Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex

Caffeine, found in many foods, beverages, and pharmaceuticals, is the most used chemical compound for mental alertness. It is originally a natural product of plants and exists widely in environmental soil. Some bacteria, such as Pseudomonas putida CBB5, utilize caffeine as a sole carbon and nitrogen source by degrading it through sequential N-demethylation catalyzed by five enzymes (NdmA, NdmB, NdmC, NdmD, and NdmE). The environmentally friendly enzymatic reaction products, methylxanthines, are high-value biochemicals that are used in the pharmaceutical and cosmetic industries. However, the structures and biochemical properties of bacterial N-demethylases remain largely unknown. Here, we report the structures of NdmA and NdmB, the initial N₁- and N₃-specific demethylases, respectively. Reverse-oriented substrate bindings were observed in the substrate-complexed structures, offering methyl position specificity for proper N-demethylation. For efficient sequential degradation of caffeine, these enzymes form a unique heterocomplex with 3:3 stoichiometry, which was confirmed by enzymatic assays, fluorescent labeling, and small-angle x-ray scattering. The binary structure of NdmA with the ferredoxin domain of NdmD, which is the first structural information for the plant-type ferredoxin domain in a complex state, was also determined to better understand electron transport during N-demethylation. These findings broaden our understanding of the caffeine degradation mechanism by bacterial enzymes and will enable their use for industrial applications.     

Structural Insights into Functional Overlapping and Differentiation among Myosin V Motors

Myosin V (MyoV) motors have been implicated in the intracellular transport of diverse cargoes including vesicles, organelles, RNA-protein complexes, and regulatory proteins. Here, we have solved the cargo-binding domain (CBD) structures of the three human MyoV paralogs (Va, Vb, and Vc), revealing subtle structural changes that drive functional differentiation and a novel redox mechanism controlling the CBD dimerization process, which is unique for the MyoVc subclass. Moreover, the cargo- and motor-binding sites were structurally assigned, indicating the conservation of residues involved in the recognition of adaptors for peroxisome transport and providing high resolution insights into motor domain inhibition by CBD. These results contribute to understanding the structural requirements for cargo transport, autoinhibition, and regulatory mechanisms in myosin V motors.     

Structural and Mechanistic Insights into the Pseudomonas fluorescens 2-Nitrobenzoate 2-Nitroreductase NbaA

The bacterial 2-nitroreductase NbaA is the primary enzyme initiating the degradation of 2-nitrobenzoate (2-NBA), and its activity is controlled by posttranslational modifications. To date, the structure of NbaA remains to be elucidated. In this study, the crystal structure of a Cys194Ala NbaA mutant was determined to a 1.7-Å resolution. The substrate analog 2-NBA methyl ester was used to decipher the substrate binding site by inhibition of the wild-type NbaA protein. Tandem mass spectrometry showed that 2-NBA methyl ester produced a 2-NBA ester bond at the Tyr193 residue in the wild-type NbaA but not residues in the Tyr193Phe mutant. Moreover, covalent binding of the 2-NBA methyl ester to Tyr193 reduced the reactivity of the Cys194 residue on the peptide link. The Tyr193 hydroxyl group was shown to be essential for enzyme catalysis, as a Tyr193Phe mutant resulted in fast dissociation of flavin mononucleotide (FMN) from the protein with the reduced reactivity of Cys194. FMN binding to NbaA varied with solution NaCl concentration, which was related to the catalytic activity but not to cysteine reactivity. These observations suggest that the Cys194 reactivity is negatively affected by a posttranslational modification of the adjacent Tyr193 residue, which interacts with FMN and the substrate in the NbaA catalytic site.     

