Programmable protein circuit design.

A fundamental challenge in synthetic biology is to create molecular circuits that can program complex cellular functions. Because proteins can bind, cleave, and chemically modify one another and interface directly and rapidly with endogenous pathways, they could extend the capabilities of synthetic circuits beyond what is possible with gene regulation alone. However, the very diversity that makes proteins so powerful also complicates efforts to harness them as well-controlled synthetic circuit components. Recent work has begun to address this challenge, focusing on principles such as orthogonality and composability that permit construction of diverse circuit-level functions from a limited set of engineered protein components. These approaches are now enabling the engineering of circuits that can sense, transmit, and process information; dynamically control cellular behaviors; and enable new therapeutic strategies, establishing a powerful paradigm for programming biology.

Programmable design of orthogonal protein heterodimers.

Specificity of interactions between two DNA strands, or between protein and DNA, is often achieved by varying bases or side chains coming off the DNA or protein backbone-for example, the bases participating in Watson-Crick pairing in the double helix, or the side chains contacting DNA in TALEN-DNA complexes. By contrast, specificity of protein-protein interactions usually involves backbone shape complementarity1, which is less modular and hence harder to generalize. Coiled-coil heterodimers are an exception, but the restricted geometry of interactions across the heterodimer interface (primarily at the heptad a and d positions2) limits the number of orthogonal pairs that can be created simply by varying side-chain interactions3,4. Here we show that protein-protein interaction specificity can be achieved using extensive and modular side-chain hydrogen-bond networks. We used the Crick generating equations5 to produce millions of four-helix backbones with varying degrees of supercoiling around a central axis, identified those accommodating extensive hydrogen-bond networks, and used Rosetta to connect pairs of helices with short loops and to optimize the remainder of the sequence. Of 97 such designs expressed in Escherichia coli, 65 formed constitutive heterodimers, and the crystal structures of four designs were in close agreement with the computational models and confirmed the designed hydrogen-bond networks. In cells, six heterodimers were fully orthogonal, and in vitro-following mixing of 32 chains from 16 heterodimer designs, denaturation in 5 M guanidine hydrochloride and reannealing-almost all of the interactions observed by native mass spectrometry were between the designed cognate pairs. The ability to design orthogonal protein heterodimers should enable sophisticated protein-based control logic for synthetic biology, and illustrates that nature has not fully explored the possibilities for programmable biomolecular interaction modalities.

De novo design of bioactive protein switches.

Allosteric regulation of protein function is widespread in biology, but is challenging for de novo protein design as it requires the explicit design of multiple states with comparable free energies. Here we explore the possibility of designing switchable protein systems de novo, through the modulation of competing inter- and intramolecular interactions. We design a static, five-helix 'cage' with a single interface that can interact either intramolecularly with a terminal 'latch' helix or intermolecularly with a peptide 'key'. Encoded on the latch are functional motifs for binding, degradation or nuclear export that function only when the key displaces the latch from the cage. We describe orthogonal cage-key systems that function in vitro, in yeast and in mammalian cells with up to 40-fold activation of function by key. The ability to design switchable protein functions that are controlled by induced conformational change is a milestone for de novo protein design, and opens up new avenues for synthetic biology and cell engineering.

Converting Commercial Zn Foils into Single (002)-Textured Zn with Millimeter-Sized Grains for Highly Reversible Aqueous Zinc Batteries.

Rechargeable aqueous zinc batteries are promising but hindered by unfavorable dendrite growth and side reactions on zinc anodes. In this study, we demonstrate a fast melting-solidification approach for effectively converting commercial Zn foils into single (002)-textured Zn featuring millimeter-sized grains. The melting process eliminates initial texture, residual stress, and grain size variations in diverse commercial Zn foils, guaranteeing the uniformity of commercial Zn foils into single (002)-textured Zn. The single (002)-texture ensures large-scale epitaxial and dense Zn deposition, while the reduction in grain boundaries significantly minimizes intergranular reactions. These features enable large grain single (002)-textured Zn shows planar and dense Zn deposition under harsh conditions (100 mA cm-2, 100 mAh cm-2), impressive reversibility in Zn||Zn symmetric cell (3280 h under 1 mA cm-2, 830 h under 10 mAh cm-2), and long cycling stability over 180 h with a high depth of discharge value of 75 %. This study successfully addresses the issue of uncontrollable texture formation in Zn foils following routine annealing treatments with temperatures below the Zn melting point. The findings of this study establish a highly efficient strategy for fabricating highly reversible single (002)-textured Zn anodes.

