled network, which resulted in the formation of a hydrogel (1 w/v%). In addition, the nanostructures obtained using the ultrafast self-assembly process were investigated to study their hydrolase enzyme activity mimicking performance against a model substrate (p-NPA) reaction. Intriguingly, we found that our nanostructures were suitably well ordered, and when taking molecular mass into consideration, showed improved catalytic efficiency as compared to the native enzymes.

Recent Advances in Peptides-Based Stimuli-Responsive Materials for Biomedical and Therapeutic Applications: A Review

Smart materials are engineered materials that have one or more properties that are introduced in a controlled fashion by surrounding stimuli. Engineering of biomacromolecules like proteins into a smart material call for meticulous artistry. Peptides have grabbed notable attention as a preferred source for smart materials in the medicinal field, promoted by their versatile chemical and biophysical attributes of biocompatibility, and biodegradability. Recent advances in the synthesis of multifunctional peptides have proliferated their application in diverse domains: agriculture, nanotechnology, medicines, biosensors, therapeutics, and soft robotics. Stimuli such as pH, temperature, light, metal ions, and enzymes have vitalized physicochemical properties of peptides by augmented sensitivity, stability, and selectivity. This review elucidates recent (2018-2021) advances in the design and synthesis of smart materials, from stimuli-responsive peptides followed by their biomedical and therapeutic applications.

Dimension switchable auto-fluorescent peptide-based 1D and 2D nano-assemblies and their self-influence on intracellular fate and drug delivery

The production of dynamic, environment-responsive shape-tunable biomaterials marks a significant step forward in the construction of synthetic materials that can easily rival their natural counterparts. Significant progress has been made in the self-assembly of bio-materials. However, the self-assembly of a peptide into morphologically distinct auto-fluorescent nanostructures, without the incorporation of any external moiety is still in its infancy. Hence, in this study, we have developed peptide-based self-assembled auto-fluorescent nanostructures that can shuttle between 1D and 2D morphologies. Different morphological nanostructures are well known to have varied cellular internalization efficiencies. Taking advantage of our morphologically different particles emanating from the same peptide monomer, we further explored the intracellular fate of our nanostructures. We observed that the nanostructures' cellular internalization is a complex process that gets influenced by particle morphology and this might further affect their intracellular drug delivery potential. Overall, this study provides initial cues for the preparation of environment-responsive shape-shifting peptide-nano assemblies. Efforts have also been made to understand their shape driven cellular uptake behaviour, along with establishing them as nanocarriers for the cellular delivery of therapeutic molecules.

Peptide-modified substrate enhances cell migration and migrasome formation

Extracellular vesicles (EVs) are cell-to-cell communication tools. Migrasomes are recently discovered microscale EVs formed at the rear ends of migrating cells, and thus are suggested to be involved in communicating with neighboring cells. In cell culture, peptide scaffolds on substrates have been used to demonstrate cellular function for regenerative medicine. In this study, we evaluated peptide scaffolds, including cell penetrating, virus fusion, and integrin-binding peptides, for their potential to enable the formation of migrasome-like vesicles. Through structural and functional analyses, we confirmed that the EVs formed on these peptide-modified substrates were migrasomes. We further noted that the peptide interface comprising cell-penetrating peptides (pVEC and R9) and virus fusion peptide (SIV) have superior properties for enabling cell migration and migrasome formation than fibronectin protein, integrin-binding peptide (RGD), or bare substrate. This is the first report of migrasome formation on peptide-modified substrates. Additionally, the combination of 95% RGD and 5% pVEC peptides provided a functional interface for effective migrasome formation and desorption of cells from the substrate via a simple ethylenediaminetetraacetic acid treatment. These results provide a functional substrate for the enhancement of migrasome formation and functional analysis.

Protein Assembly by Design

Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.

