De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity.

Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency of de novo protein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in viscoelastic biomaterials exhibiting fluid-like properties under rest and low shear, but solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and show via fluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly in a manner similar to formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology.

Computational design of transmembrane pores.

Transmembrane channels and pores have key roles in fundamental biological processes1 and in biotechnological applications such as DNA nanopore sequencing2-4, resulting in considerable interest in the design of pore-containing proteins. Synthetic amphiphilic peptides have been found to form ion channels5,6, and there have been recent advances in de novo membrane protein design7,8 and in redesigning naturally occurring channel-containing proteins9,10. However, the de novo design of stable, well-defined transmembrane protein pores that are capable of conducting ions selectively or are large enough to enable the passage of small-molecule fluorophores remains an outstanding challenge11,12. Here we report the computational design of protein pores formed by two concentric rings of α-helices that are stable and monodisperse in both their water-soluble and their transmembrane forms. Crystal structures of the water-soluble forms of a 12-helical pore and a 16-helical pore closely match the computational design models. Patch-clamp electrophysiology experiments show that, when expressed in insect cells, the transmembrane form of the 12-helix pore enables the passage of ions across the membrane with high selectivity for potassium over sodium; ion passage is blocked by specific chemical modification at the pore entrance. When incorporated into liposomes using in vitro protein synthesis, the transmembrane form of the 16-helix pore-but not the 12-helix pore-enables the passage of biotinylated Alexa Fluor 488. A cryo-electron microscopy structure of the 16-helix transmembrane pore closely matches the design model. The ability to produce structurally and functionally well-defined transmembrane pores opens the door to the creation of designer channels and pores for a wide variety of applications.

Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers.

To enable enhanced paper-based diagnostics with improved detection capabilities, new methods are needed to immobilize affinity reagents to porous substrates, especially for capture molecules other than IgG. To this end, we have developed and characterized three novel methods for immobilizing protein-based affinity reagents to nitrocellulose membranes. We have demonstrated these methods using recombinant affinity proteins for the influenza surface protein hemagglutinin, leveraging the customizability of these recombinant "flu binders" for the design of features for immobilization. The three approaches shown are: (1) covalent attachment of thiolated affinity protein to an epoxide-functionalized nitrocellulose membrane, (2) attachment of biotinylated affinity protein through a nitrocellulose-binding streptavidin anchor protein, and (3) fusion of affinity protein to a novel nitrocellulose-binding anchor protein for direct coupling and immobilization. We also characterized the use of direct adsorption for the flu binders, as a point of comparison and motivation for these novel methods. Finally, we demonstrated that these novel methods can provide improved performance to an influenza hemagglutinin assay, compared to a traditional antibody-based capture system. Taken together, this work advances the toolkit available for the development of next-generation paper-based diagnostics.

Intracellular delivery system for antibody-Peptide drug conjugates.

Antibodies armed with biologic drugs could greatly expand the therapeutic potential of antibody-drug conjugates for cancer therapy, broadening their application to disease targets currently limited by intracellular delivery barriers. Additional selectivity and new therapeutic approaches could be realized with intracellular protein drugs that more specifically target dysregulated pathways in hematologic cancers and other malignancies. A multifunctional polymeric delivery system for enhanced cytosolic delivery of protein drugs has been developed that incorporates endosomal-releasing activity, antibody targeting, and a biocompatible long-chain ethylene glycol component for optimized safety, pharmacokinetics, and tumor biodistribution. The pH-responsive polymeric micelle carrier, with an internalizing anti-CD22 monoclonal targeting antibody, effectively delivered a proapoptotic Bcl-2 interacting mediator (BIM) peptide drug that suppressed tumor growth for the duration of treatment and prolonged survival in a xenograft mouse model of human B-cell lymphoma. Antitumor drug activity was correlated with a mechanistic induction of the Bcl-2 pathway biomarker cleaved caspase-3 and a marked decrease in the Ki-67 proliferation biomarker. Broadening the intracellular target space by more effective delivery of protein/peptide drugs could expand the repertoire of antibody-drug conjugates to currently undruggable disease-specific targets and permit tailored drug strategies to stratified subpopulations and personalized medicines.

