Structural basis for the regulation of plant transcription factor WRKY33 by the VQ protein SIB1.

The WRKY transcription factors play essential roles in a variety of plant signaling pathways associated with biotic and abiotic stress response. The transcriptional activity of many WRKY members are regulated by a class of intrinsically disordered VQ proteins. While it is known that VQ proteins interact with the WRKY DNA-binding domains (DBDs), also termed as the WRKY domains, structural information regarding VQ-WRKY interaction is lacking and the regulation mechanism remains unknown. Herein we report a solution NMR study of the interaction between Arabidopsis WRKY33 and its regulatory VQ protein partner SIB1. We uncover a SIB1 minimal sequence neccessary for forming a stable complex with WRKY33 DBD, which comprises not only the consensus "FxxhVQxhTG" VQ motif but also its preceding region. We demonstrate that the ßN-strand and the extended ßN-ß1 loop of WRKY33 DBD form the SIB1 docking site, and build a structural model of the complex based on the NMR paramagnetic relaxation enhancement and mutagenesis data. Based on this model, we further identify a cluster of positively-charged residues in the N-terminal region of SIB1 to be essential for the formation of a SIB1-WRKY33-DNA ternary complex. These results provide a framework for the mechanism of SIB1-enhanced WRKY33 transcriptional activity.

Interior-Confined Vacancy in Potassium Manganese Hexacyanoferrate for Ultra-Stable Potassium-Ion Batteries.

Metal hexacyanoferrates (HCFs) are viewed as promising cathode materials for potassium-ion batteries (PIBs) because of their high theoretical capacities and redox potentials. However, the development of an HCF cathode with high cycling stability and voltage retention is still impeded by the unavoidable Fe(CN)6 vacancies (VFeCN) and H2O in the materials. Here, a repair method is proposed that significantly reduces the VFeCN content in potassium manganese hexacyanoferrate (KMHCF) enabled by the reducibility of sodium citrate and removal of ligand H2O at high temperature (KMHCF-H). The KMHCF-H obtained at 90 °C contains only 2% VFeCN, and the VFeCN is concentrated in the lattice interior. Such an integrated Fe-CN-Mn surface structure of the KMHCF-H cathode with repaired surface VFeCN allows preferential decomposition of potassium bis(fluorosulfonyl)imide (KFSI) in the electrolyte, which constitutes a dense anion-dominated cathode electrolyte interphase (CEI) , inhibiting effectively Mn dissolution into the electrolyte. Consequently, the KMHCF-H cathode exhibits excellent cycling performance for both half-cell (95.2 % at 0.2 Ag-1 after 2000 cycles) and full-cell (99.4 % at 0.1 Ag-1 after 200 cycles). This thermal repair method enables scalable preparation of KMHCF with a low content of vacancies, holding substantial promise for practical applications of PIBs.

Distinct activation mechanisms of ß-arrestin-1 revealed by 19F NMR spectroscopy.

ß-Arrestins (ßarrs) are functionally versatile proteins that play critical roles in the G-protein-coupled receptor (GPCR) signaling pathways. While it is well established that the phosphorylated receptor tail plays a central role in ßarr activation, emerging evidence highlights the contribution from membrane lipids. However, detailed molecular mechanisms of ßarr activation by different binding partners remain elusive. In this work, we present a comprehensive study of the structural changes in critical regions of ßarr1 during activation using 19F NMR spectroscopy. We show that phosphopeptides derived from different classes of GPCRs display different ßarr1 activation abilities, whereas binding of the membrane phosphoinositide PIP2 stabilizes a distinct partially activated conformational state. Our results further unveil a sparsely-populated activation intermediate as well as complex cross-talks between different binding partners, implying a highly multifaceted conformational energy landscape of ßarr1 that can be intricately modulated during signaling.

The substrate selectivity of papain-like proteases from human-infecting coronaviruses correlates with innate immune suppression.