CT-707 overcomes hypoxia-mediated sorafenib resistance in Hepatocellular carcinoma by inhibiting YAP signaling.

BACKGROUND: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Sorafenib is the first-line treatment for advanced HCC, but the anti-cancer effects remain to be improved as indicated by its low response rates and failure to prolong the progression-free survival (PFS). Thus, it is urgent to explore approaches to improve the clinical outcome. MATERIALS AND METHODS: The effect of Sorafenib in HCC was analyzed by SRB (sulforhodamine B) assay in normoxia and hypoxia, respectively. The different dose combination effect of CT707 and sorafenib was analyzed by SRB assay in hypoxia. Flow cytometry assay was used to detect the cell apoptosis rate with CT707 and sorafenib treatment in hypoxia. Western blotting was used to detect the expression levels of apoptosis -related proteins and the mechanism of CT707 overcome the resistance of sorafenib in hypoxia. RESULTS: Our study showed that the characteristic intratumor hypoxia of advanced HCC is one of the major factors which mediated the drug resistance towards sorafenib in HCC. And CT-707, a novel multi-kinase inhibitor, could sensitize the hypoxic HCC cells towards sorafenib. Further studies showed that CT-707 abolished the nuclear translocation of Yes Associate-Protein (YAP), which has been demonstrated as one of mechanism of hypoxia-mediated sorafenib-resistance in HCC. CONCLUSIONS: Overall, this study not only favors the development of this novel multi-kinase inhibitor CT-707 as a therapeutic agent against HCC, but also provides a potential strategy to overcome the hypoxia-mediated resistance to sorafenib in HCC patients.

Functional expression and characterization of the envelope glycoprotein E1E2 heterodimer of hepatitis C virus.

Hepatitis C virus (HCV) is a member of Hepacivirus and belongs to the family of Flaviviridae. HCV infects millions of people worldwide and may lead to cirrhosis and hepatocellular carcinoma. HCV envelope proteins, E1 and E2, play critical roles in viral cell entry and act as major epitopes for neutralizing antibodies. However, unlike other known flaviviruses, it has been challenging to study HCV envelope proteins E1E2 in the past decades as the in vitro expressed E1E2 heterodimers are usually of poor quality, making the structural and functional characterization difficult. Here we express the ectodomains of HCV E1E2 heterodimer with either an Fc-tag or a de novo designed heterodimeric tag and are able to isolate soluble E1E2 heterodimer suitable for functional and structural studies. Then we characterize the E1E2 heterodimer by electron microscopy and model the structure by the coevolution based modeling strategy with Rosetta, revealing the potential interactions between E1 and E2. Moreover, the E1E2 heterodimer is applied to examine the interactions with the known HCV receptors, neutralizing antibodies as well as the inhibition of HCV infection, confirming the functionality of the E1E2 heterodimer and the binding profiles of E1E2 with the cellular receptors. Therefore, the expressed E1E2 heterodimer would be a valuable target for both viral studies and vaccination against HCV.

Self-Assembling 2D Arrays with de Novo Protein Building Blocks.

Modular self-assembly of biomolecules in two dimensions (2D) is straightforward with DNA but has been difficult to realize with proteins, due to the lack of modular specificity similar to Watson-Crick base pairing. Here we describe a general approach to design 2D arrays using de novo designed pseudosymmetric protein building blocks. A homodimeric helical bundle was reconnected into a monomeric building block, and the surface was redesigned in Rosetta to enable self-assembly into a 2D array in the C12 layer symmetry group. Two out of ten designed arrays assembled to micrometer scale under negative stain electron microscopy, and displayed the designed lattice geometry with assembly size up to 100 nm under atomic force microscopy. The design of 2D arrays with pseudosymmetric building blocks is an important step toward the design of programmable protein self-assembly via pseudosymmetric patterning of orthogonal binding interfaces.