Dopamine-Substituted Multidomain Peptide Hydrogel with Inherent Antimicrobial Activity and Antioxidant Capability for Infected Wound Healing

Wound infection can cause a delay in wound healing or even wound deterioration, threatening patients' lives. The excessive accumulation of reactive oxygen species (ROS) in infected wounds activates a strong inflammatory response to delay wound healing. Therefore, it is highly desired to develop hydrogels with inherent antimicrobial activity and antioxidant capability for infected wound healing. Herein, a dopamine-substituted multidomain peptide (DAP) with inherent antimicrobial activity, strong skin adhesion, and ROS scavenging has been developed. DAP can form bilayer β-sheets with dopamine residues on the surface of nanofibers. The enhanced rheological properties of DAP-based hydrogel can be achieved not only through UV irradiation but also by incorporation of multivalent ions (e.g., PO₄^3-). Furthermore, the DAP hydrogel shows a broad spectrum of antimicrobial activity due to the high positive charges of lysine residues and the β-sheet formation. When applied to full-thickness dermal wounds in mice, the DAP hydrogel results in a significantly shortened inflammatory stage of the healing process because of its remarkable antimicrobial activity and antioxidant capability. Accelerated wound closure with thick granulation tissue, uniform collagen arrangement, and dense vascularization can be achieved. This work suggests that the DAP hydrogel can serve as antimicrobial coating and ROS-scavenging wound dressing for bacterial-infected wound treatment.

The 'Shape-Shifter' Peptide from the Disulphide Isomerase PmScsC Shows Context-Dependent Conformational Preferences

Multiple crystal structures of the homo-trimeric protein disulphide isomerase PmScsC reveal that the peptide which links the trimerization stalk and catalytic domain can adopt helical, β-strand and loop conformations. This region has been called a 'shape-shifter' peptide. Characterisation of this peptide using NMR experiments and MD simulations has shown that it is essentially disordered in solution. Analysis of the PmScsC crystal structures identifies the role of intermolecular contacts, within an assembly of protein molecules, in stabilising the different linker peptide conformations. These context-dependent conformational properties may be important functionally, allowing for the binding and disulphide shuffling of a variety of protein substrates to PmScsC. They also have a relevance for our understanding of protein aggregation and misfolding showing how intermolecular quaternary interactions can lead to β-sheet formation by a sequence that in other contexts adopts a helical structure. This 'shape-shifting' peptide region within PmScsC is reminiscent of one-to-many molecular recognition features (MoRFs) found in intrinsically disordered proteins which are able to adopt different conformations when they fold upon binding to their protein partners.

Thermoresponsive Polypeptoids

Stimuli-responsive polymers have been widely studied in many applications such as biomedicine, nanotechnology, and catalysis. Temperature is one of the most commonly used external triggers, which can be highly controlled with excellent reversibility. Thermoresponsive polymers exhibiting a reversible phase transition in a controlled manner to temperature are a promising class of smart polymers that have been widely studied. The phase transition behavior can be tuned by polymer architectures, chain-end, and various functional groups. Particularly, thermoresponsive polypeptoid is a type of promising material that has drawn growing interest because of its excellent biocompatibility, biodegradability, and bioactivity. This paper summarizes the recent advances of thermoresponsive polypeptoids, including the synthetic methods and functional groups as well as their applications.

Electrokinetic characterization of synthetic protein nanoparticles

The application of nanoparticle in medicine is promising for the treatment of a wide variety of diseases. However, the slow progress in the field has resulted in relatively few therapies being translated into the clinic. Anisotropic synthetic protein nanoparticles (ASPNPs) show potential as a next-generation drug-delivery technology, due to their biocompatibility, biodegradability, and functionality. Even though ASPNPs have the potential to be used in a variety of applications, such as in the treatment of glioblastoma, there is currently no high-throughput technology for the processing of these particles. Insulator-based electrokinetics employ microfluidics devices that rely on electrokinetic principles to manipulate micro- and nanoparticles. These miniaturized devices can selectively trap and enrich nanoparticles based on their material characteristics, and subsequently release them, which allows for particle sorting and processing. In this study, we use insulator-based electrokinetic (EK) microdevices to characterize ASPNPs. We found that anisotropy strongly influences electrokinetic particle behavior by comparing compositionally identical anisotropic and non-anisotropic SPNPs. Additionally, we were able to estimate the empirical electrokinetic equilibrium parameter (eE EEC) for all SPNPs. This particle-dependent parameter can allow for the design of various separation and purification processes. These results show how promising the insulator-based EK microdevices are for the analysis and purification of clinically relevant SPNPs.