Coronaviruses that can infect humans can cause either common colds (HCoV-NL63, HCoV-229E, HCoV-HKU1, and HCoV-OC43) or severe respiratory symptoms (SARS-CoV-2, SARS-CoV, and MERS-CoV). The papain-like proteases (PLPs) of SARS-CoV, SARS-CoV-2, MERS-CoV, and HCoV-NL63 function in viral innate immune evasion and have deubiquitinating (DUB) and deISGylating activities. We identified the PLPs of HCoV-229E, HCoV-HKU1, and HCoV-OC43 and found that their enzymatic properties correlated with their ability to suppress innate immune responses. A conserved noncatalytic aspartic acid residue was critical for both DUB and deISGylating activities, but the PLPs had differing ubiquitin (Ub) chain cleavage selectivities and binding affinities for Ub, K48-linked diUb, and interferon-stimulated gene 15 (ISG15) substrates. The crystal structure of HKU1-PLP2 in complex with Ub revealed binding interfaces that accounted for the unusually high binding affinity between this PLP and Ub. In cellular assays, the PLPs from the severe disease-causing coronaviruses strongly suppressed innate immune IFN-I and NF-κB signaling and stimulated autophagy, whereas the PLPs from the mild disease-causing coronaviruses generally showed weaker effects on immune suppression and autophagy induction. In addition, a PLP from a SARS-CoV-2 variant of concern showed increased suppression of innate immune signaling pathways. Overall, these results demonstrated that the DUB and deISGylating activities and substrate selectivities of these PLPs differentially contribute to viral innate immune evasion and may affect viral pathogenicity.

Function and dynamics of the intrinsically disordered carboxyl terminus of ß2 adrenergic receptor.

Advances in structural biology have provided important mechanistic insights into signaling by the transmembrane core of G-protein coupled receptors (GPCRs); however, much less is known about intrinsically disordered regions such as the carboxyl terminus (CT), which is highly flexible and not visible in GPCR structures. The ß2 adrenergic receptor's (ß2AR) 71 amino acid CT is a substrate for GPCR kinases and binds ß-arrestins to regulate signaling. Here we show that the ß2AR CT directly inhibits basal and agonist-stimulated signaling in cell lines lacking ß-arrestins. Combining single-molecule fluorescence resonance energy transfer (FRET), NMR spectroscopy, and molecular dynamics simulations, we reveal that the negatively charged ß2AR-CT serves as an autoinhibitory factor via interacting with the positively charged cytoplasmic surface of the receptor to limit access to G-proteins. The stability of this interaction is influenced by agonists and allosteric modulators, emphasizing that the CT plays important role in allosterically regulating GPCR activation.

Structural and dynamic insights into supra-physiological activation and allosteric modulation of a muscarinic acetylcholine receptor.

The M2 muscarinic receptor (M2R) is a prototypical G-protein-coupled receptor (GPCR) that serves as a model system for understanding GPCR regulation by both orthosteric and allosteric ligands. Here, we investigate the mechanisms governing M2R signaling versatility using cryo-electron microscopy (cryo-EM) and NMR spectroscopy, focusing on the physiological agonist acetylcholine and a supra-physiological agonist iperoxo, as well as a positive allosteric modulator LY2119620. These studies reveal that acetylcholine stabilizes a more heterogeneous M2R-G-protein complex than iperoxo, where two conformers with distinctive G-protein orientations were determined. We find that LY2119620 increases the affinity for both agonists, but differentially modulates agonists efficacy in G-protein and ß-arrestin pathways. Structural and spectroscopic analysis suggest that LY211620 stabilizes distinct intracellular conformational ensembles from agonist-bound M2R, which may enhance ß-arrestin recruitment while impairing G-protein activation. These results highlight the role of conformational dynamics in the complex signaling behavior of GPCRs, and could facilitate design of better drugs.

Highly Active and Stable Li2 S-Cu Nanocomposite Cathodes Enabled by Kinetically Favored Displacement Interconversion between Cu2 S and Li2 S.

The high activation barrier, inferior rate performance, and short cycling life severely constrain the practical applications of the high-capacity Li2 S cathode. Herein, we fabricate a Li2 S-Cu nanocomposite with a drastically reduced activation potential, fast rate capability, and extraordinary cycling stability even under a practically relevant areal capacity of 2.96 mAh cm-2 . Detailed experimental investigations aided by theoretical calculations indicate that instead of converting to S8 via troublesome soluble lithium polysulfides, Li2 S is thermodynamically and kinetically more favorable to react with Cu by the displacement reaction, which alters the redox couple from Li2 S/S to Cu/Cu2 S, leading to the excellent electrochemical performance. Moreover, the stability of the composite is demonstrated in the full-cell configuration consisting of commercial graphite anodes. This work provides an innovative and effective approach to realize highly activated and stable Li2 S cathode materials.

