Effects of Cell-Adhesive Ligand Presentation on Pentapeptide Supramolecular Assembly and Gelation: Simulations and Experiments.

The extracellular matrix (ECM) is a complex, hierarchical material containing structural and bioactive components. This complexity makes decoupling the effects of biomechanical properties and cell-matrix interactions difficult, especially when studying cellular processes in a 3D environment. Matrix mechanics and cell adhesion are both known regulators of specific cellular processes such as stem cell proliferation and differentiation. However, more information is required about how such variables impact various neural lineages that could, upon transplantation, therapeutically improve neural function after a central nervous system injury or disease. Rapidly Assembling Pentapeptides for Injectable Delivery (RAPID) hydrogels are one biomaterial approach to meet these goals, consisting of a family of peptide sequences that assemble into physical hydrogels in physiological media. In this study, we studied our previously reported supramolecularly-assembling RAPID hydrogels functionalized with the ECM-derived cell-adhesive peptide ligands RGD, IKVAV, and YIGSR. Using molecular dynamics simulations and experimental rheology, we demonstrated that these integrin-binding ligands at physiological concentrations (3-12 mm) did not impact the assembly of the KYFIL peptide system. In simulations, molecular measures of assembly such as hydrogen bonding and pi-pi interactions appeared unaffected by cell-adhesion sequence or concentration. Visualizations of clustering and analysis of solvent-accessible surface area indicated that the integrin-binding domains remained exposed. KYFIL or AYFIL hydrogels containing 3 mm of integrin-binding domains resulted in mechanical properties consistent with their non-functionalized equivalents. This strategy of doping RAPID gels with cell-adhesion sequences allows for the precise tuning of peptide ligand concentration, independent of the rheological properties. The controllability of the RAPID hydrogel system provides an opportunity to investigate the effect of integrin-binding interactions on encapsulated neural cells to discern how hydrogel microenvironment impacts growth, maturation, or differentiation.

Understanding how transmembrane domains regulate interactions between human BST-2 and the SARS-CoV-2 accessory protein ORF7a.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID, replicates at intracellular membranes. Bone marrow stromal antigen 2 (BST-2; tetherin) is an antiviral response protein that inhibits transport of viral particles after budding within infected cells. RNA viruses such as SARS-CoV-2 use various strategies to disable BST-2, including use of transmembrane 'accessory' proteins that interfere with BST-2 oligomerization. ORF7a is a small, transmembrane protein present in SARS-CoV-2 shown previously to alter BST-2 glycosylation and function. In this study, we investigated the structural basis for BST-2 ORF7a interactions, with a particular focus on transmembrane and juxtamembrane interactions. Our results indicate that transmembrane domains play an important role in BST-2 ORF7a interactions and mutations to the transmembrane domain of BST-2 can alter these interactions, particularly single-nucleotide polymorphisms in BST-2 that result in mutations such as I28S. Using molecular dynamics simulations, we identified specific interfaces and interactions between BST-2 and ORF7a to develop a structural basis for the transmembrane interactions. Differences in glycosylation are observed for BST-2 transmembrane mutants interacting with ORF7a, consistent with the idea that transmembrane domains play a key role in their heterooligomerization. Overall, our results indicate that ORF7a transmembrane domain interactions play a key role along with extracellular and juxtamembrane domains in modulating BST-2 function.

Engineering human liver fatty acid binding protein for detection of poly- and perfluoroalkyl substances.