Characterizing aggregate growth and morphology of alanine-rich polypeptides as a function of sequence chemistry and solution temperature from scattering, spectroscopy, and microscopy

The aggregation behavior and stability of a series of alanine-rich peptides, which are included as components of peptide-polymer conjugates, were characterized using a combination of biophysical techniques. Light scattering techniques were used to monitor changes in peptide morphology and size distributions as a function of time and temperature. The results show large particles immediately upon dissolution in buffer. At room temperature, these particles relaxed to reach a mostly monomeric peptide state, while at higher temperatures, they grew to form aggregates. Circular dichroism spectroscopy (CD) was used to monitor temperature- and time-dependent conformational changes as a function of peptide sequence and incubation time. CD measurements reveal that all of the sequences are helical at low temperatures with transitions to non-helical conformation with increased temperature. Samples incubated at room temperature were able to recover their original helicity. At increased temperature, the shorter and longer peptide sequences showed notable changes in conformation, and were not able to recover their original helicity after 72 h. After incubation for up to one week, β-sheet conformations were observed in these two cases, while only α-helical conformation loss was observed for the peptide of intermediate molecular weight. Transmission electron microscopy measurements reveal the formation of fibrils after 72 h of incubation at 60 °C for all samples, in agreement with the scattering measurements. Additional quenching experiments show that peptide aggregation can be stalled when solutions are cooled to room temperature.

A thermo-responsive, self-assembling biointerface for on demand release of surface-immobilised proteins

Dedicated chemistries for on-demand capture and release of biomolecules at the solid-liquid interface are required for applications in drug delivery, for the synthesis of switchable surfaces used in analytical devices and for the assembly of next-generation biomaterials with complex architectures and functions. Here we report the engineering of a binary self-assembling polypeptide system for reversible protein capture, immobilisation and controlled thermo-responsive release from a solid surface. The first element of the binary system is a universal protein substrate immobilised on a solid surface. This protein is bio-inspired by the neuronal SNAP25, which is the protein involved in the docking and fusion of synaptic vesicles to the synaptic membrane. The second element is an artificial chimeric protein engineered to include distinct domains from three different proteins: Syntaxin, VAMP and SNAP25. These native proteins constitute the machinery dedicated to vesicle trafficking in eukaryotes. We removed approximately 70% of native protein sequence from these proteins and constructed a protein chimera capable of high affinity interaction and self-assembly with immobilised substrate. The interaction of the two parts of the engineered protein complex is strong but fully-reversible and therefore the chimera can be recombinantly fused as a tag to a protein of interest, to allow spontaneous assembly and stimuli-sensitive release from the surface upon heating at a predetermined temperature. Two thermo-responsive tags are reported: the first presents remarkable thermal stability with melting temperature of the order of 80 °C; the second disassembles at a substantially lower temperature of about 45 °C. The latter is a promising candidate for remote-controlled localised delivery of therapeutic proteins, as physiologically tolerable local increase of temperatures in the 40-45 °C range can be achieved using magnetic fields, infra-red light or focused ultrasound. Importantly, these two novel polypeptides provide a broader blueprint for the engineering of future functional proteins with predictable folding and response to external stimuli.

Modular Fabrication of Intelligent Material-Tissue Interfaces for Bioinspired and Biomimetic Devices

One of the goals of biomaterials science is to reverse engineer aspects of human and nonhuman physiology. Similar to the body's regulatory mechanisms, such devices must transduce changes in the physiological environment or the presence of an external stimulus into a detectable or therapeutic response. This review is a comprehensive evaluation and critical analysis of the design and fabrication of environmentally responsive cell-material constructs for bioinspired machinery and biomimetic devices. In a bottom-up analysis, we begin by reviewing fundamental principles that explain materials' responses to chemical gradients, biomarkers, electromagnetic fields, light, and temperature. Strategies for fabricating highly ordered assemblies of material components at the nano to macro-scales via directed assembly, lithography, 3D printing and 4D printing are also presented. We conclude with an account of contemporary material-tissue interfaces within bioinspired and biomimetic devices for peptide delivery, cancer theranostics, biomonitoring, neuroprosthetics, soft robotics, and biological machines.

