ADP Complex Research Articles

Crystal Structure and Enzymology of Solanum tuberosum Inositol Tris/Tetrakisphosphate Kinase 1 (StITPK1).

Inositol phosphates and their pyrophosphorylated derivatives are responsive to the phosphate supply and are agents of phosphate homeostasis and other aspects of physiology. It seems likely that the enzymes that interconvert these signals work against the prevailing milieu of mixed populations of competing substrates and products. The synthesis of inositol pyrophosphates is mediated in plants by two classes of ATP-grasp fold kinase: PPIP5 kinases, known as VIH, and members of the inositol tris/tetrakisphosphate kinase (ITPK) family, specifically ITPK1/2. A molecular explanation of the contribution of ITPK1/2 to inositol pyrophosphate synthesis and turnover in plants is incomplete: the absence of nucleotide in published crystal structures limits the explanation of phosphotransfer reactions, and little is known of the affinity of potential substrates and competitors for ITPK1. Herein, we describe a complex of ADP and StITPK1 at 2.26 Å resolution and use a simple fluorescence polarization approach to compare the affinity of binding of diverse inositol phosphates, inositol pyrophosphates, and analogues. By simple HPLC, we reveal the novel catalytic capability of ITPK1 for different inositol pyrophosphates and show Ins(3,4,5,6)P4 to be a potent inhibitor of the inositol pyrophosphate-synthesizing activity of ITPK1. We further describe the exquisite specificity of ITPK1 for the myo-isomer among naturally occurring inositol hexakisphosphates.

Crystal structure of adenosine 5ʹ-phosphosulfate kinase isolated from Archaeoglobus fulgidus

The 3′-phosphoadenosine-5′-phosphosulfate (PAPS) molecule is essential during enzyme-catalyzed sulfation reactions as a sulfate donor and is an intermediate in the reduction of sulfate to sulfite in the sulfur assimilation pathway. PAPS is produced through a two-step reaction involving ATP sulfurylase and adenosine 5′-phosphosulfate (APS) kinase enzymes/domains. However, archaeal APS kinases have not yet been characterized and their mechanism of action remains unclear. Here, we first structurally characterized APS kinase from the hyperthermophilic archaeon Archaeoglobus fulgidus, (AfAPSK). We demonstrated the PAPS production activity of AfAPSK at the optimal growth temperature (83 °C). Furthermore, we determined the two crystal structures of AfAPSK: ADP complex and ATP analog adenylyl-imidodiphosphate (AMP-PNP)/Mg2+/APS complex. Structural and complementary mutational analyses revealed the catalytic and substrate recognition mechanisms of AfAPSK. This study also hints at the molecular basis behind the thermal stability of AfAPSK.

ADP-Induced Conformational Transition of Human Adenylate Kinase 1 Is Triggered by Suppressing Internal Motion of α3α4 and α7α8 Fragments on the ps-ns Timescale.

Human adenylate kinase 1 (hAK1) plays a vital role in the energetic and metabolic regulation of cell life, and impaired functions of hAK1 are closely associated with many diseases. In the presence of Mg2+ ions, hAK1 in vivo can catalyze two ADP molecules into one ATP and one AMP molecule, activating the downstream AMP signaling. The ADP-binding also initiates AK1 transition from an open conformation to a closed conformation. However, how substrate binding triggers the conformational transition of hAK1 is still unclear, and the underlying molecular mechanisms remain elusive. Herein, we determined the solution structure of apo-hAK1 and its key residues for catalyzing ADP, and characterized backbone dynamics characteristics of apo-hAK1 and hAK1-Mg2+-ADP complex (holo-hAK1) using NMR relaxation experiments. We found that ADP was primarily bound to a cavity surrounded by the LID, NMP, and CORE domains of hAK1, and identified several critical residues for hAK1 catalyzing ADP including G16, G18, G20, G22, T39, G40, R44, V67, D93, G94, D140, and D141. Furthermore, we found that apo-hAK1 adopts an open conformation with significant ps-ns internal mobility, and Mg2+-ADP binding triggered conformational transition of hAK1 by suppressing the ps-ns internal motions of α3α4 in the NMP domain and α7α8 in the LID domain. Both α3α4 and α7α8 fragments became more rigid so as to fix the substrate, while the catalyzing center of hAK1 experiences promoted µs-ms conformational exchange, potentially facilitating catalysis reaction and conformational transition. Our results provide the structural basis of hAK1 catalyzing ADP into ATP and AMP, and disclose the driving force that triggers the conformational transition of hAK1, which will deepen understanding of the molecular mechanisms of hAK1 functions.