Structural and Mechanistic Insights into the Interaction between Pyk2 and Paxillin LD Motifs

Proline-rich tyrosine kinase 2 (Pyk2) is a member of the focal adhesion kinase (FAK) subfamily of cytoplasmic tyrosine kinases. The C-terminal Pyk2-focal adhesion targeting (FAT) domain binds to paxillin, an adhesion molecule. Paxillin has five leucine-aspartate (LD) motifs (LD1–LD5). Here, we show that the second LD motif of paxillin, LD2, interacts with Pyk2-FAT, similar to the known Pyk2-FAT/LD4 interaction. Both LD motifs can target two ligand binding sites on Pyk2-FAT. Interestingly, they also share similar binding affinity for Pyk2-FAT with preferential association to one site relative to the other. Nevertheless, the LD2-LD4 region of paxillin (paxillin^133 -290) binds to Pyk2-FAT as a 1:1 complex. However, our data suggest that the Pyk2-FAT and paxillin complex is dynamic and it appears to be a mixture of two distinct conformations of paxillin that almost equally compete for Pyk2-FAT binding. These studies provide insight into the underlying selectivity of paxillin for Pyk2 and FAK that may influence the differing behavior of these two closely related kinases in focal adhesion sites.     

Structural and Functional Studies of a Klebsiella Phage Capsule Depolymerase Tailspike: Mechanistic Insights into Capsular Degradation

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Structural Insights into the Assembly of CARMA1 and BCL10

The CBM complex (CARMA1, BCL10 and MALT1) plays a crucial role in B and T lymphocyte activation. CARMA1 serves as a scaffold for BCL10, MALT1 and other effector proteins and regulates various signaling pathways related to the immune response. The assembly of CARMA1 and BCL10 is mediated through a CARD-CARD interaction. Here, we report the crystal structure of the CARD domain of CARMA1 at a resolution of 1.75 Å. The structure consists of six helices, as previously determined for CARD domains. Structural and computational analysis identified the binding interface between CARMA1-CARD and BCL10-CARD, which consists of a basic patch in CARMA1 and an acidic patch in BCL10. Site-directed mutagenesis, co-immunoprecipitation and an NF-κB activation assay confirmed that the interface is necessary for association and downstream signaling. Our studies provide molecular insight into the assembly of CARMA1 and BCL10.     

Functional Insights into Recombinant TROSPA Protein from Ixodes ricinus

Lyme disease (also called borreliosis) is a prevalent chronic disease transmitted by ticks and caused by Borrelia burgdorferi s. l. spirochete. At least one tick protein, namely TROSPA from I. scapularis, commonly occurring in the USA, was shown to be required for colonization of the vector by bacteria. Located in the tick gut, TROSPA interacts with the spirochete outer surface protein A (OspA) and initiates the tick colonization. Ixodes ricinus is a primary vector involved in B. burgdorferi s. l. transmission in most European countries. In this study, we characterized the capacities of recombinant TROSPA protein from I. ricinus to interact with OspA from different Borrelia species and to induce an immune response in animals. We also showed that the N-terminal part of TROSPA (a putative transmembrane domain) is not involved in the interaction with OspA and that reduction of the total negative charge on the TROSPA protein impaired TROSPA-OspA binding. In general, the data presented in this paper indicate that recombinant TROSPA protein retains the capacity to form a complex with OspA and induces a significant level of IgG in orally immunized rats. Thus, I. ricinus TROSPA may be considered a good candidate component for an animal vaccine against Borrelia.     

Structural Insights into Ca2+-dependent Regulation of Inositol 1,4,5-Trisphosphate Receptors by CaBP1