[Sunitinib suppresses migration of ovarian cancer cells through negative modulation of TGF-ß-mediated epithelial-mesenchymal transition].

OBJECTIVE: To investigate the effect of sunitinib on the migration of ovarian cells and its mechanism of the negative regulation TGF-ß mediated of epithelial-mesenchymal transition(EMT) by sunitinib to inhibit ovarian cancer metastasis. METHODS: The migration of human ovarian cancer cells SKOV3 was evaluated by wound-healing and transwell assays. The effects of sunitinib on TGF-ß-induced E-cadherin expression was assessed by Western-blotting, real time RT-PCR and immunofluorescence assay. The protein levels of Snail and the transcriptional activity of Smad in sunitinib-treated cells were examined by Western-blotting and SBE-luciferase assay. RESULTS: Sunitinib suppressed the migration of SKOV3 cells in a concentration-dependent manner. TGF-ß stimulation reduced E-cadherin protein level, which was attenuated by sunitinib. Sunitinib inhibited the up-regulation of Snail protein level induced by TGF-ß treatment. The SBE reporter was constructed by linking the Smad-binding elements promoter upstream of luciferase reporter gene. A remarkable increment of transcriptional activity of Smads complexes was observed in SKOV3 cells exposed to TGF-ß, which was significantly prohibited by sunitinib. CONCLUSION: Sunitinib can inhibit the migration of SKOV3 cells and attenuate the down-regulation of E-cadherin protein level induced by TGF-ß. Sunitinib can abolish TGF-ß-induced up-regulation of Snail protein and decrease the transcriptional activity of Smad complexes. The results indicate that sunitinib suppresses migration of ovarian cancer cells through negative modulation of TGF-ß-mediated epithelial-mesenchymal transition.

Boosting the Performance of Aluminum-Air Batteries by Interface Modification.

The large-scale application of aqueous Al-air batteries is highly restricted by the performance of Al anodes. The severe self-corrosion and hydrogen evolution of the Al anode in a concentrated alkaline electrolyte are the main reason. Here, aimed at relieving side reactions and enhancing the utilization of metal Al, we propose a hybrid electrolyte additive of 2-mercaptobenzothiazole (MBT) and ZnO to form a protective film at the anode/electrolyte interface and to decrease the hydrogen evolution active site. The strong absorption capability of MBT on the metal surface, along with the reduced Zn-containing layer, enables a compact protective film with high hydrogen evolution potential on the Al surface. With this benefit, the hydrogen evolution reaction (HER) inhibition efficiency is up to 83.58%, endowing a superior Al-air battery with an energy density of 2376.71 Wh kgAl-1 under a current density of 25 mA cm-2. The conception of constructing a hybrid protective film on the metal surface not only favors the development of metal-air batteries but also facilitates metal corrosion protection.

Effects of the Biomimetic Microstructure in Electrospun Fiber Sutures and Mechanical Tension on Tissue Repair.

Electrospun microfibers, designed to emulate the extracellular matrix (ECM), play a crucial role in regulating the cellular microenvironment for tissue repair. Understanding their mechanical influence and inherent biological interactions at the ECM interface, however, remains a complex challenge. This study delves into the role of mechanical cues in tissue repair by fabricating Col/PLCL microfibers with varying chemical compositions and alignments that mimic the structure of the ECM. Furthermore, we optimized these microfibers to create the Col/PLCL@PDO aligned suture, with a specific emphasis on mechanical tension in tissue repair. The result reveals that within fibers of identical chemical composition, fibroblast proliferation is more pronounced in aligned fibers than in unaligned ones. Moreover, cells on aligned fibers exhibit an increased aspect ratio. In vivo experiments demonstrated that as the tension increased to a certain level, cell proliferation augmented, cells assumed more elongated morphologies with distinct protrusions, and there was an elevated secretion of collagen III and tension suture, facilitating soft tissue repair. This research illuminates the structural and mechanical dynamics of electrospun fiber scaffolds; it will provide crucial insights for the advancement of precise and controllable tissue engineering materials.