Discovery and Characterization of Rubrinodin Provide Clues into the Evolution of Lasso Peptides.

Lasso peptides are unique natural products that comprise a class of ribosomally synthesized and post-translationally modified peptides. Their defining three-dimensional structure is a lariat knot, in which the C-terminal tail is threaded through a macrolactam ring formed between the N-terminal amino group and an Asp or Glu side chain (i.e., an isopeptide bond). Recent genome mining strategies have revealed various types of lasso peptide biosynthetic gene clusters and have thus redefined the known chemical space of lasso peptides. To date, over 20 different types of these gene clusters have been discovered, including several different clades from Proteobacteria. Despite the diverse architectures of these gene clusters, which may or may not encode various tailoring enzymes, most currently known lasso peptides are synthesized by two discrete clades defined by the presence of an ATP-binding cassette transporter or its absence and (sometimes) concurrent appearance of an isopeptidase, raising questions about their evolutionary history. Herein, we discovered and characterized the lasso peptide rubrinodin, which is assembled by a gene cluster encoding both an ATP-binding cassette transporter and an isopeptidase. Our bioinformatics analyses of this and other representative cluster types provided new clues into the evolutionary history of lasso peptides. Furthermore, our structural and biochemical investigations of rubrinodin permitted the conversion of this thermolabile lasso peptide into a more thermostable scaffold.

Identification of Small Molecule Inhibitors of RNase L by Fragment-Based Drug Discovery.

The pseudokinase-endoribonuclease RNase L plays important roles in antiviral innate immunity and is also implicated in many other cellular activities. The inhibition of RNase L showed therapeutic potential for Aicardi-Goutières syndrome (AGS). Thus, RNase L is a promising drug target. In this study, using an enzyme assay and NMR screening, we discovered 13 inhibitory fragments against RNase L. Cocrystal structures of RNase L separately complexed with two different fragments were determined in which both fragments bound to the ATP-binding pocket of the pseudokinase domain. Myricetin, vitexin, and hyperoside, three natural products sharing similar scaffolds with the fragment AC40357, demonstrated a potent inhibitory activity in vitro. In addition, myricetin has a promising cellular inhibitory activity. A cocrystal structure of RNase L with myricetin provided a structural basis for inhibitor design by allosterically modulating the ribonuclease activity. Our findings demonstrate that fragment screening can lead to the discovery of natural product inhibitors of RNase L.

Sulfurized Polyacrylonitrile as a High-Performance and Low-Volume Change Anode for Robust Potassium Storage.

Potassium-ion batteries (KIBs) are considered as low-cost electrochemical energy storage technologies because of the abundant potassium resources. However, the practical applications of KIBs are mainly hampered by the unsatisfactory electrochemical performance of anode materials which often undergo large volume variations during potassiation-depotassiation, limiting their cycling life. Here, low-cost sulfurized polyacrylonitrile (S-PAN) is reported as an attractive anode candidate for KIBs. It provides a high potassium storage capacity of 569 mAh g(S-PAN)-1 with decent rate capability and cycling stability (no capacity loss after 1500 cycles, running time ∼188 days). Detailed ex situ spectroscopic and in situ microscopic characterizations reveal that the distinguished electrochemical performance of S-PAN is attributed to the high reversibility of its covalent C-S and S-S bonds which undergo repeated cleavage-redimerization during potassiation-depotassiation concomitant with relatively small volume variation (less than 24.2%). Subsequently, a full-cell constructed by pairing high-voltage K2MnFe(CN)6 cathode with high-capacity S-PAN anode demonstrates an attractive energy density (290.9 Wh kg-1) and long-term cycling stability (1200 cycles with 95.4% capacity retention). Given the high performance and low cost of both anode and cathode materials, it is believed that the present full-cell promises it as a competitive energy storage system for the cost-sensitive grid-scale applications.