Calcium-binding protein 1 (CaBP1), a neuron-specific member of the calmodulin (CaM) superfamily, modulates Ca²⁺-dependent activity of inositol 1,4,5-trisphosphate receptors (InsP₃Rs). Here we present NMR structures of CaBP1 in both Mg²⁺-bound and Ca²⁺-bound states and their structural interaction with InsP₃Rs. CaBP1 contains four EF-hands in two separate domains. The N-domain consists of EF1 and EF2 in a closed conformation with Mg²⁺ bound at EF1. The C-domain binds Ca²⁺ at EF3 and EF4, and exhibits a Ca²⁺-induced closed to open transition like that of CaM. The Ca²⁺-bound C-domain contains exposed hydrophobic residues (Leu¹³², His¹³⁴, Ile¹⁴¹, Ile¹⁴⁴, and Val¹⁴⁸) that may account for selective binding to InsP₃Rs. Isothermal titration calorimetry analysis reveals a Ca²⁺-induced binding of the CaBP1 C-domain to the N-terminal region of InsP₃R (residues 1-587), whereas CaM and the CaBP1 N-domain did not show appreciable binding. CaBP1 binding to InsP₃Rs requires both the suppressor and ligand-binding core domains, but has no effect on InsP₃ binding to the receptor. We propose that CaBP1 may regulate Ca²⁺-dependent activity of InsP₃Rs by promoting structural contacts between the suppressor and core domains.Calcium ion (Ca²⁺) in the cell functions as an important messenger that controls neurotransmitter release, gene expression, muscle contraction, apoptosis, and disease processes (1). Receptor stimulation in neurons promotes large increases in intracellular Ca²⁺ levels controlled by Ca²⁺ release from intracellular stores through InsP₃Rs (2). The neuronal type-1 receptor (InsP₃R1)² is positively and negatively regulated by cytosolic Ca²⁺ (3-6), important for the generation of repetitive Ca²⁺ transients known as Ca²⁺ spikes and waves (1). Ca²⁺-dependent activation of InsP₃R1 contributes to the fast rising phase of Ca²⁺ signaling known as Ca²⁺-induced Ca²⁺ release (7). Ca²⁺-induced inhibition of InsP₃R1, triggered at higher cytosolic Ca²⁺ levels, coordinates the temporal decay of Ca²⁺ transients (6). The mechanism of Ca²⁺-dependent regulation of InsP₃Rs is complex (8, 9), and involves direct Ca²⁺ binding sites (5, 10) as well as remote sensing by extrinsic Ca²⁺-binding proteins such as CaM (11, 12), CaBP1 (13, 14), CIB1 (15), and NCS-1 (16).Neuronal Ca²⁺-binding proteins (CaBP1-5 (17)) represent a new sub-branch of the CaM superfamily (18) that regulate various Ca²⁺ channel targets. Multiple splice variants and isoforms of CaBPs are localized in different neuronal cell types (19-21) and perform specialized roles in signal transduction. CaBP1, also termed caldendrin (22), has been shown to modulate the Ca²⁺-sensitive activity of InsP₃Rs (13, 14). CaBP1 also regulates P/Q-type voltage-gated Ca²⁺ channels (23), L-type channels (24), and the transient receptor potential channel, TRPC5 (25). CaBP4 regulates Ca²⁺-dependent inhibition of L-type channels in the retina and may be genetically linked to retinal degeneration (26). Thus, the CaBP proteins are receiving increased attention as a family of Ca²⁺ sensors that control a variety of Ca²⁺ channel targets implicated in neuronal degenerative diseases.CaBP proteins contain four EF-hands, similar in sequence to those found in CaM and troponin C (18) (Fig. 1). By analogy to CaM (27), the four EF-hands are grouped into two domains connected by a central linker that is four residues longer in CaBPs than in CaM. In contrast to CaM, the CaBPs contain non-conserved amino acids within the N-terminal region that may confer target specificity. Another distinguishing property of CaBPs is that the second EF-hand lacks critical residues required for high affinity Ca²⁺ binding (17). CaBP1 binds Ca²⁺ only at EF3 and EF4, whereas it binds Mg²⁺ at EF1 that may serve a functional role (28). Indeed, changes in cytosolic Mg²⁺ levels have been detected in cortical neurons after treatment with neurotransmitter (29). Other neuronal Ca²⁺-binding proteins such as DREAM (30), CIB1 (31), and NCS-1 (32) also bind Mg²⁺ and exhibit Mg²⁺-induced physiological effects. Mg²⁺ binding in each of these proteins helps stabilize their Ca²⁺-free state to interact with signaling targets.Open in a separate windowFIGURE 1.Amino acid sequence alignment of human CaBP1 with CaM. Secondary structural elements (α-helices and β-strands) were derived from NMR analysis. The four EF-hands (EF1, EF2, EF3, and EF4) are highlighted green, red, cyan, and yellow. Residues in the 12-residue Ca²⁺-binding loops are underlined and chelating residues are highlighted bold. Non-conserved residues in the hydrophobic patch are colored red.Despite extensive studies on CaBP1, little is known about its structure and target binding properties, and regulation of InsP₃Rs by CaBP1 is somewhat controversial and not well understood. Here, we present the NMR solution structures of both Mg²⁺-bound and Ca²⁺-bound conformational states of CaBP1 and their structural interactions with InsP₃R1. These CaBP1 structures reveal important Ca²⁺-induced structural changes that control its binding to InsP₃R1. Our target binding analysis demonstrates that the C-domain of CaBP1 exhibits Ca²⁺-induced binding to the N-terminal cytosolic region of InsP₃R1. We propose that CaBP1 may regulate Ca²⁺-dependent channel activity in InsP₃Rs by promoting a structural interaction between the N-terminal suppressor and ligand-binding core domains that modulates Ca²⁺-dependent channel gating (8, 33, 34).     