Photoelectrochemistry of photosystem I bound in nafion.

Developing a solid state Photosystem I (PSI) modified electrode is attractive for photoelectrochemical applications because of the quantum yield of PSI, which approaches unity in the visible spectrum. Electrodes are constructed using a Nafion film to encapsulate PSI as well as the hole-scavenging redox mediator Os(bpy)2Cl2. The photoactive electrodes generate photocurrents of 4 µA/cm(2) when illuminated with 1.4 mW/cm(2) of 676 nm band-pass filtered light. Methyl viologen (MV(2+)) is present in the electrolyte to scavenge photoelectrons from PSI in the Nafion film and transport charges to the counter electrode. Because MV(2+) is positively charged in both reduced and oxidized states, it is able to diffuse through the cation permeable channels of Nafion. Photocurrent is produced when the working electrode is set to voltages negative of the Os(3+)/Os(2+) redox potential. Charge transfer through the Nafion film and photohole scavenging at the PSI luminal surface by Os(bpy)2Cl2 depends on the reduction of Os redox centers to Os(2+) via hole scavenging from PSI. The optimal film densities of Nafion (10 µg/cm(2) Nafion) and PSI (100 µg/cm(2) PSI) are determined to provide the highest photocurrents. These optimal film densities force films to be thin to allow the majority of PSI to have productive electrical contact with the backing electrode.

Enhancing extracellular vesicle cargo loading and functional delivery by engineering protein-lipid interactions.

Naturally generated lipid nanoparticles termed extracellular vesicles (EVs) hold significant promise as engineerable therapeutic delivery vehicles. However, active loading of protein cargo into EVs in a manner that is useful for delivery remains a challenge. Here, we demonstrate that by rationally designing proteins to traffic to the plasma membrane and associate with lipid rafts, we can enhance loading of protein cargo into EVs for a set of structurally diverse transmembrane and peripheral membrane proteins. We then demonstrate the capacity of select lipid tags to mediate increased EV loading and functional delivery of an engineered transcription factor to modulate gene expression in target cells. We envision that this technology could be leveraged to develop new EV-based therapeutics that deliver a wide array of macromolecular cargo.

Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes.

The organization of membrane proteins between and within membrane-bound compartments is critical to cellular function. Yet we lack approaches to regulate this organization in a range of membrane-based materials, such as engineered cells, exosomes, and liposomes. Uncovering and leveraging biophysical drivers of membrane protein organization to design membrane systems could greatly enhance the functionality of these materials. Towards this goal, we use de novo protein design, molecular dynamic simulations, and cell-free systems to explore how membrane-protein hydrophobic mismatch could be used to tune protein cotranslational integration and organization in synthetic lipid membranes. We find that membranes must deform to accommodate membrane-protein hydrophobic mismatch, which reduces the expression and co-translational insertion of membrane proteins into synthetic membranes. We use this principle to sort proteins both between and within membranes, thereby achieving one-pot assembly of vesicles with distinct functions and controlled split-protein assembly, respectively. Our results shed light on protein organization in biological membranes and provide a framework to design self-organizing membrane-based materials with applications such as artificial cells, biosensors, and therapeutic nanoparticles.

In vivo evaluation of medical device-associated inflammation using a macrophage-specific positron emission tomography (PET) imaging probe.

To image implant-surrounding activated macrophages, a macrophage-specific PET probe was prepared by conjugating folic acid (FA) and 2,2',2″,2‴-(1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrayl)tetracetic acid (DOTA) to polyethylene glycol (PEG) and then labeling the conjugate with Ga-68. In vivo PET imaging evaluations demonstrate that the probe is able to detect foreign body reactions, and more importantly, quantify the degree of inflammatory responses to an implanted medical device. These results were further validated by histological analysis.