A Polymorphic FeS2 Cathode Enabled by Copper Current Collector Induced Displacement Redox Mechanism.

In this contribution, we fabricated a composite consisting of two polymorphs of FeS2, pyrite (P-FeS2) and marcasite (M-FeS2), for high-performance Li-FeS2 battery. A series of electrochemical, microscopic, and spectroscopic characterizations indicate that the introduction of metastable M-FeS2 into P-FeS2 enables the four-electron reduction between FeS2 and lithium to generate Fe and Li2S, providing a high specific capacity of 894 mAh/g with specific energy over 1300 Wh/kg. Moreover, it is verified that the electrochemical irreversibility of this composite toward lithium storage is mainly rooted in the shuttle effect, caused by the elemental sulfur which is inevitably produced during the oxidation process of Li2S and Fe. To tackle this issue, copper (Cu) current collector is adopted to chemically immobilize the soluble lithium polysulfides and fundamentally alter the reaction pathway. It is shown that compared with Fe, Li2S prefers to react with Cu current collector to generate Cu2S through the thermodynamically facile displacement reaction mechanism benefiting from the similar lattice framework between Cu2S and Li2S. Such displacement reaction without lattice reconstruction renders the composite superior rate capability (∼730 mAh/g@2 A/g) and long lifespan (89.7% capacity retention after 3200 cycles). Present work allows for the fabrication of high-performance electrodes based on metal chalcogenides.

Structural studies of phosphorylation-dependent interactions between the V2R receptor and arrestin-2.

Arrestins recognize different receptor phosphorylation patterns and convert this information to selective arrestin functions to expand the functional diversity of the G protein-coupled receptor (GPCR) superfamilies. However, the principles governing arrestin-phospho-receptor interactions, as well as the contribution of each single phospho-interaction to selective arrestin structural and functional states, are undefined. Here, we determined the crystal structures of arrestin2 in complex with four different phosphopeptides derived from the vasopressin receptor-2 (V2R) C-tail. A comparison of these four crystal structures with previously solved Arrestin2 structures demonstrated that a single phospho-interaction change results in measurable conformational changes at remote sites in the complex. This conformational bias introduced by specific phosphorylation patterns was further inspected by FRET and 1H NMR spectrum analysis facilitated via genetic code expansion. Moreover, an interdependent phospho-binding mechanism of phospho-receptor-arrestin interactions between different phospho-interaction sites was unexpectedly revealed. Taken together, our results provide evidence showing that phospho-interaction changes at different arrestin sites can elicit changes in affinity and structural states at remote sites, which correlate with selective arrestin functions.

Defect-free potassium manganese hexacyanoferrate cathode material for high-performance potassium-ion batteries.

Potassium-ion batteries (KIBs) are promising electrochemical energy storage systems because of their low cost and high energy density. However, practical exploitation of KIBs is hampered by the lack of high-performance cathode materials. Here we report a potassium manganese hexacyanoferrate (K2Mn[Fe(CN)6]) material, with a negligible content of defects and water, for efficient high-voltage K-ion storage. When tested in combination with a K metal anode, the K2Mn[Fe(CN)6]-based electrode enables a cell specific energy of 609.7 Wh kg-1 and 80% capacity retention after 7800 cycles. Moreover, a K-ion full-cell consisting of graphite and K2Mn[Fe(CN)6] as anode and cathode active materials, respectively, demonstrates a specific energy of 331.5 Wh kg-1, remarkable rate capability, and negligible capacity decay for 300 cycles. The remarkable electrochemical energy storage performances of the K2Mn[Fe(CN)6] material are attributed to its stable frameworks that benefit from the defect-free structure.

The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery.