The Structural Basis of IKs Ion-Channel Activation: Mechanistic Insights from Molecular Simulations

Relating ion channel (iCh) structural dynamics to physiological function remains a challenge. Current experimental and computational techniques have limited ability to explore this relationship in atomistic detail over physiological timescales. A framework associating iCh structure to function is necessary for elucidating normal and disease mechanisms. We formulated a modeling schema that overcomes the limitations of current methods through applications of artificial intelligence machine learning. Using this approach, we studied molecular processes that underlie human IKs voltage-mediated gating. IKs malfunction underlies many debilitating and life-threatening diseases. Molecular components of IKs that underlie its electrophysiological function include KCNQ1 (a pore-forming tetramer) and KCNE1 (an auxiliary subunit). Simulations, using the IKs structure-function model, reproduced experimentally recorded saturation of gating-charge displacement at positive membrane voltages, two-step voltage sensor (VS) movement shown by fluorescence, iCh gating statistics, and current-voltage relationship. Mechanistic insights include the following: 1) pore energy profile determines iCh subconductance; 2) the entire protein structure, not limited to the pore, contributes to pore energy and channel subconductance; 3) interactions with KCNE1 result in two distinct VS movements, causing gating-charge saturation at positive membrane voltages and current activation delay; and 4) flexible coupling between VS and pore permits pore opening at lower VS positions, resulting in sequential gating. The new modeling approach is applicable to atomistic scale studies of other proteins on timescales of physiological function.     

Structural Insights into Serine-rich Fimbriae from Gram-positive Bacteria

The serine-rich repeat family of fimbriae play important roles in the pathogenesis of streptococci and staphylococci. Despite recent attention, their finer structural details and precise adhesion mechanisms have yet to be determined. Fap1 (Fimbriae-associated protein 1) is the major structural subunit of serine-rich repeat fimbriae from Streptococcus parasanguinis and plays an essential role in fimbrial biogenesis, adhesion, and the early stages of dental plaque formation. Combining multidisciplinary, high resolution structural studies with biological assays, we provide new structural insight into adhesion by Fap1. We propose a model in which the serine-rich repeats of Fap1 subunits form an extended structure that projects the N-terminal globular domains away from the bacterial surface for adhesion to the salivary pellicle. We also uncover a novel pH-dependent conformational change that modulates adhesion and likely plays a role in survival in acidic environments.     