Flexible, Transparent and Conductive Metal Mesh Films with Ultra-High FoM for Stretchable Heating and Electromagnetic Interference Shielding.

Despite the growing demand for transparent conductive films in smart and wearable electronics for electromagnetic interference (EMI) shielding, achieving a flexible EMI shielding film, while maintaining a high transmittance remains a significant challenge. Herein, a flexible, transparent, and conductive copper (Cu) metal mesh film for EMI shielding is fabricated by self-forming crackle template method and electroplating technique. The Cu mesh film shows an ultra-low sheet resistance (0.18 Ω â–¡-1), high transmittance (85.8%@550 nm), and ultra-high figure of merit (> 13,000). It also has satisfactory stretchability and mechanical stability, with a resistance increases of only 1.3% after 1,000 bending cycles. As a stretchable heater (ε > 30%), the saturation temperature of the film can reach over 110 °C within 60 s at 1.00 V applied voltage. Moreover, the metal mesh film exhibits outstanding average EMI shielding effectiveness of 40.4 dB in the X-band at the thickness of 2.5 µm. As a demonstration, it is used as a transparent window for shielding the wireless communication electromagnetic waves. Therefore, the flexible and transparent conductive Cu mesh film proposed in this work provides a promising candidate for the next-generation EMI shielding applications.

Tunnel-Oriented VO2 (B) Cathode for High-Rate Aqueous Zinc-Ion Batteries.

Tunnel-type vanadium oxides are promising cathodes for aqueous zinc ion batteries. However, unlike layer-type cathodes with adjustable layer distances, enhancing ion-transport kinetics in tunnels characterized by fixed sizes poses a considerable challenge. This study highlights that the macroscopic arrangement of the electrode crucially determines tunnel orientation, thereby influencing ion transport. By changing the material morphology, the tunnel orientation can be optimized to facilitate rapid ion diffusion. In a proof-of-concept demonstration, it is revealed that (00l) facets-dominated VO2 (B) nanobelts with dispersive morphology (VO2-D) tend to adopt a stacking pattern with directional ion transport along the c-axis on the electrode and guarantee fast ion diffusion. Compared with the aggregated sample (VO2-A) that tends to random arrangement on the electrode with isotropic and slow ion transfer behavior, the electrode featuring dispersive (00l) facets-dominated VO2 (B) nanobelts displays directional and fast ion diffusion behavior, thus exhibits an ultrahigh-rate performance (420.8 and 344.8 mAh g-1 at 0.1 and 10 A g-1, respectively) and long cycling stability (84.3% capacity retention under 5000 cycles at 10 A g-1). The results suggest that simultaneous manipulation of exposed crystal facet and morphology-related electrode arrangement should be promising for boosting the ion-transport kinetics in tunnel-type vanadium oxide cathodes.

Stretchable, Transparent, and Ultra-Broadband Terahertz Shielding Thin Films Based on Wrinkled MXene Architectures.

With the increasing demand for terahertz (THz) technology in security inspection, medical imaging, and flexible electronics, there is a significant need for stretchable and transparent THz electromagnetic interference (EMI) shielding materials. Existing EMI shielding materials, like opaque metals and carbon-based films, face challenges in achieving both high transparency and high shielding efficiency (SE). Here, a wrinkled structure strategy was proposed to construct ultra-thin, stretchable, and transparent terahertz shielding MXene films, which possesses both isotropous wrinkles (height about 50 nm) and periodic wrinkles (height about 500 nm). Compared to flat film, the wrinkled MXene film (8 nm) demonstrates a remarkable 36.5% increase in SE within the THz band. The wrinkled MXene film exhibits an EMI SE of 21.1 dB at the thickness of 100 nm, and an average EMI SE/t of 700 dB µm-1 over the 0.1-10 THz. Theoretical calculations suggest that the wrinkled structure enhances the film's conductivity and surface plasmon resonances, resulting in an improved THz wave absorption. Additionally, the wrinkled structure enhances the MXene films' stretchability and stability. After bending and stretching (at 30% strain) cycles, the average THz transmittance of the wrinkled film is only 0.5% and 2.4%, respectively. The outstanding performances of the wrinkled MXene film make it a promising THz electromagnetic shielding materials for future smart windows and wearable electronics.

