Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation.

Post-translational modifications (PTMs) play key roles in regulating cell signaling and physiology in both normal and cancer cells. Advances in mass spectrometry enable high-throughput, accurate, and sensitive measurement of PTM levels to better understand their role, prevalence, and crosstalk. Here, we analyze the largest collection of proteogenomics data from 1,110 patients with PTM profiles across 11 cancer types (10 from the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium [CPTAC]). Our study reveals pan-cancer patterns of changes in protein acetylation and phosphorylation involved in hallmark cancer processes. These patterns revealed subsets of tumors, from different cancer types, including those with dysregulated DNA repair driven by phosphorylation, altered metabolic regulation associated with immune response driven by acetylation, affected kinase specificity by crosstalk between acetylation and phosphorylation, and modified histone regulation. Overall, this resource highlights the rich biology governed by PTMs and exposes potential new therapeutic avenues.

The intrinsic substrate specificity of the human tyrosine kinome.

Phosphorylation of proteins on tyrosine (Tyr) residues evolved in metazoan organisms as a mechanism of coordinating tissue growth1. Multicellular eukaryotes typically have more than 50 distinct protein Tyr kinases that catalyse the phosphorylation of thousands of Tyr residues throughout the proteome1-3. How a given Tyr kinase can phosphorylate a specific subset of proteins at unique Tyr sites is only partially understood4-7. Here we used combinatorial peptide arrays to profile the substrate sequence specificity of all human Tyr kinases. Globally, the Tyr kinases demonstrate considerable diversity in optimal patterns of residues surrounding the site of phosphorylation, revealing the functional organization of the human Tyr kinome by substrate motif preference. Using this information, Tyr kinases that are most compatible with phosphorylating any Tyr site can be identified. Analysis of mass spectrometry phosphoproteomic datasets using this compendium of kinase specificities accurately identifies specific Tyr kinases that are dysregulated in cells after stimulation with growth factors, treatment with anti-cancer drugs or expression of oncogenic variants. Furthermore, the topology of known Tyr signalling networks naturally emerged from a comparison of the sequence specificities of the Tyr kinases and the SH2 phosphotyrosine (pTyr)-binding domains. Finally we show that the intrinsic substrate specificity of Tyr kinases has remained fundamentally unchanged from worms to humans, suggesting that the fidelity between Tyr kinases and their protein substrate sequences has been maintained across hundreds of millions of years of evolution.

An atlas of substrate specificities for the human serine/threonine kinome.

Protein phosphorylation is one of the most widespread post-translational modifications in biology1,2. With advances in mass-spectrometry-based phosphoproteomics, 90,000 sites of serine and threonine phosphorylation have so far been identified, and several thousand have been associated with human diseases and biological processes3,4. For the vast majority of phosphorylation events, it is not yet known which of the more than 300 protein serine/threonine (Ser/Thr) kinases encoded in the human genome are responsible3. Here we used synthetic peptide libraries to profile the substrate sequence specificity of 303 Ser/Thr kinases, comprising more than 84% of those predicted to be active in humans. Viewed in its entirety, the substrate specificity of the kinome was substantially more diverse than expected and was driven extensively by negative selectivity. We used our kinome-wide dataset to computationally annotate and identify the kinases capable of phosphorylating every reported phosphorylation site in the human Ser/Thr phosphoproteome. For the small minority of phosphosites for which the putative protein kinases involved have been previously reported, our predictions were in excellent agreement. When this approach was applied to examine the signalling response of tissues and cell lines to hormones, growth factors, targeted inhibitors and environmental or genetic perturbations, it revealed unexpected insights into pathway complexity and compensation. Overall, these studies reveal the intrinsic substrate specificity of the human Ser/Thr kinome, illuminate cellular signalling responses and provide a resource to link phosphorylation events to biological pathways.

Maximized electron interactions at the magic angle in twisted bilayer graphene.