Droplet Microfluidics-Enabled High-Throughput Screening for Protein Engineering

Protein engineering—the process of developing useful or valuable proteins—has successfully created a wide range of proteins tailored to specific agricultural, industrial, and biomedical applications. Protein engineering may rely on rational techniques informed by structural models, phylogenic information, or computational methods or it may rely upon random techniques such as chemical mutation, DNA shuffling, error prone polymerase chain reaction (PCR), etc. The increasing capabilities of rational protein design coupled to the rapid production of large variant libraries have seriously challenged the capacity of traditional screening and selection techniques. Similarly, random approaches based on directed evolution, which relies on the Darwinian principles of mutation and selection to steer proteins toward desired traits, also requires the screening of very large libraries of mutants to be truly effective. For either rational or random approaches, the highest possible screening throughput facilitates efficient protein engineering strategies. In the last decade, high-throughput screening (HTS) for protein engineering has been leveraging the emerging technologies of droplet microfluidics. Droplet microfluidics, featuring controlled formation and manipulation of nano- to femtoliter droplets of one fluid phase in another, has presented a new paradigm for screening, providing increased throughput, reduced reagent volume, and scalability. We review here the recent droplet microfluidics-based HTS systems developed for protein engineering, particularly directed evolution. The current review can also serve as a tutorial guide for protein engineers and molecular biologists who need a droplet microfluidics-based HTS system for their specific applications but may not have prior knowledge about microfluidics. In the end, several challenges and opportunities are identified to motivate the continued innovation of microfluidics with implications for protein engineering.

Comparative Study of Photoswitchable Zinc-Finger Domain and AT-Hook Motif for Light-Controlled Peptide-DNA Binding

DNA-peptide interactions are involved in key life processes, including DNA recognition, replication, transcription, repair, organization, and modification. Development of tools that can influence DNA-peptide binding non-invasively with high spatiotemporal precision could aid in determining its role in cells and tissues. Here, the design, synthesis, and study of photocontrolled tools for sequence-specific small peptide-DNA major and minor groove interactions are reported, shedding light on DNA binding by transcriptionally active peptides. In particular, photoswitchable moieties were implemented in the peptide backbone or turn region. In each case, DNA binding was affected by photochemical isomerization, as determined in fluorescent displacement assays on model DNA strands, which provides promising tools for DNA modulation.

Self-Assembling Multidomain Peptides: Design and Characterization of Neutral Peptide-Based Materials with pH and Ionic Strength Independent Self-Assembly

Self-assembly of peptides is a powerful method of preparing nanostructured materials. These peptides frequently utilize charged groups as a convenient switch for controlling self-assembly in which pH or ionic strength determines the assembly state. Multidomain peptides have been previously designed with charged domains of amino acids, which create molecular frustration between electrostatic repulsion and a combination of supramolecular forces including hydrogen bonding and hydrophobic packing. This frustration is eliminated by the addition of multivalent ions or pH adjustment, resulting in a self-assembled hydrogel. However, these charged functionalities can have profound, unintended effects on the properties of the resulting material. Access to neutral self-assembled nanostructured hydrogels may allow for distinct biological properties that are not available to highly charged analogues. Here, we designed a series of peptides to determine if self-assembly could be mediated by the steric interactions created by neutral hydroxyproline (O) domains, eliminating the need for charged residues and creating a neutral peptide hydrogel. The series of peptides, O _n (SL)₆O _n , was studied to determine the effect of oligo-hydroxyproline on peptide self-assembly and nanostructure. We show that peptide solubility and nanofiber length increase with a higher number of hydroxyproline residues. Within this series, O₅(SL)₆O₅ displayed the optimal properties for self-assembly and hydrogelation. In vitro, this hydrogel supports cell viability of fibroblasts, while in vivo it is infiltrated with cells and easily degraded over time without promoting a strong inflammatory response. This neutral self-assembling peptide hydrogel shows promising properties for biomedical, cell preservation, and tissue regeneration applications.