Protein circuit design using de novo proteins.

Protein-based biological circuits enable customized control of cellular functions, and de novo protein design enables circuit functionalities that are not possible by repurposing natural proteins. Here, I highlight recent progress in protein circuit design, including CHOMP, developed by Gao et al., and SPOC, developed by Fink et al.

Flexible, Transparent, and Wafer-Scale Artificial Synapse Array Based on TiOx /Ti3 C2 Tx Film for Neuromorphic Computing.

A high-density neuromorphic computing memristor array based on 2D materials paves the way for next-generation information-processing components and in-memory computing systems. However, the traditional 2D-materials-based memristor devices suffer from poor flexibility and opacity, which hinders the application of memristors in flexible electronics. Here, a flexible artificial synapse array based on TiOx /Ti3 C2 Tx film is fabricated by a convenient and energy-efficient solution-processing technique, which realizes high transmittance (≈90%) and oxidation resistance (>30 days). The TiOx /Ti3 C2 Tx memristor shows low device-to-device variability, long memory retention and endurance, a high ON/OFF ratio, and fundamental synaptic behavior. Furthermore, satisfactory flexibility (R = 1.0 mm) and mechanical endurance (104 bending cycles) of the TiOx /Ti3 C2 Tx memristor are achieved, which is superior to other film memristors prepared by chemical vapor deposition. In addition, high-precision (>96.44%) MNIST handwritten digits recognition classification simulation indicates that the TiOx /Ti3 C2 Tx artificial synapse array holds promise for future neuromorphic computing applications, and provides excellent high-density neuron circuits for new flexible intelligent electronic equipment.

CDK2 inhibition disorders centrosome stoichiometry and alters cellular outcomes in aneuploid cancer cells.

Cyclin-dependent Kinase 2 (CDK2) inhibition prevents supernumerary centrosome clustering. This causes multipolarity, anaphase catastrophe and apoptotic death of aneuploid cancers. This study elucidated how CDK2 antagonism affected centrosome stoichiometry. Focused ion beam scanning electron microscopy (FIB-SEM) and immunofluorescent imaging were used. Studies interrogated multipolar mitosis after pharmacologic or genetic repression of CDK2. CDK2/9 antagonism with CYC065 (Fadraciclib)-treatment disordered centrosome stoichiometry in aneuploid cancer cells, preventing centrosome clustering. This caused ring-like chromosomes or multipolar cancer cells to form before onset of cell death. Intriguingly, CDK2 inhibition caused a statistically significant increase in single centrioles rather than intact centrosomes with two centrioles in cancer cells having chromosome rings or multipolarity. Statistically significant alterations in centrosome stoichiometry were undetected in other mitotic cancer cells. To confirm this pharmacodynamic effect, CDK2 but not CDK9 siRNA-mediated knockdown augmented cancer cells with chromosome ring or multipolarity formation. Notably, engineered gain of CDK2, but not CDK9 expression, reversed emergence of cancer cells with chromosome rings or multipolarity, despite CYC065-treatment. In marked contrast, CDK2 inhibition of primary human alveolar epithelial cells did not confer statistically significant increases of cells with ring-like chromosomes or multipolarity. Hence, CDK2 antagonism caused differential effects in malignant versus normal alveolar epithelial cells. Translational relevance was confirmed by CYC065-treatment of syngeneic lung cancers in mice. Mitotic figures in tumors exhibited chromosome rings or multipolarity. Thus, CDK2 inhibition preferentially disorders centrosome stoichiometry in cancer cells. Engaging this disruption is a strategy to explore against aneuploid cancers in future clinical trials.

A novel retinoic acid receptor-γ agonist antagonizes immune checkpoint resistance in lung cancers by altering the tumor immune microenvironment.