A mutation in the switch 1 region of myosin VA alters the load-dependence of phosphate rebinding

The load-dependence of reversible product release in myosins is key to understanding how it converts chemical energy into mechanical force. Following the powerstroke and phosphate (Pi) release, the rebinding of Pi to the actomyosin⋅ADP complex is highly load-dependent, but the underlying mechanisms/structures involved remain unclear. Therefore, we introduced a mutation (S217A) into the switch I region of the active site to examine its impact on the load dependence of Pi rebinding to single-headed myosin Va (MV) in a mini-ensemble (∼10 heads) three-bead laser trap assay at 100 uM ATP.

Tuning the Properties of Azadipyrromethene-Based Near-Infrared Dyes Using Intramolecular BO Chelation and Peripheral Substitutions.

Tetraphenylazadipyrromethenes (ADPs) are attractive near-infrared (NIR) dyes because of their simple synthesis and exceptional optical and electronic properties. The typical BF2 and less explored intramolecular BO coordination planarize the molecule, making them promising π-conjugated materials for organic electronic applications. However, their use has been mostly limited to vacuum-deposited devices. To improve the properties, we synthesized and characterized a series of ADP complexes and used density functional theory calculations to further explain the properties. Hexyloxy solubilizing groups increase the complexes' solubility in organic solvents and enable film formation from solution. Phenylethynyls at the pyrrolic positions extend π conjugation, red-shift absorption and emission peaks, and increase the ionization potential (IP) and electron affinity. When the properties of complexes with hexyloxy and phenyethynyl substitutions are compared, the BO complex is more planar and has a smaller IP than the corresponding BF2 complex because of increased electron density on the proximal phenyls. The BO complex has an unusual combination of properties: a solution λmax of 781 nm, emission at 805 nm, a small Stokes shift, and a quantum yield of 6%. It forms transparent films with a low optical gap of 1.22 eV. This new complex is a promising candidate for transparent solar cells and NIR photodetectors.

Azadipyrromethene-Based Materials: From Synthesis to Electronic and Photovoltaic Properties