The electronic properties of heterostructures of atomically thin van der Waals crystals can be modified substantially by moiré superlattice potentials from an interlayer twist between crystals1,2. Moiré tuning of the band structure has led to the recent discovery of superconductivity3,4 and correlated insulating phases5 in twisted bilayer graphene (TBG) near the 'magic angle' of twist of about 1.1 degrees, with a phase diagram reminiscent of high-transition-temperature superconductors. Here we directly map the atomic-scale structural and electronic properties of TBG near the magic angle using scanning tunnelling microscopy and spectroscopy. We observe two distinct van Hove singularities (VHSs) in the local density of states around the magic angle, with an energy separation of 57 millielectronvolts that drops to 40 millielectronvolts with high electron/hole doping. Unexpectedly, the VHS energy separation continues to decrease with decreasing twist angle, with a lowest value of 7 to 13 millielectronvolts at a magic angle of 0.79 degrees. More crucial to the correlated behaviour of this material, we find that at the magic angle, the ratio of the Coulomb interaction to the bandwidth of each individual VHS (U/t) is maximized, which is optimal for electronic Cooper pairing mechanisms. When doped near the half-moiré-band filling, a correlation-induced gap splits the conduction VHS with a maximum size of 6.5 millielectronvolts at 1.15 degrees, dropping to 4 millielectronvolts at 0.79 degrees. We capture the doping-dependent and angle-dependent spectroscopy results using a Hartree-Fock model, which allows us to extract the on-site and nearest-neighbour Coulomb interactions. This analysis yields a U/t of order unity indicating that magic-angle TBG is moderately correlated. In addition, scanning tunnelling spectroscopy maps reveal an energy- and doping-dependent three-fold rotational-symmetry breaking of the local density of states in TBG, with the strongest symmetry breaking near the Fermi level and further enhanced when doped to the correlated gap regime. This indicates the presence of a strong electronic nematic susceptibility or even nematic order in TBG in regions of the phase diagram where superconductivity is observed.

Moiréless correlations in ABCA graphene.

Atomically thin van der Waals materials stacked with an interlayer twist have proven to be an excellent platform toward achieving gate-tunable correlated phenomena linked to the formation of flat electronic bands. In this work we demonstrate the formation of emergent correlated phases in multilayer rhombohedral graphene--a simple material that also exhibits a flat electronic band edge but without the need of having a moiré superlattice induced by twisted van der Waals layers. We show that two layers of bilayer graphene that are twisted by an arbitrary tiny angle host large (micrometer-scale) regions of uniform rhombohedral four-layer (ABCA) graphene that can be independently studied. Scanning tunneling spectroscopy reveals that ABCA graphene hosts an unprecedentedly sharp van Hove singularity of 3-5-meV half-width. We demonstrate that when this van Hove singularity straddles the Fermi level, a correlated many-body gap emerges with peak-to-peak value of 9.5 meV at charge neutrality. Mean-field theoretical calculations for model with short-ranged interactions indicate that two primary candidates for the appearance of this broken symmetry state are a charge-transfer excitonic insulator and a ferrimagnet. Finally, we show that ABCA graphene hosts surface topological helical edge states at natural interfaces with ABAB graphene which can be turned on and off with gate voltage, implying that small-angle twisted double-bilayer graphene is an ideal programmable topological quantum material.

Approaching the Intrinsic Limit in Transition Metal Diselenides via Point Defect Control.

Two dimensional (2D) transition-metal dichalcogenide (TMD) based semiconductors have generated intense recent interest due to their novel optical and electronic properties and potential for applications. In this work, we characterize the atomic and electronic nature of intrinsic point defects found in single crystals of these materials synthesized by two different methods, chemical vapor transport and self-flux growth. Using a combination of scanning tunneling microscopy (STM) and scanning transmission electron microscopy (STEM), we show that the two major intrinsic defects in these materials are metal vacancies and chalcogen antisites. We show that by control of the synthetic conditions, we can reduce the defect concentration from above 1013/cm2 to below 1011/cm2. Because these point defects act as centers for nonradiative recombination of excitons, this improvement in material quality leads to a hundred-fold increase in the radiative recombination efficiency.

Absence of a Band Gap at the Interface of a Metal and Highly Doped Monolayer MoS2.