De novo design of monomeric helical bundles for pH-controlled membrane lysis.

Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here, we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of the 30 designs that were experimentally tested, all expressed in Escherichia coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0-5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.

Single Cell RNA Sequencing Reveals Human Tooth Type Identity and Guides In Vitro hiPSC Derived Odontoblast Differentiation (iOB).

Over 90% of the U.S. adult population suffers from tooth structure loss due to caries. Most of the mineralized tooth structure is composed of dentin, a material produced and mineralized by ectomesenchyme derived cells known as odontoblasts. Clinicians, scientists, and the general public share the desire to regenerate this missing tooth structure. To bioengineer missing dentin, increased understanding of human tooth development is required. Here we interrogate at the single cell level the signaling interactions that guide human odontoblast and ameloblast development and which determine incisor or molar tooth germ type identity. During human odontoblast development, computational analysis predicts that early FGF and BMP activation followed by later HH signaling is crucial. Application of this sci-RNA-seq analysis generates a differentiation protocol to produce mature hiPSC derived odontoblasts in vitro (iOB). Further, we elucidate the critical role of FGF signaling in odontoblast maturation and its biomineralization capacity using the de novo designed FGFR1/2c isoform specific minibinder scaffolded as a C6 oligomer that acts as a pathway agonist. We find that FGFR1c is upregulated in functional odontoblasts and specifically plays a crucial role in driving odontoblast maturity. Using computational tools, we show on a molecular level how human molar development is delayed compared to incisors. We reveal that enamel knot development is guided by FGF and WNT in incisors and BMP and ROBO in the molars, and that incisor and molar ameloblast development is guided by FGF, EGF and BMP signaling, with tooth type specific intensity of signaling interactions. Dental ectomesenchyme derived cells are the primary source of signaling ligands responsible for both enamel knot and ameloblast development.

Single-cell census of human tooth development enables generation of human enamel.

Tooth enamel secreted by ameloblasts (AMs) is the hardest material in the human body, acting as a shield to protect the teeth. However, the enamel is gradually damaged or partially lost in over 90% of adults and cannot be regenerated due to a lack of ameloblasts in erupted teeth. Here, we use single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) to establish a spatiotemporal single-cell census for the developing human tooth and identify regulatory mechanisms controlling the differentiation process of human ameloblasts. We identify key signaling pathways involved between the support cells and ameloblasts during fetal development and recapitulate those findings in human ameloblast in vitro differentiation from induced pluripotent stem cells (iPSCs). We furthermore develop a disease model of amelogenesis imperfecta in a three-dimensional (3D) organoid system and show AM maturation to mineralized structure in vivo. These studies pave the way for future regenerative dentistry.

Novel thermogelling dispersions of polymer nanoparticles for controlled protein release.

A novel poly(oligo(ethylene glycol) methyl ether methacrylate-co-oligo(ethylene glycol) ethyl ether methacrylate)-poly(acrylic acid) interpenetrating network (IPN) nanoparticle was synthesized. The temperature-responsive properties of the IPN nanoparticles were investigated by a dynamic light scattering method. Atomic force microscopic images confirmed the homogenous and monodisperse morphology of the IPN nanoparticles. Both visual observation and viscosity testing demonstrated that the IPN nanoparticles exhibit thermogelling properties at body temperature, 37 °C. Subsequent studies verified that such temperature-sensitive properties of IPN nanoparticles allow their ease of injection and then slow release of model proteins, both in vitro and in vivo. Histological analysis showed that our IPN implants exerted minimal inflammation following subcutaneous implantation. Our results support the idea that, by simply mixing with proteins of interest, the novel IPN nanoparticles can be used to form in situ thermogelling devices for controlled protein release. FROM THE CLINICAL EDITOR: This paper discusses a temperature responsive interpenetrating network (IPN) polymeric nanoparticle that can be used to form in situ thermogelling devices for controlled protein release by simply mixing them with proteins of interest.