Azadipyrromethene (ADP, see image) is an aromatic monoanionic bidentate ligand whose core resembles half of a phthalocyanine ligand. Complexes of ADP have strong visible to near-IR absorption, high electron affinity and easy synthesis, making them attractive for a variety of applications. We have demonstrated that homoleptic zinc(II) complexes of ADP with phenylethynyl pyrrolic substituents (Zn(WS3)2, see image), are promising candidates as non-fullerene acceptors for solution-processed organic photovoltaics (OPVs). The complexe’s distorted tetrahedral structure (non-planar) facilitates favorable phase separation from the common conjugated polymer donor, poly(3-hexylthiophene) (P3HT), yielding good performance in OPVs. The phenylethynyl groups also contribute to increase the electron affinity of the complex. To further increase electron affinity, we installed electronegative fluorine at various positions of the ADP ligands. To our surprise, the electrochemical properties are relatively unaffected by the substitutions, but the electron mobility and performance in OPVs improves. On the other hand, substitution with nitrile groups anodically shifts the redox potentials and thus increases electronegativity. The substitutions also improve electron mobility in diodes as compared to the un-substituted analogue. However, OPV performance is poor, possibly due to unfavorable blend morphology with P3HT, demonstrating the difficulties in optimizing all properties simultaneously.To further enhance charge transport and OPV performance, we investigated replacing the phenyl in the phenylethynyl pyrrolic substituents with larger aromatic groups such as naphthyl and phenanthrenyl groups. Because these larger aromatic groups reduced solubility in organic solvents, we added hexyl solubilizing groups at the para position of the proximal phenyls. We found that the hexyl and the larger aromatic groups both contribute to improving crystallinity of the zinc(II) complexes, electron mobility and OPV performance. The best performance was obtained with 1-naphthyl substitution, Zn(L2)2 shown in the image. OPVs using P3HT as the donor gave a high power conversion efficiency (PCE) of 5.5% and the PCE was not very sensitive to the P3HT:Zn(L2)2 weight ratio. Additionally, Zn(L2)2 can be synthesized on the gram scale using inexpensive starting materials without chromatography column purification, increasing its industrial accessibility. Due to its non-planar structure, Zn(L2)2 shows isotropic charge transport. Interestingly, it had high hole mobility, making it a good candidate as donor for OPVs. This combination of properties demonstrates the potential of these types of molecules for optoelectronic devices. Selected references: Z. Mao; W. Senevirathna; J. Y. Liao; J. Gu; S. V. Kesava; C. Guo; E. D. Gomez; G. Sauvé, “Azadipyrromethene-Based Zn(II) Complexes as Nonplanar Conjugated Electron Acceptors for Organic Photovoltaics.” Adv. Mater. 26 (2014), 6290-6294. S. Pejić; A. M. Thomsen; F. S. Etheridge; R. Fernando; C. Wang; G. Sauvé, “Fluorination Increases the Electron Mobility of Zinc Azadipyrromethene-Based Electron Acceptors and Enhances the Performance of Fullerene-Free Organic Solar Cells.” J. Mater. Chem. C 6 (2018), 3990-3998. G. Sauvé, “Designing Alternative Non-Fullerene Molecular Electron Acceptors for Solution-Processable Organic Photovoltaics.” Chem. Rec. 19 (2019), 1-16. C. Wang; P. Wei; J. H. L. Ngai; A. L. Rheingold; T. G. Gray; Y. Li; E. Pentzer; R. Li; L. Zhu; G. Sauvé, “A Zinc(Ii) Complex of Di(Naphthylethynyl)Azadipyrromethene with Low Synthetic Complexity Leads to OPV with High Industrial Accessibility.” J. Mater. Chem. A 7 (2019), 24614-24625. C. Wang, C. Daddario, S. Pejić, G. Sauvé, “Synthesis and Properties of Azadipyrromethene-based Complexes with Nitrile Substitution” Submitted to Eur. JOC. Figure 1

Myosin motor domains carrying mutations implicated in early or late onset hypertrophic cardiomyopathy have similar properties

Hypertrophic cardiomyopathy (HCM) is a common genetic disorder characterized by left ventricular hypertrophy and cardiac hyper-contractility. Mutations in the β-cardiac myosin heavy chain gene (β-MyHC) are a major cause of HCM, but the specific mechanistic changes to myosin function that lead to this disease remain incompletely understood. Predicting the severity of any β-MyHC mutation is hindered by a lack of detailed examinations at the molecular level. Moreover, because HCM can take ≥20 years to develop, the severity of the mutations must be somewhat subtle. We hypothesized that mutations that result in early onset disease would have more severe changes in function than do later onset mutations. Here, we performed steady-state and transient kinetic analyses of myosins carrying one of seven missense mutations in the motor domain. Of these seven, four were previously identified in early onset cardiomyopathy screens. We used the parameters derived from these analyses to model the ATP-driven cross-bridge cycle. Contrary to our hypothesis, the results indicated no clear differences between early and late onset HCM mutations. Despite the lack of distinction between early and late onset HCM, the predicted occupancy of the force-holding actin·myosin·ADP complex at [Actin] = 3 Kapp along with the closely related duty ratio (the fraction of myosin in strongly attached force-holding states), and the measured ATPases all changed in parallel (in both sign and degree of change) compared with wildtype (WT) values. Six of the seven HCM mutations were clearly distinct from a set of previously characterized DCM mutations.

Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties.

Nucleoside diphosphate kinases (NDKs) are implicated in a wide variety of cellular functions owing to their enzymatic conversion of NDP to NTP. NDK from Borrelia burgdorferi (BbNDK) was selected for functional and structural analysis to determine whether its activity is required for infection and to assess its potential for therapeutic inhibition. The Seattle Structural Genomics Center for Infectious Diseases (SSGCID) expressed recombinant BbNDK protein. The protein was crystallized and structures were solved of both the apoenzyme and a liganded form with ADP and vanadate ligands. This provided two structures and allowed the elucidation of changes between the apo and ligand-bound enzymes. Infectivity studies with ndk transposon mutants demonstrated that NDK function was important for establishing a robust infection in mice, and provided a rationale for therapeutic targeting of BbNDK. The protein structure was compared with other NDK structures found in the Protein Data Bank and was found to have similar primary, secondary, tertiary and quaternary structures, with conserved residues acting as the catalytic pocket, primarily using His132 as the phosphohistidine-transfer residue. Vanadate and ADP complexes model the transition state of this phosphoryl-transfer reaction, demonstrating that the pocket closes when bound to ADP, while allowing the addition or removal of a γ-phosphate. This analysis provides a framework for the design of potential therapeutics targeting BbNDK inhibition.

Effects of GSH1 and GSH2 Gene Mutation on Glutathione Synthetases Activity of Saccharomyces cerevisiae.

In this paper, three mutants from wild Saccharomyces cerevisiae HBU2.558, called U2.558, UN2.558, and UNA2.558, were screened by UV, sodium nitrite, Atmospheric and room temperature plasma, respectively. Glutathione production of the three mutants increased by 41.86, 72.09 and 56.76%, respectively. We detected the activity of glutathione synthetases and found that its activity was improved. Amino acid sequences of three mutant colonies were compared with HBU2.558. Four mutants: Leu51→Pro51 (L51P), Glu62→Val62 (E62V), Ala332→Glu332 (A332E) and Ser653→Gly653 (S653G) were found in the analysis of γ-glutamylcysteine ligase. L51 is located adjacently to the two active sites of GCL/E/Mg2+/ADP complex in the overall GCL structure. L51P mutant spread distortion on the β-sheet due to the fact that the φ was changed from -50.4° to -40.2°. A mutant Leu54→Pro54 (L54P) was found in the analysis of glutathione synthetase, and L54 was an amino acid located between an α-helix and a β-sheet. The results confirm that introduction of proline located at the middle of the β-sheet or at the N- or C-terminal between α-helix and β-sheet or, i.e., L51P and L54P, changed the φ, rigidity, hydrophobicity and conformational entropy, thus increased protein stability and improved the enzyme activity.

Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis.

A free serine kinase (SerK) is involved in l-cysteine biosynthesis in the hyperthermophilic archaeon Thermococcus kodakarensis. The enzyme converts ADP and l-serine (Ser) into AMP and O-phospho-l-serine (Sep), which is a precursor of l-cysteine. SerK is the first identified enzyme that phosphorylates free serine, while serine/threonine protein kinases have been well studied. SerK displays low sequence similarities to known kinases, suggesting that its reaction mechanism is different from those of known kinases. Here, we determined the crystal structures of SerK from T. kodakarensis (Tk-SerK). The overall structure is divided into two domains. A large cleft is found between the two domains in the AMP complex and in the ADP complex. The cleft is closed in the ternary product complex (Sep, AMP, and Tk-SerK) and may also be in the ternary substrate complex (Ser, ADP, and Tk-SerK). The closure may reorient the carboxyl group of E30 near to the Oγ atom of Ser. The Oγ atom is considered to be deprotonated by E30 and to attack the β-phosphate of ADP to form Sep. The substantial decrease in the activity of the E30A mutant is consistent with this mechanism. Our structures also revealed the residues that contribute to the ligand binding. The conservation of these residues in uncharacterized proteins from bacteria may raise the possibility of the presence of free Ser kinases not only in archaea but also in bacteria.