SARS-CoV-2 is the pathogen responsible for the COVID-19 pandemic. The SARS-CoV-2 papain-like cysteine protease (PLpro) has been implicated in playing important roles in virus maturation, dysregulation of host inflammation, and antiviral immune responses. The multiple functions of PLpro render it a promising drug target. Therefore, we screened a library of approved drugs and also examined available inhibitors against PLpro. Inhibitor GRL0617 showed a promising in vitro IC50 of 2.1 µM and an effective antiviral inhibition in cell-based assays. The co-crystal structure of SARS-CoV-2 PLproC111S in complex with GRL0617 indicates that GRL0617 is a non-covalent inhibitor and it resides in the ubiquitin-specific proteases (USP) domain of PLpro. NMR data indicate that GRL0617 blocks the binding of ISG15 C-terminus to PLpro. Using truncated ISG15 mutants, we show that the C-terminus of ISG15 plays a dominant role in binding PLpro. Structural analysis reveals that the ISG15 C-terminus binding pocket in PLpro contributes a disproportionately large portion of binding energy, thus this pocket is a hot spot for antiviral drug discovery targeting PLpro.

DeSiphering receptor core-induced and ligand-dependent conformational changes in arrestin via genetic encoded trimethylsilyl 1H-NMR probe.

Characterization of the dynamic conformational changes in membrane protein signaling complexes by nuclear magnetic resonance (NMR) spectroscopy remains challenging. Here we report the site-specific incorporation of 4-trimethylsilyl phenylalanine (TMSiPhe) into proteins, through genetic code expansion. Crystallographic analysis revealed structural changes that reshaped the TMSiPhe-specific amino-acyl tRNA synthetase active site to selectively accommodate the trimethylsilyl (TMSi) group. The unique up-field 1H-NMR chemical shift and the highly efficient incorporation of TMSiPhe enabled the characterization of multiple conformational states of a phospho-ß2 adrenergic receptor/ß-arrestin-1(ß-arr1) membrane protein signaling complex, using only 5 µM protein and 20 min of spectrum accumulation time. We further showed that extracellular ligands induced conformational changes located in the polar core or ERK interaction site of ß-arr1 via direct receptor transmembrane core interactions. These observations provided direct delineation and key mechanism insights that multiple receptor ligands were able to induce distinct functionally relevant conformational changes of arrestin.

Analysis of ß2AR-Gs and ß2AR-Gi complex formation by NMR spectroscopy.

The ß2-adrenergic receptor (ß2AR) is a prototypical G protein-coupled receptor (GPCR) that preferentially couples to the stimulatory G protein Gs and stimulates cAMP formation. Functional studies have shown that the ß2AR also couples to inhibitory G protein Gi, activation of which inhibits cAMP formation [R. P. Xiao, Sci. STKE 2001, re15 (2001)]. A crystal structure of the ß2AR-Gs complex revealed the interaction interface of ß2AR-Gs and structural changes upon complex formation [S. G. Rasmussen et al., Nature 477, 549-555 (2011)], yet, the dynamic process of the ß2AR signaling through Gs and its preferential coupling to Gs over Gi is still not fully understood. Here, we utilize solution nuclear magnetic resonance (NMR) spectroscopy and supporting molecular dynamics (MD) simulations to monitor the conformational changes in the G protein coupling interface of the ß2AR in response to the full agonist BI-167107 and Gs and Gi1 These results show that BI-167107 stabilizes conformational changes in four transmembrane segments (TM4, TM5, TM6, and TM7) prior to coupling to a G protein, and that the agonist-bound receptor conformation is different from the G protein coupled state. While most of the conformational changes observed in the ß2AR are qualitatively the same for Gs and Gi1, we detected distinct differences between the ß2AR-Gs and the ß2AR-Gi1 complex in intracellular loop 2 (ICL2). Interactions with ICL2 are essential for activation of Gs These differences between the ß2AR-Gs and ß2AR-Gi1 complexes in ICL2 may be key determinants for G protein coupling selectivity.

Conformational Dynamics of the Periplasmic Chaperone SurA.

The periplasmic protein SurA is the primary chaperone involved in the biogenesis of bacterial outer membrane proteins and is a potential antibacterial drug target. The three-dimensional structure of SurA can be divided into three parts, a core module formed by the N- and C-terminal regions and two peptidyl-prolyl isomerase (PPIase) domains, P1 and P2. Despite the determination of the structures of several SurA-peptide complexes, the functional mechanism of this chaperone remains elusive and the roles of the two PPIase domains are yet unclear. Herein, we characterize the conformational dynamics of SurA by using solution nuclear magnetic resonance and single-molecule fluorescence resonance energy transfer methods. We demonstrate a "closed-to-open" structural transition of the P1 domain that is correlated with both chaperone activity and peptide binding and show that the flexible P2 domain can also occupy conformations that closely contact the NC core module. Our results offer a structural basis for the counteracting roles of the two PPIase domains in regulating the SurA chaperone activity.