High quality electrical contact to semiconducting transition metal dichalcogenides (TMDCs) such as MoS2 is key to unlocking their unique electronic and optoelectronic properties for fundamental research and device applications. Despite extensive experimental and theoretical efforts reliable ohmic contact to doped TMDCs remains elusive and would benefit from a better understanding of the underlying physics of the metal-TMDC interface. Here we present measurements of the atomic-scale energy band diagram of junctions between various metals and heavily doped monolayer MoS2 using ultrahigh vacuum scanning tunneling microscopy (UHV-STM). Our measurements reveal that the electronic properties of these junctions are dominated by two-dimensional metal-induced gap states (MIGS). These MIGS are characterized by a spatially growing measured gap in the local density of states (L-DOS) of the MoS2 within 2 nm of the metal-semiconductor interface. Their decay lengths extend from a minimum of ∼0.55 nm near midgap to as long as 2 nm near the band edges and are nearly identical for Au, Pd, and graphite contacts, indicating that it is a universal property of the monolayer semiconductor. Our findings indicate that even in heavily doped semiconductors, the presence of MIGS sets the ultimate limit for electrical contact.

Nanofilament Formation and Regeneration During Cu/Al2O3 Resistive Memory Switching.

Conductive bridge random access memory (CBRAM) is a leading candidate to supersede flash memory, but poor understanding of its switching process impedes widespread implementation. The underlying physics and basic, unresolved issues such as the connecting filament's growth direction can be revealed with direct imaging, but the nanoscale target region is completely encased and thus difficult to access with real-time, high-resolution probes. In Pt/Al2O3/Cu CBRAM devices with a realistic topology, we find that the filament grows backward toward the source metal electrode. This observation, consistent over many cycles in different devices, corroborates the standard electrochemical metallization model of CBRAM operation. Time-resolved scanning transmission electron microscopy (STEM) reveals distinct nucleation-limited and potential-limited no-growth periods occurring before and after a connection is made, respectively. The subfemtoampere ionic currents visualized move some thousands of atoms during a switch and lag the nanoampere electronic currents.

Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication.

Multiple coronaviruses have emerged independently in the past 20 years that cause lethal human diseases. Although vaccine development targeting these viruses has been accelerated substantially, there remain patients requiring treatment who cannot be vaccinated or who experience breakthrough infections. Understanding the common host factors necessary for the life cycles of coronaviruses may reveal conserved therapeutic targets. Here, we used the known substrate specificities of mammalian protein kinases to deconvolute the sequence of phosphorylation events mediated by three host protein kinase families (SRPK, GSK-3, and CK1) that coordinately phosphorylate a cluster of serine and threonine residues in the viral N protein, which is required for viral replication. We also showed that loss or inhibition of SRPK1/2, which we propose initiates the N protein phosphorylation cascade, compromised the viral replication cycle. Because these phosphorylation sites are highly conserved across coronaviruses, inhibitors of these protein kinases not only may have therapeutic potential against COVID-19 but also may be broadly useful against coronavirus-mediated diseases.

Moiré metrology of energy landscapes in van der Waals heterostructures.

The emerging field of twistronics, which harnesses the twist angle between two-dimensional materials, represents a promising route for the design of quantum materials, as the twist-angle-induced superlattices offer means to control topology and strong correlations. At the small twist limit, and particularly under strain, as atomic relaxation prevails, the emergent moiré superlattice encodes elusive insights into the local interlayer interaction. Here we introduce moiré metrology as a combined experiment-theory framework to probe the stacking energy landscape of bilayer structures at the 0.1 meV/atom scale, outperforming the gold-standard of quantum chemistry. Through studying the shapes of moiré domains with numerous nano-imaging techniques, and correlating with multi-scale modelling, we assess and refine first-principle models for the interlayer interaction. We document the prowess of moiré metrology for three representative twisted systems: bilayer graphene, double bilayer graphene and H-stacked MoSe2/WSe2. Moiré metrology establishes sought after experimental benchmarks for interlayer interaction, thus enabling accurate modelling of twisted multilayers.

Visualization of moiré superlattices.