Kinetic analysis of gluconate phosphorylation by human gluconokinase using isothermal titration calorimetry

Gluconate is a commonly encountered nutrient, which is degraded by the enzyme gluconokinase to generate 6-phosphogluconate. Here we used isothermal titration calorimetry to study the properties of this reaction. ΔH, KM and kcat are reported along with substrate binding data. We propose that the reaction follows a ternary complex mechanism, with ATP binding first. The reaction is inhibited by gluconate, as it binds to an Enzyme–ADP complex forming a dead-end complex. The study exemplifies that ITC can be used to determine mechanisms of enzyme catalyzed reactions, for which it is currently not commonly applied.

Open–close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase

Infant gut-associated bifidobacteria possess a metabolic pathway to utilize lacto-N-biose (Gal-β1,3-GlcNAc) and galacto-N-biose (Gal-β1,3-GalNAc) from human milk and glycoconjugates specifically. In this pathway, N-acetylhexosamine 1-kinase (NahK) catalyzes the phosphorylation of GlcNAc or GalNAc at the anomeric C1 position with ATP. Crystal structures of NahK have only been determined in the closed state. In this study, we determined open state structures of NahK in three different forms (apo, ADP complex, and ATP complex). A comparison of the open and closed state structures revealed an induced fit structural change defined by two rigid domains. ATP binds to the small N-terminal domain, and binding of the N-acetylhexosamine substrate to the large C-terminal domain induces a closing conformational change with a rotation angle of 16°. In the nucleotide binding site, two magnesium ions bridging the α-γ and β-γ phosphates were identified. A mutational analysis indicated that a residue coordinating both of the two magnesium ions (Asp228) is essential for catalysis. The involvement of two magnesium ions in the catalytic machinery is structurally similar to the catalytic structures of protein kinases and aminoglycoside phosphotransferases, but distinct from the structures of other anomeric kinases or sugar 6-kinases. These findings help to elucidate the possible evolutionary adaptation of substrate specificities and induced fit mechanism.

Chapter Nine - Use of Safranin for the Assessment of Mitochondrial Membrane Potential by High-Resolution Respirometry and Fluorometry

The mitochondrial transmembrane potential (Δψmt or mtMP) is directly influenced by oxidative phosphorylation (OXPHOS). The exact nature of the interactions between respiration (flux) and mtMP (force) under various physiological and pathological conditions remains unclear, partially due to methodological limitations. Here, we describe a combination of high-resolution respirometry and fluorometry based on the OROBOROS Oxygraph-2k and the widely applied mtMP indicator safranin. The analysis of OXPHOS in mouse brain homogenates revealed that, at commonly applied concentrations, safranin inhibits Complex I-driven OXPHOS capacity, primarily targeting the phosphorylation system, but has no effects on LEAK respiration. Conversely, Complex II-driven OXPHOS capacity was inhibited by <20% by safranin concentrations normally used for mtMP monitoring. The mtMP was higher in the LEAK state without adenylates than at identical LEAK respiration after ADP stimulation and Complex V inhibition with oligomycin. The maximal electron transfer system (ETS) capacity was reached in uncoupler titrations before the mtMP fully collapsed, whereas respiration was inhibited at increasing uncoupler concentrations, resulting in the progressive reduction of mtMP. In a pharmacologically induced state of Complex II dysfunction, mtMP was rather insensitive to the inhibition of OXPHOS to 50% of its normal capacity, but robustly responded to inhibitors when respiration was limited by substrate depletion. The optimal concentration of uncoupler supporting maximal ETS capacity varied as a function of pharmacological intervention. Taken together, the combined measurement of respiration and mtMP greatly enhances the informative potential of OXPHOS studies. The respirometric validation of inhibitory and uncoupling effects is mandatory for any fluorophore employed to assess mtMP in any respiratory state, tissue type, and pathophysiological condition. The methodological issues analyzed herein are relevant for the study of mitochondrial respiration in a wide variety of setting, including cancer cell metabolism.