Backbone 1H, 13C and 15N resonance assignments of the proteasome lid subunit Rpn12 from Saccharomyces cerevisiae.

The 26S proteasome degrades selected polyubiquitinated proteins in the ubiquitin-proteasome system, which is the major pathway for programmed protein degradation in eukaryotic cells. The Saccharomyces cerevisiae Rpn12 locates in the lid of the 19S regulatory particle within the 26S proteasome and plays a role in recruiting the extrinsic ubiquitin receptor Rpn10. Rpn12 contains a N-terminal TPR (tetratrico peptide repeat)-like domain and a C-terminal WH (winged helix) domain. Interaction of Rpn12 with several subunits of 19S has been observed and it may play an important role in the 19S regulatory particle rearrangement after ubiquitylated substrate binding to the proteasome. Herein, we report the resonance assignments of backbone 1H, 13C and 15N atoms of the Saccharomyces cerevisiae Rpn12, which provide valuable information for further studies of the dynamics and interactions of the Rpn12 subunit using NMR techniques.

K0.83V2O5: A New Layered Compound as a Stable Cathode Material for Potassium-Ion Batteries.

Recently, potassium-ion batteries (PIBs) are being actively investigated. The development of PIBs calls for cathode materials with a rigid framework, reversible electrochemical reactivity, and a high amount of extractable K ions, which is extremely challenging due to the large size of potassium. Herein, a new layered compound K0.83V2O5 is reported as a potential cathode material for PIBs. It delivers an initial depotassiation capacity of 86 mAh g-1 and exhibits a reversible capacity of 90 mAh g-1 with a high redox potential of 3.5 V (vs K+/K) and a capacity retention of more than 80% after 200 cycles. Experimental investigations combined with theoretical calculation indicate that depotassiation-potassiation is accommodated by contraction-expansion of the interlayer spacing along with unpuckering-puckering of the layers. Additionally, the calculated electronic structure suggests the (semi)metallic feature of KxV2O5 (0 < x ≤ 0.875) and K-ion transport in the material is predicted to be one-dimensional with the experimentally estimated chemical diffusion coefficient in the order of 10-15-10-12 cm2 s-1. Finally, a K-ion full cell consisting of the K0.83V2O5 cathode and a graphite anode is demonstrated to deliver an energy density of 136 Wh kg-1. This study will provide insights for further designing novel layered cathodes with high K-ion content for PIBs.

Computational strategy for intrinsically disordered protein ligand design leads to the discovery of p53 transactivation domain I binding compounds that activate the p53 pathway.

Intrinsically disordered proteins or intrinsically disordered regions (IDPs) have gained much attention in recent years due to their vital roles in biology and prevalence in various human diseases. Although IDPs are perceived as attractive therapeutic targets, rational drug design targeting IDPs remains challenging because of their conformational heterogeneity. Here, we propose a hierarchical computational strategy for IDP drug virtual screening (IDPDVS) and applied it in the discovery of p53 transactivation domain I (TAD1) binding compounds. IDPDVS starts from conformation sampling of the IDP target, then it combines stepwise conformational clustering with druggability evaluation to identify potential ligand binding pockets, followed by multiple docking screening runs and selection of compounds that can bind multi-conformations. p53 is an important tumor suppressor and restoration of its function provides an opportunity to inhibit cancer cell growth. TAD1 locates at the N-terminus of p53 and plays key roles in regulating p53 function. No compounds that directly bind to TAD1 have been reported due to its highly disordered structure. We successfully used IDPDVS to identify two compounds that bind p53 TAD1 and restore wild-type p53 function in cancer cells. Our study demonstrates that IDPDVS is an efficient strategy for IDP drug discovery and p53 TAD1 can be directly targeted by small molecules.