Post-assembly α-helix to β-sheet structural transformation within SAF-p1/p2a peptide nanofibers

We report an unanticipated helix-to-sheet structural transformation within an assembly of SAF-p1 and SAF-p2a designer peptides. Solid-state NMR spectroscopic data support the assembled structure that was targeted by rational peptide design: an α-helical coiled-coil co-assembly of both peptides. Subsequent to assembly, however, the system converts to a β-sheet structure that continues to exhibit nearest-neighbor interactions between the two peptide components. The structural transition occurs at pH 7.4 and exhibits strongly temperature-dependent kinetics between room temperature (weeks) and 40 °C (minutes). We further observed evidence of reversibility on the timescale of months at 4 °C. The structural conversion from the anticipated structure to an unexpected structure highlights an important aspect to the challenge of designing peptide assemblies. Furthermore, the conformational switching mechanism mediated by a prerequisite α-helical nanostructure represents a previously unknown route for β-sheet designer peptide assembly.

Two Engineered OBPs with opposite temperature-dependent affinities towards 1-aminoanthracene

Engineered odorant-binding proteins (OBPs) display tunable binding affinities triggered by temperature alterations. We designed and produced two engineered proteins based on OBP-I sequence: truncated OBP (tOBP) and OBP::GQ20::SP-DS3. The binding affinity of 1-aminoanthracene (1-AMA) to these proteins revealed that tOBP presents higher affinity at 25 °C (kd = 0.45 μM) than at 37 °C (kd = 1.72 μM). OBP::GQ20::SP-DS3 showed an opposite behavior, revealing higher affinity at 37 °C (kd = 0.58 μM) than at 25 °C (kd = 1.17 μM). We set-up a system containing both proteins to evaluate their temperature-dependent binding. Our data proved the 1-AMA differential and reversible affinity towards OBPs, triggered by temperature changes. The variations of the binding pocket size with temperature, confirmed by molecular modelling studies, were determinant for the differential binding of the engineered OBPs. Herein we described for the first time a competitive temperature-dependent mechanism for this class of proteins.

Using single molecule force spectroscopy to facilitate a rational design of Ca2+-responsive β-roll peptide-based hydrogels

Mechanical stability of Ca²⁺-responsive β-roll peptides (RTX) is largely responsible for the Ca²⁺-dependent mechanical properties of the RTX-based hydrogels.

Block V RTX Domain of Adenylate Cyclase from Bordetella pertussis: A Conformationally Dynamic Scaffold for Protein Engineering Applications

The isolated Block V repeats-in-toxin (RTX) peptide domain of adenylate cyclase (CyaA) from Bordetella pertussis reversibly folds into a β-roll secondary structure upon calcium binding. In this review, we discuss how the conformationally dynamic nature of the peptide is being engineered and employed as a switching mechanism to mediate different protein functions and protein-protein interactions. The peptide has been used as a scaffold for diverse applications including: a precipitation tag for bioseparations, a cross-linking domain for protein hydrogel formation and as an alternative scaffold for biomolecular recognition applications. Proteins and peptides such as the RTX domains that exhibit natural stimulus-responsive behavior are valuable building blocks for emerging synthetic biology applications.

Catch and Release: Engineered Allosterically Regulated β-Roll Peptides Enable On/Off Biomolecular Recognition

Alternative scaffolds for biomolecular recognition are being developed to overcome some of the limitations associated with immunoglobulin domains. The repeat-in-toxin (RTX) domain is a repeat protein sequence that reversibly adopts the β-roll secondary structure motif specifically upon calcium binding. This conformational change was exploited for controlled biomolecular recognition. Using ribosome display, an RTX peptide library was selected to identify binders to a model protein, lysozyme, exclusively in the folded state of the peptide. Several mutants were identified with low micromolar dissociation constants. After concatenation of the mutants, a 500-fold increase in the overall affinity for lysozyme was achieved leading to a peptide with an apparent dissociation constant of 65 nM. This mutant was immobilized for affinity chromatography experiments, and the on/off nature of the molecular recognition was demonstrated as the target is captured from a mixture in the presence of calcium and is released in the absence of calcium as the RTX peptides lose their β-roll structure. This work presents the design of a new stimulus-responsive scaffold that can be used for environmentally responsive specific molecular recognition and self-assembly.