A Role for Glutathione Transferase Omega 1 (GSTO1-1) in the Glutathionylation Cycle

The glutathionylation of intracellular protein thiols can protect against irreversible oxidation and can act as a redox switch regulating metabolic pathways. In this study we discovered that the Omega class glutathione transferase GSTO1-1 plays a significant role in the glutathionylation cycle. The catalytic activity of GSTO1-1 was determined in vitro by assaying the deglutathionylation of a synthetic peptide by tryptophan fluorescence quenching and in T47-D epithelial breast cancer cells by both immunoblotting and the direct determination of total glutathionylation. Mutating the active site cysteine residue (Cys-32) ablated the deglutathionylating activity of GSTO1-1. Furthermore, we demonstrate that the expression of GSTO1-1 in T47-D cells that are devoid of endogenous GSTO1-1 resulted in a 50% reduction in total glutathionylation levels. Mass spectrometry and immunoprecipitation identified β-actin as a protein that is specifically deglutathionylated by GSTO1-1 in T47-D cells. In contrast to the deglutathionylation activity, we also found that GSTO1-1 is associated with the rapid glutathionylation of cellular proteins when the cells are exposed to S-nitrosoglutathione. The common A140D genetic polymorphism in GSTO1 was found to have significant effects on the kinetics of both the deglutathionylation and glutathionylation reactions. Genetic variation in GSTO1-1 has been associated with a range of diseases, and the discovery that a frequent GSTO1-1 polymorphism affects glutathionylation cycle reactions reveals a common mechanism where it can act on multiple proteins and pathways.

Specialized Hsp70 Chaperone (HscA) Binds Preferentially to the Disordered Form, whereas J-protein (HscB) Binds Preferentially to the Structured Form of the Iron-Sulfur Cluster Scaffold Protein (IscU)

The Escherichia coli protein IscU serves as the scaffold for Fe-S cluster assembly and the vehicle for Fe-S cluster transfer to acceptor proteins, such as apoferredoxin. IscU populates two conformational states in solution, a structured conformation (S) that resembles the conformation of the holoprotein IscU-[2Fe-2S] and a dynamically disordered conformation (D) that does not bind metal ions. NMR spectroscopic results presented here show that the specialized Hsp70 chaperone (HscA), alone or as the HscA-ADP complex, preferentially binds to and stabilizes the D-state of IscU. IscU is released when HscA binds ATP. By contrast, the J-protein HscB binds preferentially to the S-state of IscU. Consistent with these findings, we propose a mechanism in which cluster transfer is coupled to hydrolysis of ATP bound to HscA, conversion of IscU to the D-state, and release of HscB.

Evaluation of competing J domain:Hsp70 complex models in light of existing mutational and NMR data

Ahmad et al. recently presented an NMR-based model for a bacterial DnaJ J domain:DnaK(Hsp70):ADP complex(1) that differs significantly from the crystal structure of a disulfide linked mammalian auxilin J domain:Hsc70 complex that we previously published(2). They claimed that their model could better account for existing mutational data, was in better agreement with previous NMR studies, and that the presence of a cross-link in our structure made it irrelevant to understanding J:Hsp70 interactions. Here we detail extensive NMR and mutational data relevant to understanding J:Hsp70 function and show that, in fact, our structure is much better able to account for the mutational data and is in much better agreement with a previous NMR study of a mammalian polyoma virus T-ag J domain:Hsc70 complex than is the Ahmad et al. complex, and that our structure is predictive and provides insight into J:Hsp70 interactions and mechanism of ATPase activation.