Real-time Analysis of Conformation-sensitive Antibody Binding Provides New Insights into Integrin Conformational Regulation

Integrins are heterodimeric adhesion receptors that regulate immune cell adhesion. Integrin-dependent adhesion is controlled by multiple conformational states that include states with different affinity to the ligand, states with various degrees of molecule unbending, and others. Affinity change and molecule unbending play major roles in the regulation of cell adhesion. The relationship between different conformational states of the integrin is unclear. Here we have used conformationally sensitive antibodies and a small LDV-containing ligand to study the role of the inside-out signaling through formyl peptide receptor and CXCR4 in the regulation of α₄β₁ integrin conformation. We found that in the absence of ligand, activation by formyl peptide or SDF-1 did not result in a significant exposure of HUTS-21 epitope. Occupancy of the ligand binding pocket without cell activation was sufficient to induce epitope exposure. EC₅₀ for HUTS-21 binding in the presence of LDV was identical to a previously reported ligand equilibrium dissociation constant at rest and after activation. Furthermore, the rate of HUTS-21 binding was also related to the VLA-4 activation state even at saturating ligand concentration. We propose that the unbending of the integrin molecule after guanine nucleotide-binding protein-coupled receptor-induced signaling accounts for the enhanced rate of HUTS-21 binding. Taken together, current results support the existence of multiple conformational states independently regulated by both inside-out signaling and ligand binding. Our data suggest that VLA-4 integrin hybrid domain movement does not depend on the affinity state of the ligand binding pocket.In the bloodstream circulating leukocytes respond to inflammatory signals by rapid changes of cell adhesive properties. These include cell tethering, rolling, arrest, and firm adhesion, all of which are well described steps of leukocyte recruitment to the sites of inflammation (1). Leukocyte arrest and firm adhesion are mediated exclusively by integrin receptors (2). At the same time integrins can also mediate tethering and rolling (3). These largely diverse cell adhesive properties are achieved by sophisticated conformational regulation; multiple states of the same molecule with different affinity for its ligand and different degrees of molecular unbending are attributed to various types of “cellular behavior.” It is proposed that the low affinity bent state translates into a non-adhesive resting cell, the low affinity unbent or extended state of integrin results in cell rolling, and the high affinity state promotes cell arrest (4, 5). However, the exact sequence of conformational events and the relationship between integrin conformational and functional activity remain key questions (6).Integrin conformation is regulated through G-protein-coupled receptors by a signaling pathway which is initiated by ligand binding to a GPCR,³ propagated inside the cell, and results in the binding of signaling proteins (such as talin and others) to cytoplasmic domains of integrin subunits. This binding leads to a separation of the integrin cytoplasmic domains and inside-out activation (6). Chemokines (chemotactic cytokines) as well as “classical” chemoattractants (such as formyl peptide) preferentially signal through heterotrimeric G-proteins coupled to the Gα_i subunit (1). Activation by these ligands results in up-regulation of integrin affinity and/or conformational unbending (extension) of the integrin molecule. These conformational changes lead to cell arrest and firm adhesion. G-protein receptors coupled to Gα_s-coupled subunit (adenylyl cyclase/cAMP signaling pathway) can actively down-regulate the affinity state of the ligand binding pocket without changing integrin conformational unbending. This provides an anti-adhesive signal and results in cell de-adhesion (7). Thus, interaction of multiple G-protein-coupled receptors on a single cell creates a plethora of conformational states. Understanding of the relationship between inside-out signaling through GPCRs and integrin conformational regulation will provide valuable insight into the dynamic regulation of cell adhesion.One technique to study conformational changes of integrins uses conformationally sensitive mAbs that bind to epitopes which are hidden in one conformation and exposed under certain conditions. Lately, it has been accepted that integrins exhibit two major conformations, resting and activated. A number of mAbs for “activated” integrins have been described, and the epitopes have been mapped. Together with mapping of these epitopes into three-dimensional structures of integrin (8), epitope exposure can provide helpful information about integrin conformational changes upon signaling. Moreover, because integrin inside-out activation through different signaling pathways can result in different activation states, the use of previously mapped mAbs can help dissect conformational changes upon activation.Although it is clear that inside-out activation results in a conformational rearrangement of the integrin molecule, the relationship between affinity state of the ligand binding pocket and overall molecule conformation is still debated. Currently, two contrasting models of integrin inside-out integrin activation are described. The “switchblade” model implies that an open head structure with swung-out β-hybrid domain represents the high (or at least intermediate) affinity state. A feature of this model is that integrin extension provides space for hybrid domain swing. The “deadbolt” model proposes that the movement of β-hybrid domain is not related to the inside-out signal. Ligand binding by itself can provide the energy for the hybrid domain swing out (for details, see Ref. 9 and references therein). Because these two models assign different roles to the hybrid domain motion, we evaluated the exposure of VLA-4 hybrid domain epitopes upon activation through two Gα_i-coupled GPCRs (FPR and CXCR4) and ligand binding using the conformationally sensitive HUTS-21 mAb with an epitope mapped to the hybrid domain of β1-integrin (10).We found that contrary to previous reports, where these mAbs were reported to bind or used for the detection of activated integrin (10–13), formyl peptide or SDF-1 treatment alone did not result in any significant exposure of HUTS-21 epitope despite the fact that the VLA-4 affinity up-regulation was detected in parallel on the same batch of cells. Quantitative analysis of mAb binding in real time on live cells suggests that for both the low (resting) and high affinity (induced by inside-out pathway) states, occupancy of the ligand binding pocket rather than inside-out signaling by itself causes the conformational change. Thus, these data support the idea that the hybrid domain movement, which results in the exposure of the mAb epitope, and the high affinity state of the binding pocket are regulated separately and independently of each other, a feature of the deadbolt model of inside-out activation.     

