Conformational Complexity and Dynamics in a Muscarinic Receptor Revealed by NMR Spectroscopy.

The M2 muscarinic acetylcholine receptor (M2R) is a prototypical GPCR that plays important roles in regulating heart rate and CNS functions. Crystal structures provide snapshots of the M2R in inactive and active states, but the allosteric link between the ligand binding pocket and cytoplasmic surface remains poorly understood. Here we used solution NMR to examine the structure and dynamics of the M2R labeled with 13CH3-ε-methionine upon binding to various orthosteric and allosteric ligands having a range of efficacy for both G protein activation and arrestin recruitment. We observed ligand-specific changes in the NMR spectra of 13CH3-ε-methionine probes in the M2R extracellular domain, transmembrane core, and cytoplasmic surface, allowing us to correlate ligand structure with changes in receptor structure and dynamics. We show that the M2R has a complex energy landscape in which ligands with different efficacy profiles stabilize distinct receptor conformations.

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.

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.

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.

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.

The Flexibility of an Amorphous Cobalt Hydroxide Nanomaterial Promotes the Electrocatalysis of Oxygen Evolution Reaction.

Structural flexibility can be a desirable trait of an operating catalyst because it adapts itself to a given catalytic process for enhanced activity. Here, amorphous cobalt hydroxide nanocages are demonstrated to be a promising electrocatalyst with an overpotential of 0.28 V at 10 mA cm-2 , far outperforming the crystalline counterparts and being in the top rank of the catalysts of their kind, under the condition of electrocatalytic oxygen evolution reaction. From the direct experimental in situ and ex situ results, this enhanced activity is attributed to its high structural flexibility in terms of 1) facile and holistic transformation into catalytic active phase; 2) hosting oxygen vacancies; and 3) structure self-regulation in a real-time process. Significantly, based on plausible catalytic mechanism and computational simulation results, it is disclosed how this structural flexibility facilitates the kinetics of oxygen evolution reaction. This work deepens the understanding of the structure-activity relationship of the Co-based catalysts in electrochemical catalysis, and it inspires more applications that require flexible structures enabled by such amorphous nanomaterials.

Characterizations of the Interactions between Escherichia coli Periplasmic Chaperone HdeA and Its Native Substrates during Acid Stress.

The bacterial acid-resistant chaperone HdeA is a "conditionally disordered" protein that functions at low pH when it undergoes a transition from a well-folded dimer to an unfolded monomer. The dimer dissociation and unfolding processes result in exposure of hydrophobic surfaces that allows binding to a broad range of client proteins. To fully elucidate the chaperone mechanism of HdeA, it is crucial to understand how the activated HdeA interacts with its native substrates during acid stress. Herein, we present a nuclear magnetic resonance study of the pH-dependent HdeA-substrate interactions. Our results show that the activation of HdeA is not only induced by acidification but also regulated by the presence of unfolded substrates. The variable extent of unfolding of substrates differentially regulates the HdeA-substrate interaction, and the binding further affects the HdeA conformation. Finally, we show that HdeA binds its substrates heterogeneously, and the "amphiphilic" model for HdeA-substrate interaction is discussed.

Conformation switching of AIM2 PYD domain revealed by NMR relaxation and MD simulation.

Protein absent in melanoma 2 (AIM2) is a double-strand DNA (ds DNA) sensor mainly located in cytoplasm of cell. It includes one N terminal PYD domain and one C terminal HIN domain. When the ds DNA such as DNA viruses and bacteria entered cytoplasm, the HIN domain of AIM2 will recognize and bind to DNA, and the PYD domain will bind to ASC protein which will result in the formation of AIM2 inflammasome. Three AIM2 PYD domain structures have been solved, but every structure yields a unique conformation around the α3 helix region. To understand why different AIM2 PYD structures show different conformations in this region, we use NMR relaxation techniques to study the backbone dynamics of mouse AIM2 PYD domain and perform molecular dynamics (MD) simulations on both mouse and human AIM2 PYD structures. Our results indicate that this region is highly flexible in both mouse and human AIM2 PYD domains, and the PYD domain may exist as a conformation ensemble in solution. Different environment makes the population vary among pre-existing conformational substrates of the ensemble, which may be the reason why different AIM2 PYD structures were observed under different conditions. Further docking analysis reveals that the conformation switching may be important for the autoinhibition of the AIM2 protein.