Nonequilibrium Isotope Exchange Reveals a Catalytically Significant Enzyme–Phosphate Complex in the ATP Hydrolysis Pathway of the AAA+ ATPase Magnesium Chelatase

Magnesium chelatase is an AAA(+) ATPase that catalyzes the first committed step in chlorophyll biosynthesis. Using nonequilibrium isotope exchange, we show that the ATP hydrolysis reaction proceeds via an enzyme-phosphate complex. Exchange from radiolabeled phosphate to ATP was not observed, offering no support for an enzyme-ADP complex.

Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1

BackgroundIre1 is a signal transduction protein in the endoplasmic reticulum (ER) membrane that serves to adjust the protein-folding capacity of the ER according to the needs of the cell. Ire1 signals, in a transcriptional program, the unfolded protein response (UPR) via the coordinated action of its protein kinase and RNase domains. In this study, we investigated how the binding of cofactors to the kinase domain of Ire1 modulates its RNase activity.ResultsOur results suggest that the kinase domain of Ire1 initially binds cofactors without activation of the RNase domain. RNase is activated upon a subsequent conformational rearrangement of Ire1 governed by the chemical properties of bound cofactors. The conformational step can be selectively inhibited by chemical perturbations of cofactors. Substitution of a single oxygen atom in the terminal β-phosphate group of a potent cofactor ADP by sulfur results in ADPβS, a cofactor that binds to Ire1 as well as to ADP but does not activate RNase. RNase activity can be rescued by thiophilic metal ions such as Mn2+ and Cd2+, revealing a functional metal ion-phosphate interaction which controls the conformation and RNase activity of the Ire1 ADP complex. Mutagenesis of the kinase domain suggests that this rearrangement involves movement of the αC-helix, which is generally conserved among protein kinases. Using X-ray crystallography, we show that oligomerization of Ire1 is sufficient for placing the αC-helix in the active, cofactor-bound-like conformation, even in the absence of cofactors.ConclusionsOur structural and biochemical evidence converges on a model that the cofactor-induced conformational change in Ire1 is coupled to oligomerization of the receptor, which, in turn, activates RNase. The data reveal that cofactor-Ire1 interactions occur in two independent steps: binding of a cofactor to Ire1 and subsequent rearrangement of Ire1 resulting in its self-association. The pronounced allosteric effect of cofactors on protein-protein interactions involving Ire1's kinase domain suggests that protein kinases and pseudokinases encoded in metazoan genomes may use ATP pocket-binding ligands similarly to exert signaling roles other than phosphoryl transfer.

The Structure of Lombricine Kinase: IMPLICATIONS FOR PHOSPHAGEN KINASE CONFORMATIONAL CHANGES

Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309-317, which is disordered in substrate-free structures of homologs and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His(178). Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates.

Binding and recognition of AMP, ADP, ATP and related inorganic phosphate anions by a tren-based ligand containing a pyrimidine functionality

The interaction of AMP, ADP, ATP and related phosphate, diphosphate and triphosphate anions with the positively charged forms of the HL ligand, constituted by a tren molecule functionalized with a pyrimidine residue, was studied by potentiometric titrations, affording the stability constants of the formed anion complexes, 31P and 1H NMR spectroscopy in aqueous solutions and modelling calculations. The equilibrium data show that electrostatic forces make an important, but not decisive contribution, to the stability of the anion complexes. For nucleotides, 1H NMR spectra showed that the formation of π-stacking interactions between nucleotide adenine and ligand pyrimidine moieties contribute to the stability of these complexes, being very important for those complexes of higher stability. The synergistic action of the different binding groups of the polyfunctional HL receptor leads to a marked recognition of ADP over ATP with a selectivity coefficient as high as 116 at pH 3.3, which is unprecedented in the context of synthetic receptor in water. According to modelling calculations, such exceptional binding selectivity has a strong relation with the increase of stability experienced by ADP complexes upon ADP protonation. A similar phenomenon is observed for HAMP− whose interaction with H3L2+ is at least as strong as that of the more charged HATP3− anion, which is another rare occurrence.