Mechanistic Insight into Control of CFTR by AMPK

The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP and protein kinase A (PKA)-regulated Cl^– channel in the apical membrane of epithelial cells. The metabolically regulated and adenosine monophosphate-stimulated kinase (AMPK) is colocalized with CFTR and attenuates its function. However, the sites for CFTR phosphorylation and the precise mechanism of inhibition of CFTR by AMPK remain obscure. We demonstrate that CFTR normally remains closed at baseline, but nevertheless, opens after inhibition of AMPK. AMPK phosphorylates CFTR in vitro at two essential serines (Ser⁷³⁷ and Ser⁷⁶⁸) in the R domain, formerly identified as “inhibitory” PKA sites. Replacement of both serines by alanines (i) reduced phosphorylation of the R domain, with Ser⁷⁶⁸ having dramatically greater impact, (ii) produced CFTR channels that were partially open in the absence of any stimulation, (iii) significantly augmented their activation by IBMX/forskolin, and (iv) eliminated CFTR inhibition post AMPK activation. Attenuation of CFTR by AMPK activation was detectable in the absence of cAMP-dependent stimulation but disappeared in maximally stimulated oocytes. Our data also suggest that AMP is produced by local phosphodiesterases in close proximity to CFTR. Thus we propose that CFTR channels are kept closed in nonstimulated epithelia with high baseline AMPK activity but CFTR may be basally active in tissues with lowered endogenous AMPK activity.The cystic fibrosis transmembrane regulator (CFTR)² gene is mutated in patients with cystic fibrosis. CFTR has an adapted ABC transporter structural motif thereby creating an anion channel at the apical surface of secretory epithelia (1). The consequent CFTR-mediated ion transport is tightly controlled by ATP binding and phosphorylation by protein kinase A (PKA). However, a number of other protein kinases including PKC, Ca²⁺/calmodulin-dependent kinase, and cGMP-dependent kinase also control the activity of CFTR (2–4). These kinases converge on the regulatory domain of CFTR that is unique not only within the large ABC transporter family but among all known sequences, and may be considered as a “phosphorylation control module” (3). Regulation of CFTR by an inhibitory kinase, the adenosine monophosphate-dependent kinase (AMPK), has been described recently but the regulatory sites within CFTR, the mechanism of regulation, and the physiological relevance have all remained obscure (5–8). Additionally, CFTR mutation is linked to inflammation and a lack of functional CFTR expression has itself been suggested to up-regulate AMPK activity in epithelial cells carrying the cystic fibrosis (CF) defect. Pharmacologic AMPK activation was shown to inhibit secretion of inflammatory mediators (9). Thus AMPK may play multiple roles in CF pathophysiology making the mechanism of interaction an important problem in biology.AMPK is a ubiquitous serine/threonine kinase that exists as a heterotrimer with a catalytic α subunit and regulatory β and γ subunits, each with multiple isoforms. In response to metabolic depletion and a consequent increase in the cellular AMP to ATP ratio, AMPK phosphorylates numerous proteins and activates catabolic pathways that generate ATP, whereas inhibiting cell growth, protein biosynthesis, and a number of other ATP-consuming processes, thereby operating as a cellular “low-fuel” sensor (10, 11). AMPK also controls signaling pathways involved in apoptosis, cell cycle, and tissue inflammation (12). Because AMPK is a cellular metabolic sensor that inhibits CFTR and limits cAMP activated Cl^– secretion, a coupling of membrane transport by CFTR to the cellular metabolism has been proposed (13). However, AMPK activity can also increase without detectable changes in the cytosolic AMP to ATP ratio, suggesting a contribution of additional AMP-independent signals for regulation of CFTR by AMPK (14). Drugs used to combat type 2 diabetes, such as phenformin and metformin, act in this manner to activate AMPK, AMP-independently. It is also likely that cytosolic AMP is compartmentalized depending on the distribution of AMP generating enzymes such as phosphodiesterases that convert cAMP to AMP. The concept of spatiotemporal control of cAMP signaling by anchored protein complexes is well established (15). CFTR is known to form such macromolecular complexes with a number of interacting partners (16–18). For example, competitive interaction of EBP50-PKA and Shank2-PDE4D with CFTR has been demonstrated recently (19). In addition, Barnes and co-workers (20) demonstrated that phosphodiesterase 4D generates a cAMP diffusion barrier local to the apical membrane of the airway epithelium. It is therefore likely that activator pathways through cAMP and inhibitory AMP/AMPK signaling occur in a local CFTR-organized compartment. Here we explore the functional links between CFTR, inhibition of phosphodiesterases, and AMPK focusing on the effects of mutating putative AMPK targets within the R domain on CFTR function.     