Can Simple Interaction Models Explain Sequence-Dependent Effects in Peptide Homodimerization?

The development of rapid methods to explain and predict peptide interactions, aggregation, and self-assembly has become important to understanding amyloid disease pathology, the shelf stability of peptide therapeutics, and the design of novel peptide materials. Although experimental aggregation databases have been used to develop correlative and statistical models, molecular simulations offer atomic-level details that potentially provide greater physical insight and allow one to single out the most explanatory simple models. Here, we outline one such approach using a case study that develops homodimerization models for serine-glycine peptides with various hydrophobic leucine mutations. Using detailed all-atom simulations, we calculate reference dimerization free energy profiles and binding constants for a small peptide library. We then use statistical methods to systematically assess whether simple interaction models, which do not require expensive simulations and free energy calculation, can capture them. Surprisingly, some combinations of a few simple scaling laws well recapitulate the detailed, all-atom results with high accuracy. Specifically, we find that a recently proposed phenomenological hydrophobic force law and coarse measures of entropic effects in binding offer particularly high explanatory power, underscoring the physical relevance to association that these driving forces can play.

Fabrication and characterization of hydrogels formed from designer coiled-coil fibril-forming peptides

A peptide sequence was designed to form α-helical fibrils and hydrogels at physiological pH, utilising transient buffering by carbonic acid.

Biomaterial Approaches to Enhancing Neurorestoration after Spinal Cord Injury: Strategies for Overcoming Inherent Biological Obstacles

While advances in technology and medicine have improved both longevity and quality of life in patients living with a spinal cord injury, restoration of full motor function is not often achieved. This is due to the failure of repair and regeneration of neuronal connections in the spinal cord after injury. In this review, the complicated nature of spinal cord injury is described, noting the numerous cellular and molecular events that occur in the central nervous system following a traumatic lesion. In short, postinjury tissue changes create a complex and dynamic environment that is highly inhibitory to the process of neural regeneration. Strategies for repair are outlined with a particular focus on the important role of biomaterials in designing a therapeutic treatment that can overcome this inhibitory environment. The importance of considering the inherent biological response of the central nervous system to both injury and subsequent therapeutic interventions is highlighted as a key consideration for all attempts at improving functional recovery.

A theoretical study of imine hydrocyanation catalyzed by halogen-bonding

A detailed theoretical study of the mechanism and energetics of an organocatalysis based on C=N activation by halogen-bonding is presented for the hydrocyanation of N-benzylidenemethylamine. The calculations at the level of scalar-relativistic gradient-corrected density functional theory give an insight in this catalytic concept and provide information on the characteristics of four different monodentate catalyst candidates acting as halogen-bond donors during the reaction.

A photoinduced growth system of peptide nanofibres addressed by DNA hybridization

Spatiotemporal control of peptide nanofibre growth was achieved by photocleavage of a DNA-conjugated β-sheet-forming peptide with a photoresponsive amino acid.

An16-resilin: an advanced multi-stimuli-responsive resilin-mimetic protein polymer

Engineered protein polymers that display responsiveness to multiple stimuli are emerging as a promising class of soft material with unprecedented functionality. The remarkable advancement in genetic engineering and biosynthesis has created the opportunity for precise control over the amino acid sequence, size, structure and resulting functions of such biomimetic proteins. Herein, we describe the multi-stimuli-responsive characteristics of a resilin-mimetic protein, An16-resilin (An16), derived from the consensus sequence of resilin gene in the mosquito Anopheles gambiae. We demonstrate that An16 is an intrinsically disordered protein that displays unusual dual-phase thermal transition behavior along with responsiveness to pH, ion, light and humidity. Identifying the molecular mechanisms that allow An16 to sense and switch in response to varying environments furthers the ability to design intelligent biomacromolecules.