Do bib clips pose a cross-contamination risk at the dental clinic?

Although multiple-use dental napkin holders have a relatively low risk of transmitting infection, they do require disinfection between patients. This study sought to: 1) determine the presence of bacterial load on two types of clips of reusable bib chains after dental procedures at the Endodontics and Orthodontics clinics at Tufts University School of Dental Medicine; and 2) evaluate the effectiveness of disinfecting the clips. These specialty clinics represent a wide spectrum of patients, procedures, and appointment times. Bacterial load on the bib clips was determined immediately following dental treatments-both before and after their disinfection-during morning and afternoon sessions. The results revealed that, after treatments, there was a statistically significant difference when comparing the two clinics for bacterial burden on the clips. Furthermore, there was a statistically significant difference in bacterial load on the two types of clips. Disinfection of the bib clips was highly effective in both clinics. Clinically, the results suggest that due to the nature of the treatment, the demographic population, and the type of bib clips used, patients in different clinics may be exposed to varying bacterial concentrations on the bib clips, and thus to different possible cross-contamination risks. Future analyses will be performed to identify the bacterial species in samples from both pre- and post-disinfected clips, and to determine if they harbor disease-causing bacterial species that can pose a potential, yet undetermined risk for cross-contamination.

Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.

Symmetric protein dimers, trimers, and higher-order cyclic oligomers play key roles in many biological processes. However, structural studies of oligomeric systems by solution NMR can be difficult due to slow tumbling of the system and the difficulty in identifying NOE interactions across protein interfaces. Here, we present an automated method (RosettaOligomers) for determining the solution structures of oligomeric systems using only chemical shifts, sparse NOEs, and domain orientation restraints from residual dipolar couplings (RDCs) without a need for a previously determined structure of the monomeric subunit. The method integrates previously developed Rosetta protocols for solving the structures of monomeric proteins using sparse NMR data and for predicting the structures of both nonintertwined and intertwined symmetric oligomers. We illustrated the performance of the method using a benchmark set of nine protein dimers, one trimer, and one tetramer with available experimental data and various interface topologies. The final converged structures are found to be in good agreement with both experimental data and previously published high-resolution structures. The new approach is more readily applicable to large oligomeric systems than conventional structure-determination protocols, which often require a large number of NOEs, and will likely become increasingly relevant as more high-molecular weight systems are studied by NMR.

Fibroblast/fibrocyte: surface interaction dictates tissue reactions to micropillar implants.

Micropillar technology has shown great promise for medical implants or sensors in recent years. To study the influence of surface topography on cellular responses, polydimethylsiloxane (PDMS) micropillar arrays with pillar spacing (20-70 µm) and height (14-25 µm) have been fabricated. The influence of micropillar arrays on cellular behavior was tested both in vitro and in vivo. Interestingly, in vitro, we observe a distinct response for 3T3 fibroblasts and RAW 264.7 macrophages to the topographical cues tested. Attachment and proliferation of fibroblasts was substantially enhanced by increasing pillar height, whereas macrophage adherence is significantly diminished by reduced pillar spacing. When implanted in the subcutaneous cavity of BALB/c mice for 14 days, we find a prevailing trend with capsule cell density and capsule thickness increasing, as both pillar height and spacing rise. Collagen deposition and neoangiogenesis, two pivotal factors in granulation tissue maturation, are also observed to have a stronger response to the increase in both pillar height and spacing. In contradiction to our original hypothesis, we observed that fibroblasts rather than macrophages are a key contributor to the in vivo outcome of micropillar arrays. Investigation into fibroblast activation, however, revealed that recruited fibrocytes, rather than resident fibroblasts, correspond to the in vivo outcome. The results from this work support the critical and often overlooked role of fibrocytes in tissue response to biomaterial implants with varying topography.

Treatment of experimental anthrax with pegylated circularly permuted capsule depolymerase.