Per- and polyfluoroalkyl substances (PFAS) are a large group of synthetic fluorinated chemicals with surface active and water-repellent properties. The combination of wide-spread use in numerous consumer and industrial products and extended biological half-lives arising from strong carbon-fluorine bonds has led to significant accumulation of PFAS in humans. As most human interaction with PFAS comes from ingestion, it is important to be able to detect PFAS in drinking water as well as in agricultural water. Here we present an approach to designing a fluorescence-based biosensor for the rapid detection of PFAS based on human liver fatty acid binding protein (hLFABP). Introduction of solvatochromic fluorophores within the ligand binding pocket (L50) allowed for intrinsic detection of perfluorooctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS), and perfluorohexanesulfonic acid (PFHxS) via blue-shifts in fluorescence emission spectra. Initially, a single tryptophan mutation (L50W) was found to be able to detect PFOA with a limit of detection (LOD) of 2.8 ppm. We improved the sensitivity of the biosensor by exchanging tryptophan for the thiol reactive fluorophore, acrylodan. The acrylodan conjugated C69S/F50C hLFABP variant is capable of detecting PFOA, PFOS, and PFHxS in PBS with LODs of 112 ppb, 345 ppb, and 1.09 ppm, respectively. The protein-based sensor is also capable of detecting these contaminants at similar ranges in spiked environmental water samples, including samples containing an interfering anionic surfactant sodium dodecyl sulfate. Overall, this study demonstrates engineered hLFABP is a useful platform for detection of PFAS in environmental water samples and highlights its ease of use and versatility in field applications.

Stimuli-Responsive, Pentapeptide, Nanofiber Hydrogel for Tissue Engineering.

Short peptides are uniquely versatile building blocks for self-assembly. Supramolecular peptide assemblies can be used to construct functional hydrogel biomaterials-an attractive approach for neural tissue engineering. Here, we report a new class of short, five-residue peptides that form hydrogels with nanofiber structures. Using rheology and spectroscopy, we describe how sequence variations, pH, and peptide concentration alter the mechanical properties of our pentapeptide hydrogels. We find that this class of seven unmodified peptides forms robust hydrogels from 0.2-20 kPa at low weight percent (less than 3 wt %) in cell culture media and undergoes shear-thinning and rapid self-healing. The peptides self-assemble into long fibrils with sequence-dependent fibrillar morphologies. These fibrils exhibit a unique twisted ribbon shape, as visualized by transmission electron microscopy (TEM) and Cryo-EM imaging, with diameters in the low tens of nanometers and periodicities similar to amyloid fibrils. Experimental gelation behavior corroborates our molecular dynamics simulations, which demonstrate peptide assembly behavior, an increase in ß-sheet content, and patterns of variation in solvent accessibility. Our rapidly assembling pentapeptides for injectable delivery (RAPID) hydrogels are syringe-injectable and support cytocompatible encapsulation of oligodendrocyte progenitor cells (OPCs), as well as their proliferation and three-dimensional process extension. Furthermore, RAPID gels protect OPCs from mechanical membrane disruption and acute loss of viability when ejected from a syringe needle, highlighting the protective capability of the hydrogel as potential cell carriers for transplantation therapies. The tunable mechanical and structural properties of these supramolecular assemblies are shown to be permissive to cell expansion and remodeling, making this hydrogel system suitable as an injectable material for cell delivery and tissue engineering applications.

Rapidly Assembling Pentapeptides for Injectable Delivery (RAPID) Hydrogels as Cytoprotective Cell Carriers.

Low cell survival after syringe injection hampers the success of preclinical and clinical cell transplantation trials. During syringe injection, cells experience mechanical forces that lead to cell-membrane disruption and decreased viability. To improve cell survival, we designed rapidly assembling pentapeptides for injectable delivery (RAPID) hydrogels that shear-thin, protect cells from extensional flow, form fibers, and provide mechanical properties similar to native tissue. We found that 1.5 wt % RAPID hydrogels mitigate the damaging effects of extensional flow, resulting in significantly greater cell viability (of common laboratory cell lines, primary cells, and human cells) than cells injected in PBS.

Temperature-Dependent Complex Coacervation of Engineered Elastin-like Polypeptide and Hyaluronic Acid Polyelectrolytes.