Designing unconventional Fmoc-peptide-based biomaterials: structure and related properties

We have recently employed L-amino acids in the lipase-catalyzed biofabrication of a class of self-assembling Fmoc-peptides that form 3-dimensional nanofiber scaffolds. Here we report that using d-amino acids, the homochiral self-assembling peptide Fmoc-D-Phe3 (Fmoc-F*F*F*) also forms a 3-dimensional nanofiber scaffold that is substantially distinguishable from its L-peptide and heterochiral peptide (F*FF and FF*F*) counterparts on the basis of their physico-chemical properties. Such chiral peptides self-assemble into ordered nanofibers with well defined fibrillar motifs. Circular dichroism and atomic force microscopy have been employed to study in depth such fibrillar peptide structures. Dexamethasone release kinetics from PLGA and CS-PLGA nanoparticles entrapped within the peptidic hydrogel matrix encourage its use for applications in drug controlled release.

Characterization of a highly flexible self-assembling protein system designed to form nanocages

The design of proteins that self-assemble into well-defined, higher order structures is an important goal that has potential applications in synthetic biology, materials science, and medicine. We previously designed a two-component protein system, designated A-(+) and A-(-), in which self-assembly is mediated by complementary electrostatic interactions between two coiled-coil sequences appended to the C-terminus of a homotrimeric enzyme with C3 symmetry. The coiled-coil sequences are attached through a short, flexible spacer sequence providing the system with a high degree of conformational flexibility. Thus, the primary constraint guiding which structures the system may assemble into is the symmetry of the protein building block. We have now characterized the properties of the self-assembling system as a whole using native gel electrophoresis and analytical ultracentrifugation (AUC) and the properties of individual assemblies using cryo-electron microscopy (EM). We show that upon mixing, A-(+) and A-(-) form only six different complexes in significant concentrations. The three predominant complexes have hydrodynamic properties consistent with the formation of heterodimeric, tetrahedral, and octahedral protein cages. Cryo-EM of size-fractionated material shows that A-(+) and A-(-) form spherical particles with diameters appropriate for tetrahedral or octahedral protein cages. The particles varied in diameter in an almost continuous manner suggesting that their structures are extremely flexible.

Rearranging and concatenating a native RTX domain to understand sequence modularity

The use of repetitive peptide sequences forming predictable secondary structures has been a key paradigm in recent efforts to engineer biomolecular recognition. The modularity and predictability of these scaffolds enables precise identification and mutation of the active interface, providing a level of control which non-repetitive scaffolds often lack. However, the majority of these scaffolds are well-folded stable structures. If the structures had a stimulus-responsive character, this would enable the allosteric regulation of their function. The calcium-responsive beta roll-forming repeats in toxin (RTX) domain potentially offer both of these properties. To further develop this scaffold, we synthesized a set of RTX peptides ranging in size from 5 to 17 repeats, with and without C-terminal capping. We found that while the number of repeats can be altered to tune the size of the RTX face, repeat ordering and C-terminal capping are critical for successful folding. Comparing all of the constructs, we also observed that native configuration with nine repeats exhibited the highest affinity for calcium. In addition, we performed a comparison on a set of known RTX-containing proteins and find that C-terminal repeats often possess deviations from the consensus RTX sequence which may be essential for proper folding. We further find that there seems to be a narrow size range in which RTX domains exist. These results demonstrate that the deviations from the consensus RTX sequence that are observed in natural proteins are important for high-affinity calcium binding and folding. Therefore, the RTX scaffolds will be less modular as compared with other, non-responsive scaffolds, and the sequence-dependent interactions between different repeats will need to be retained in these scaffolds as they are developed in future protein-engineering efforts.

Engineering of an environmentally responsive beta roll peptide for use as a calcium-dependent cross-linking domain for peptide hydrogel formation

We have created a set of rationally designed peptides that form calcium-dependent hydrogels based on the beta roll peptide domain. In the absence of calcium, the beta roll domain is intrinsically disordered. Upon the addition of calcium, the peptide forms a beta helix secondary structure. We have designed two variations of our beta roll domain. First, we have mutated one face of the beta roll domain to contain leucine residues so that the calcium-dependent structural formation leads to dimerization through hydrophobic interactions. Second, an α-helical leucine zipper domain is appended to the engineered beta roll domain as an additional means of forming intermolecular cross-links. This full peptide construct forms a hydrogel only in calcium-rich environments. The resulting structural and mechanical properties of the supramolecular assemblies are compared with the wild-type domain using several biophysical techniques including circular dichroism, FRET, bis-ANS binding and microrheology. The calcium responsiveness and rheological properties of the leucine beta roll containing construct confirm the potential of this allosterically regulated scaffold to serve as a cross-linking domain for stimulus-responsive biomaterials development.