Moiré superlattices in van der Waals heterostructures have given rise to a number of emergent electronic phenomena due to the interplay between atomic structure and electron correlations. Indeed, electrons in these structures have been recently found to exhibit a number of emergent properties that the individual layers themselves do not exhibit. This includes superconductivity1,2, magnetism3, topological edge states4,5, exciton trapping6 and correlated insulator phases7. However, the lack of a straightforward technique to characterize the local structure of moiré superlattices has thus far impeded progress in the field. In this work we describe a simple, room-temperature, ambient method to visualize real-space moiré superlattices with sub-5-nm spatial resolution in a variety of twisted van der Waals heterostructures including, but not limited to, conducting graphene, insulating boron nitride and semiconducting transition metal dichalcogenides. Our method uses piezoresponse force microscopy, an atomic force microscope modality that locally measures electromechanical surface deformation. We find that all moiré superlattices, regardless of whether the constituent layers have inversion symmetry, exhibit a mechanical response to out-of-plane electric fields. This response is closely tied to flexoelectricity wherein electric polarization and electromechanical response is induced through strain gradients present within moiré superlattices. Therefore, moiré superlattices of two-dimensional materials manifest themselves as an interlinked network of polarized domain walls in a non-polar background matrix.

The FDA-approved drug Alectinib compromises SARS-CoV-2 nucleocapsid phosphorylation and inhibits viral infection in vitro.

While vaccines are vital for preventing COVID-19 infections, it is critical to develop new therapies to treat patients who become infected. Pharmacological targeting of a host factor required for viral replication can suppress viral spread with a low probability of viral mutation leading to resistance. In particular, host kinases are highly druggable targets and a number of conserved coronavirus proteins, notably the nucleoprotein (N), require phosphorylation for full functionality. In order to understand how targeting kinases could be used to compromise viral replication, we used a combination of phosphoproteomics and bioinformatics as well as genetic and pharmacological kinase inhibition to define the enzymes important for SARS-CoV-2 N protein phosphorylation and viral replication. From these data, we propose a model whereby SRPK1/2 initiates phosphorylation of the N protein, which primes for further phosphorylation by GSK-3a/b and CK1 to achieve extensive phosphorylation of the N protein SR-rich domain. Importantly, we were able to leverage our data to identify an FDA-approved kinase inhibitor, Alectinib, that suppresses N phosphorylation by SRPK1/2 and limits SARS-CoV-2 replication. Together, these data suggest that repurposing or developing novel host-kinase directed therapies may be an efficacious strategy to prevent or treat COVID-19 and other coronavirus-mediated diseases.

Atomic-Scale Characterization of Graphene p-n Junctions for Electron-Optical Applications.

Graphene p-n junctions offer a potentially powerful approach toward controlling electron trajectories via collimation and focusing in ballistic solid-state devices. The ability of p-n junctions to control electron trajectories depends crucially on the doping profile and roughness of the junction. Here, we use four-probe scanning tunneling microscopy and spectroscopy (STM/STS) to characterize two state-of-the-art graphene p-n junction geometries at the atomic scale, one with CMOS polySi gates and another with naturally cleaved graphite gates. Using spectroscopic imaging, we characterize the local doping profile across and along the p-n junctions. We find that realistic junctions exhibit non-ideality both in their geometry as well as in the doping profile across the junction. We show that the geometry of the junction can be improved by using the cleaved edge of van der Waals metals such as graphite to define the junction. We quantify the geometric roughness and doping profiles of junctions experimentally and use these parameters in non-equilibrium Green's function-based simulations of focusing and collimation in these realistic junctions. We find that for realizing Veselago focusing, it is crucial to minimize lateral interface roughness which only natural graphite gates achieve and to reduce junction width, in which both devices under investigation underperform. We also find that carrier collimation is currently limited by the non-linearity of the doping profile across the junction. Our work provides benchmarks of the current graphene p-n junction quality and provides guidance for future improvements.

Imaging interfacial electrical transport in graphene-MoS2 heterostructures with electron-beam-induced-currents.

Heterostructure devices with specific and extraordinary properties can be fabricated by stacking two-dimensional crystals. Cleanliness at the inter-crystal interfaces within a heterostructure is crucial for maximizing device performance. However, because these interfaces are buried, characterizing their impact on device function is challenging. Here, we show that electron-beam induced current (EBIC) mapping can be used to image interfacial contamination and to characterize the quality of buried heterostructure interfaces with nanometer-scale spatial resolution. We applied EBIC and photocurrent imaging to map photo-sensitive graphene-MoS2 heterostructures. The EBIC maps, together with concurrently acquired scanning transmission electron microscopy images, reveal how a device's photocurrent collection efficiency is adversely affected by nanoscale debris invisible to optical-resolution photocurrent mapping.