Structural Insights into the Neutralization Mechanism of Monoclonal Antibody 6C2 against Ricin

Ricin belongs to the type II ribosome-inactivating proteins that depurinate the universally conserved α-sarcin loop of rRNA. The RNA N-glycosidase activity of ricin also largely depends on the ribosomal proteins that play an important role during the process of rRNA depurination. Therefore, the study of the interaction between ricin and the ribosomal elements will be better to understand the catalysis mechanism of ricin. The antibody 6C2 is a mouse monoclonal antibody exhibiting unusually potent neutralizing ability against ricin, but the neutralization mechanism remains unknown. Here, we report the 2.8 Å crystal structure of 6C2 Fab in complex with the A-chain of ricin (RTA), which reveals an extensive antigen-antibody interface that contains both hydrogen bonds and van der Waals contacts. The complementarity-determining region loops H1, H2, H3, and L3 form a pocket to accommodate the epitope on the RTA (residues Asp⁹⁶–Thr¹¹⁶). ELISA results show that Gln⁹⁸, Glu⁹⁹, Glu¹⁰², and Thr¹⁰⁵ (RTA) are the key residues that play an important role in recognizing 6C2. With the perturbation of the 6C2 Fab-RTA interface, 6C2 loses its neutralization ability, measured based on the inhibition of protein synthesis in a cell-free system. Finally, we propose that the neutralization mechanism of 6C2 against ricin is that the binding of 6C2 hinders the interaction between RTA and the ribosome and the surface plasmon resonance and pulldown results confirm our hypothesis. In short, our data explain the neutralization mechanism of mAb 6C2 against ricin and provide a structural basis for the development of improved antibody drugs with better specificity and higher affinity.