Crosslinked Aspartic Acids as Helix-Nucleating Templates.

Described is a facile helix-nucleating template based on a tethered aspartic acid at the N-terminus [terminal aspartic acid (TD)]. The nucleating effect of the template is subtly influenced by the substituent at the end of the side-chain-end tether as indicated by circular dichroism, nuclear magnetic resonance, and molecular dynamics simulations. Unlike most nucleating strategies, the N-terminal amine is preserved, thus enabling further modification. Peptidomimetic estrogen receptor modulators (PERMs) constructed using this strategy show improved therapeutic properties. The current strategy can be regarded as a good complement to existing helix-stabilizing methods.

The NMR solution structure of AIM2 PYD domain from Mus musculus reveals a distinct α2-α3 helix conformation from its human homologues.

The inflammasome is a key component of the innate immune system providing the initial defense against invading organisms. Failure of inflammasome formation is the main reason for many innate and acquired immune diseases. Cytosolic protein absent in melanoma 2 (AIM2) has been reported to play an essential role in double-stranded DNA (dsDNA) sensing and inflammasome formation in response to viruses or bacteria infection. The N-terminal pyrin domain (PYD) of AIM2 interacts with the ASC PYD domain, and then recruits downstream proteins to assemble the AIM2 inflammasome. The molecular mechanisms of PYD mediated signaling remain elusive as limited structural information on PYD family. Herein, we characterized the solution structure of mouse AIM2 PYD domain by NMR spectroscopy, and compared it with the crystal structures of its two human homologues. The comparison shows mAIM2 PYD adopts a unique α2-α3 helix conformation distinct from its human homologues, but similar to the pyrin domain of human NLRP10/PYNOD, which belongs to another family. In addition, the aggregation of mAIM2 PYD domain, with the increased salt concentration, reveals that both the charge surface and hydrophobic interaction play important roles in the self-association of mAIM2 PYD.

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.

Mining the Biosynthetic Landscape of Lactic Acid Bacteria Unearths a New Family of RiPPs Assembled by a Novel Type of ThiF-like Adenylyltransferases.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are chemically diverse natural products of ribosomal origin. These peptides, which frequently act as signals or antimicrobials, are biosynthesized by conserved enzymatic machinery, making genome mining a powerful strategy for unearthing previously uncharacterized members of their class. Herein, we investigate the untapped biosynthetic potential of Lactobacillales (i.e., lactic acid bacteria), an order of Gram-positive bacteria closely associated with human life, including pathogenic species and industrially relevant fermenters of dairy products. Through genome mining methods, we systematically explored the distribution and diversity of ThiF-like adenylyltransferase-utilizing RiPP systems in lactic acid bacteria and identified a number of unprecedented biosynthetic gene clusters. In one of these clusters, we found a previously undescribed group of macrocyclic imide biosynthetic pathways containing multiple transporters that may be involved in a potential quorum sensing (QS) system. Through in vitro assays, we determined that one such adenylyltransferase specifically catalyzes the intracyclization of its precursor peptide through macrocyclic imide formation. Incubating the enzyme with various primary amines revealed that it could effectively amidate the C-terminus of the precursor peptide. This new transformation adds to the growing list of Nature's peptide macrocyclization strategies and expands the impressive catalytic repertoire of the adenylyltransferase family. The diverse RiPP systems identified herein represent a vast, unexploited landscape for the discovery of a novel class of natural products and QS systems.

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.

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.

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.

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.

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.

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.

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.