All-trans-retinoic acid (ATRA), the retinoic acid receptors (RARs) agonist, regulates cell growth, differentiation, immunity, and survival. We report that ATRA-treatment repressed cancer growth in syngeneic immunocompetent, but not immunodeficient mice. The tumor microenvironment was implicated: CD8+ T cell depletion antagonized ATRA's anti-tumorigenic effects in syngeneic mice. ATRA-treatment with checkpoint blockade did not cooperatively inhibit murine lung cancer growth. To augment ATRA's anti-tumorigenicity without promoting its pro-tumorigenic potential, an RARγ agonist (IRX4647) was used since it regulates T cell biology. Treating with IRX4647 in combination with an immune checkpoint (anti-PD-L1) inhibitor resulted in a statistically significant suppression of syngeneic 344SQ lung cancers in mice-a model known for its resistance to checkpoints and characterized by low basal T cell and PD-L1 expression. This combined treatment notably elevated CD4+ T-cell presence within the tumor microenvironment and increased IL-5 and IL-13 tumor levels, while simultaneously decreasing CD38 in the tumor stroma. IL-5 and/or IL-13 treatments increased CD4+ more than CD8+ T-cells in mice. IRX4647-treatment did not appreciably affect in vitro lung cancer growth, despite RARγ expression. Pharmacokinetic analysis found IRX4647 plasma half-life was 6 h in mice. Yet, RARα antagonist (IRX6696)-treatment with anti-PD-L1 did not repress syngeneic lung cancer growth. Together, these findings provide a rationale for a clinical trial investigating an RARγ agonist to augment check point blockade response in cancers.

Optimization of Site Selection for Emergency Medical Facilities considering the SEIR Model.

Since the outbreak of COVID-19, the rapid construction and operation of Wuhan Vulcan Mountain Hospital and Raytheon Hospital have attracted positive responses from local and international observers. At the same time, it has also highlighted the urgency for the construction of emergency medical facilities for public health emergencies. Before construction, the practical location of medical facilities is the basis for improving the city's emergency management ability. Based on the classic susceptible, exposed, infected, and recovered (SEIR) epidemic model and epidemic data in Guangzhou, we established a multi-stage time-delay SEIR epidemic model that is suitable for epidemic research in Guangzhou. According to the results of the model, the five areas with the highest number of infected patients were identified, which included Baiyun District, Panyu District, Haizhu District, Tianhe District, and Zengcheng District. We then centralized infected individuals at five demand points. Based on the distribution of these points and by combining the characteristics of the emergency medical facilities, we built and solved the set covering location decision model, and considered the economy, society, and environment as the starting points to optimize the site location. Finally, based on simulations, we concluded that appropriate site selection can increase the time required to reach the maximum number of patients and reduce the proportion of infected and exposed people by 11.3% and 1.11%, respectively. This is indicative of the effectiveness of the site selection model and the rational selection of facility points in this study. It solves the optimization problem of the location decision of emergency medical facilities for public health emergencies in China, and also provides some valuable references for site selection decisions of emergency medical facilities in other areas.

Interpreting Neural Networks for Biological Sequences by Learning Stochastic Masks.

Sequence-based neural networks can learn to make accurate predictions from large biological datasets, but model interpretation remains challenging. Many existing feature attribution methods are optimized for continuous rather than discrete input patterns and assess individual feature importance in isolation, making them ill-suited for interpreting non-linear interactions in molecular sequences. Building on work in computer vision and natural language processing, we developed an approach based on deep learning - Scrambler networks - wherein the most salient sequence positions are identified with learned input masks. Scramblers learn to predict Position-Specific Scoring Matrices (PSSMs) where unimportant nucleotides or residues are scrambled by raising their entropy. We apply Scramblers to interpret the effects of genetic variants, uncover non-linear interactions between cis-regulatory elements, explain binding specificity for protein-protein interactions, and identify structural determinants of de novo designed proteins. We show that Scramblers enable efficient attribution across large datasets and result in high-quality explanations, often outperforming state-of-the-art methods.