Anthrax is considered one of the most dangerous bioweapon agents, and concern about multidrug-resistant strains has led to the development of alternative therapeutic approaches that target the antiphagocytic capsule, an essential virulence determinant of Bacillus anthracis, the causative agent. Capsule depolymerase is a γ-glutamyltransferase that anchors the capsule to the cell wall of B. anthracis. Encapsulated strains of B. anthracis can be treated with recombinant capsule depolymerase to enzymatically remove the capsule and promote phagocytosis and killing by human neutrophils. Here, we show that pegylation improved the pharmacokinetic and therapeutic properties of a previously described variant of capsule depolymerase, CapD-CP, when delivered 24 hours after exposure every 8 hours for 2 days for the treatment of mice infected with B. anthracis. Mice infected with 382 LD50 of B. anthracis spores from a nontoxigenic encapsulated strain were completely protected (10 of 10) after treatment with the pegylated PEG-CapD-CPS334C, whereas 10% of control mice (1 of 10) survived with control treatment using bovine serum albumin (P < 0.0001, log-rank analysis). Treatment of mice infected with five LD50 of a fully virulent toxigenic, encapsulated B. anthracis strain with PEG-CapD-CPS334C protected 80% (8 of 10) of the animals, whereas 20% of controls (2 of 10) survived (P = 0.0125, log-rank analysis). This strategy renders B. anthracis susceptible to innate immune responses and does not rely on antibiotics. These findings suggest that enzyme-catalyzed removal of the capsule may be a potential therapeutic strategy for the treatment of multidrug- or vaccine-resistant anthrax and other bacterial infections.

De novo design of transmembrane ß barrels.

Transmembrane ß-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a "hypothesis, design, and test" approach to determine TMB design principles, notably, the importance of negative design to slow ß-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.

Endosseous implants versus nonsurgical root canal therapy: a systematic review of the literature.

For this article, the authors identified and reviewed the current literature, addressing two treatment options for endodontically involved teeth: root canal therapy and restoration versus extraction and the placement of a dental implant. The literature was evaluated as a basis for making treatment decisions. PubMed was queried for all studies that compared nonsurgical root canal therapy (NSRCT) and restoration with the extraction of teeth and placement of a dental implant. This search was supplemented by searching the bibliographies of these studies to ensure that all relevant studies were included. A total of 38 studies were found that directly compared NSRCT and restoration with extraction and placement of a dental implant. The literature is discussed in terms of outcomes for both treatment options, considerations in treatment plan decision-making, or the opinions of the authors.

The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite.

Proteins are found to be involved in interaction with solid surfaces in numerous natural events. Acidic proteins that adsorb to crystal faces of a biomineral to control the growth and morphology of hard tissue are only one example. Deducing the mechanisms of surface recognition exercised by proteins has implications to osteogenesis, pathological calcification and other proteins functions at their adsorbed state. Statherin is an enamel pellicle protein that inhibits hydroxyapatite nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. Here, we highlight some of the insights we obtained recently using both thermodynamic and solid state NMR measurements to the adsorption process of statherin to hydroxyapatite. We combine macroscopic energy characterization with microscopic structural findings to present our views of protein adsorption mechanisms and the structural changes accompanying it and discuss the implications of these studies to understanding the functions of the protein adsorbed to the enamel surfaces.

A general computational approach for repeat protein design.

Repeat proteins have considerable potential for use as modular binding reagents or biomaterials in biomedical and nanotechnology applications. Here we describe a general computational method for building idealized repeats that integrates available family sequences and structural information with Rosetta de novo protein design calculations. Idealized designs from six different repeat families were generated and experimentally characterized; 80% of the proteins were expressed and soluble and more than 40% were folded and monomeric with high thermal stability. Crystal structures determined for members of three families are within 1Å root-mean-square deviation to the design models. The method provides a general approach for fast and reliable generation of stable modular repeat protein scaffolds.