Coacervates have enormous potential due to their diverse functional properties supporting a wide number of applications in personal care products, pharmaceuticals, and food processing. Normally, separation of coacervate phases is induced by changes in pH, ionic strength, and/or polyelectrolyte concentration. This study investigates the microphase separation and coacervate complex formation of two natural polyelectrolytes, elastin-like polypeptides (ELPs) and hyaluronic acid (HA), as simple models for biological coacervates. These complex coacervates are formed over a wide range of stoichiometric molar charge ratios without the presence of salt or changes in pH and are primarily induced by changes in temperature. Unlike pure ELP solutions, the ELP/HA coacervates result in well-formed spherical particles after the temperature-induced phase transition. We also note that the formation of these complex coacervates is reversible with low hysteresis. We have demonstrated via fluorescent imaging and dynamic light scattering that high positive/negative charge ratios at elevated temperatures produced 400-600 nm particles with relatively low polydispersity indices (PDIs) of ∼0.1. Furthermore, dynamic light scattering, fluorescence microscopy, and optical microscopy revealed that the ratio of the two polyions strongly influenced the size and structure of these ELP/HA complex coacervates. Finally, we showed that the ELP/HA coacervates were able to sequester the hydrophobic fluorescent molecule pyrene, highlighting their potential for use as delivery vehicles for hydrophobic payloads.

From de novo peptides to native proteins: advancements in biomaterial scaffolds for acute ischemic stroke repair.

An active area of research in the field of regenerative medicine involves the development of bioactive matrices that can promote cellular interactions and elicit desirable regenerative behavior in vivo. This is particularly important in the context of ischemic stroke where a focal lesion forms forestalling the regrowth of brain tissue. Protein-based molecules have been used as building blocks to create supramolecular structures that emulate the properties of the native healthy extracellular matrix (ECM) within the central nervous system (CNS). In this review, we briefly describe the relevant biological aspect of stroke and the techniques found in molecular biology and biochemical synthesis methodologies used in the design and synthesis of novel biomaterials. Within these biomaterials, researchers are able to incorporate a number of different domains that trigger assembly or promote cell growth and survival and direct transplanted or endogenous stem cell behavior within the 3D scaffolds. Such domains may also yield stimuli-responsive biomaterial scaffolds where the structure of the hydrogel undergoes a change in response to the local environment. These highly modular proteinaceous materials allow incorporation of diverse biofunctional motifs and structural elements comparable to those found in native ECM. We explore CNS relevant biomaterials that promote cell survival and host tissue integration and discuss their applications to stem cell therapy in the treatment of stroke.

Toward a Designable Extracellular Matrix: Molecular Dynamics Simulations of an Engineered Laminin-Mimetic, Elastin-Like Fusion Protein.

Native extracellular matrices (ECMs) exhibit networks of molecular interactions between specific matrix proteins and other tissue components. Guided by these naturally self-assembling supramolecular systems, we have designed a matrix-derived protein chimera that contains a laminin globular-like (LG) domain fused to an elastin-like polypeptide (ELP). This bipartite design offers a flexible protein engineering platform: (i) laminin is a key multifunctional component of the ECM in human brains and other neural tissues, making it an ideal bioactive component of our fusion, and (ii) ELPs, known to be well-tolerated in vivo, provide a self-assembly scaffold with tunable physicochemical (viscoelastic, thermoresponsive) properties. Experimental characterization of novel proteins is resource-intensive, and examining many conceivable designs would be a formidable challenge in the laboratory. Computational approaches offer a way forward: molecular dynamics (MD) simulations can be used to analyze the structural/physical behavior of candidate LG-ELP fusion proteins, particularly in terms of conformational properties salient to our design goals, such as assembly propensity in a temperature range spanning the inverse temperature transition. As a first step in examining the physical characteristics of a model LG-ELP fusion protein, including its temperature-dependent structural behavior, we simulated the protein over a range of physiologically relevant temperatures (290-320 K). We find that the ELP region, built upon the archetypal (VPGXG)5 scaffold, is quite flexible and has a propensity for ß-rich secondary structures near physiological (310-315 K) temperatures. Our trajectories indicate that the temperature-dependent burial of hydrophobic patches in the ELP region, coupled to the local water structure dynamics and mediated by intramolecular contacts between aliphatic side chains, correlates with the temperature-dependent structural transitions in known ELP polymers. Because of the link between compaction of ELP segments into ß-rich structures and differential solvation properties of this region, we posit that future variation of ELP sequence and composition can be used to systematically alter the phase transition profiles and, thus, the general functionality of our LG-ELP fusion protein system.