Self-assembly and reconfigurability of shape-shifting particles

Reconfigurability of two-dimensional colloidal crystal structures assembled by anisometric particles capable of changing their shape were studied by molecular dynamics computer simulation. We show that when particles change shape on cue, the assembled structures reconfigure into different ordered structures, structures with improved order, or more densely packed disordered structures, on faster time scales than can be achieved via self-assembly from an initially disordered arrangement. These results suggest that reconfigurable building blocks can be used to assemble reconfigurable materials, as well as to assemble structures not possible otherwise, and that shape shifting could be a promising mechanism to engineer assembly pathways to ordered and disordered structures.

Characterization of mesoscale coiled-coil peptide-porphyrin complexes

Photoelectronically conductive self-assembling peptide-porphyrin assemblies have great potential in their use as biomaterials, owing largely to their environmentally responsive properties. We have successfully designed a coiled-coil peptide that can self-assemble to form mesoscale filaments and serve as a scaffold for porphyrin interaction. In our earlier work, peptide-porphyrin-based biomaterials were formed at neutral pH, but the structures were irregular at the nano- to microscale size range, as judged by atomic force microscopy. We identified a pH in which mesoscale fibrils were formed, taking advantage of the types of porphyrin interactions that are present in well-characterized J-aggregates. We used UV-visible spectroscopy, circular dichroism spectropolarimetry, fluorescence spectroscopy, and atomic force microscopy to characterize these self-assembling biomaterials. We propose a new assembly paradigm that arises from a set of unique porphyrin-porphyrin and porphyrin-peptide interactions whose structure may be readily modulated by changes in pH or peptide concentration.

Evaluation of a symmetry-based strategy for assembling protein complexes

We evaluate a strategy for assembling proteins into large cage-like structures, based on the symmetry associated with the native protein's quaternary structure. Using a trimeric protein, KDPG aldolase, as a building block, two fusion proteins were designed that could assemble together upon mixing. The fusion proteins, designated A-(+) and A-(-), comprise the aldolase domain, a short, flexible spacer sequence, and a sequence designed to form a heterodimeric antiparallel coiled-coil between A-(+) and A-(-). The flexible spacer is included to minimize constraints on the ability of the fusion proteins to assemble into larger structures. On incubating together, A-(+) and A-(-) assembled into a mixture of complexes that were analyzed by size exclusion chromatography coupled to multi-angle laser light scattering, analytical ultracentrifugation, transmission electron microscopy and atomic force microscopy. Our analysis indicates that, despite the inherent flexibility of the assembly strategy, the proteins assemble into a limited number of globular structures. Dimeric and tetrameric complexes of A-(+) and A-(-) predominate, with some evidence for the formation of larger assemblies; e.g. octameric A-(+): A-(-) complexes.

Monitoring the conformational changes of an intrinsically disordered peptide using a quartz crystal microbalance

Intrinsically disordered peptides (IDPs) have recently garnered much interest because of their role in biological processes such as molecular recognition and their ability to undergo stimulus-responsive conformational changes. The block V repeat-in-toxin motif of the Bordetella pertussis adenylate cyclase is an example of an IDP that undergoes a transition from a disordered state to an ordered beta roll conformation in the presence of calcium ions. In solution, a C-terminal capping domain is necessary for this transition to occur. To further explore the conformational behavior and folding requirements of this IDP, we have cysteine modified three previously characterized constructs, allowing for attachment to the gold surface of a quartz crystal microbalance (QCM). We demonstrate that, while immobilized, the C-terminally capped peptide exhibits similar calcium-binding properties to what have been observed in solution. In addition, immobilization on the solid surface appears to enable calcium-responsiveness in the uncapped peptides, in contrast to the behavior observed in solution. This work demonstrates the power of QCM as a tool to study the conformational changes of IDPs immobilized on surfaces and has implications for a range of potential applications where IDPs may be engineered and used including protein purification, biosensors, and other bionanotechnology applications.