Glucose modulation of glucokinase activation by small molecules

Small molecule activators of glucokinase (GK) were used in kinetic and equilibrium binding studies to probe the biochemical basis for their allosteric effects. These small molecules decreased the glucose K 0.5 ( approximately 1 mM vs approximately 8 mM) and the glucose cooperativity (Hill coefficient of 1.2 vs 1.7) and lowered the k cat to various degrees (62-95% of the control activity). These activators relieved GK's inhibition from glucokinase regulatory protein (GKRP) in a glucose-dependent manner and activated GK to the same extent as control reactions in the absence of GKRP. In equilibrium binding studies, the intrinsic glucose affinity to the activator-bound enzyme was determined and demonstrated a 700-fold increase relative to the apoenzyme. This is consistent with a reduction in apparent glucose K D and the steady-state parameter K 0.5 as a result of enzyme equilibrium shifting to the activator-bound form. The binding of small molecules to GK was dependent on glucose, consistent with the structural evidence for an allosteric binding site which is present in the glucose-induced, active enzyme form of GK and absent in the inactive apoenzyme [Kamata et al. (2004) Structure 12, 429-438]. A mechanistic model that brings together the kinetic and structural data is proposed which allows qualitative and quantitative analysis of the glucose-dependent GK regulation by small molecules. The regulation of GK activation by glucose may have an important implication for the discovery and design of GK activators as potential antidiabetic agents.     

Direct F NMR observation of the conformational selection of optically active rotamers of the antifolate compound fluoronitropyrimethamine bound to the enzyme dihydrofolate reductase

The molecular basis of the binding of the lipophilic antifolate compound fluoronitropyrimethamine [2,4-diamino-5-(4-fluoro-3-nitrophenyl)-6-ethylpyrimidine] to its target enzyme dihydrofolate reductase has been investigated using a combination of ¹⁹F NMR spectroscopy and molecular mechanical calculations. ¹⁹F NMR reveals the presence of two different conformational states for the fluoronitropyrimethamine-Lactobacillus casei enzyme complex. MM2 molecular mechanical calculations predict restricted rotation about the C5-C1′ bond of the ligand and this gives rise to two slowly interconverting rotamers which are an enantiomeric pair. The results of ¹⁹F NMR spectroscopy reveal that both these isomers bind to the enzyme, with different affinities. There is no detectable interconversion of the bound rotamers themselves on the NMR timescale. The effect of the addition of co-enzyme to the sample is to reverse the preference the enzyme has for each rotamer.     

Structural Studies of Bcl-xL/ligand Complexes using 19F NMR

Fluorine atoms are often incorporated into drug molecules as part of the lead optimization process in order to improve affinity or modify undesirable metabolic and pharmacokinetic profiles. From an NMR perspective, the abundance of fluorinated drug leads provides an exploitable niche for structural studies using ¹⁹F NMR in the drug discovery process. As ¹⁹F has no interfering background signal from biological sources, ¹⁹F NMR studies of fluorinated drugs bound to their protein receptors can yield easily interpretable and unambiguous structural constraints. ¹⁹F can also be selectively incorporated into proteins to obtain additional constraints for structural studies. Despite these advantages, ¹⁹F NMR has rarely been exploited for structural studies due to its broad lines in macromolecules and their ligand complexes, leading to weak signals in ¹H/¹⁹F heteronuclear NOE experiments. Here we demonstrate several different experimental strategies that use ¹⁹F NMR to obtain ligand–protein structural constraints for ligands bound to the anti-apoptotic protein Bcl-xL, a drug target for anti-cancer therapy. These examples indicate the applicability of these methods to typical structural problems encountered in the drug development process.     

Functional characterization of MODY2 mutations highlights the importance of the fine-tuning of glucokinase and its role in glucose sensing

Glucokinase (GK) acts as a glucose sensor in the pancreatic beta-cell and regulates insulin secretion. Heterozygous mutations in the human GK-encoding GCK gene that reduce the activity index increase the glucose-stimulated insulin secretion threshold and cause familial, mild fasting hyperglycaemia, also known as Maturity Onset Diabetes of the Young type 2 (MODY2). Here we describe the biochemical characterization of five missense GK mutations: p.Ile130Thr, p.Asp205His, p.Gly223Ser, p.His416Arg and p.Ala449Thr. The enzymatic analysis of the corresponding bacterially expressed GST-GK mutant proteins show that all of them impair the kinetic characteristics of the enzyme. In keeping with their position within the protein, mutations p.Ile130Thr, p.Asp205His, p.Gly223Ser, and p.His416Arg strongly decrease the activity index of GK, affecting to one or more kinetic parameters. In contrast, the p.Ala449Thr mutation, which is located in the allosteric activator site, does not affect significantly the activity index of GK, but dramatically modifies the main kinetic parameters responsible for the function of this enzyme as a glucose sensor. The reduced Kcat of the mutant (3.21±0.28 s⁻¹ vs 47.86±2.78 s⁻¹) is balanced by an increased glucose affinity (S_0.5 = 1.33±0.08 mM vs 7.86±0.09 mM) and loss of cooperativity for this substrate. We further studied the mechanism by which this mutation impaired GK kinetics by measuring the differential effects of several competitive inhibitors and one allosteric activator on the mutant protein. Our results suggest that this mutation alters the equilibrium between the conformational states of glucokinase and highlights the importance of the fine-tuning of GK and its role in glucose sensing.     

Ca2+-independent form of protein kinase C may regulate Na+ transport across frog skin

Summary Activators of protein kinase C (PKC) stimulate Na^– transport (J _Na) across frog skin. We have examined the effect of Ca²⁺ on PKC stimulation ofJ _Na. Both the phorbol ester 12-O-tetradecanoylglycerol (DiC₈) were used as PKC activators. Blocking Ca²⁺ entry into the cytosol (either from external or internal stores) reduced the subsequent natriferic effect of the PKC activators. This negative interaction did not simply reflect saturation of activation of the apical Na⁺ channels, since the stimulations produced by blocking Ca²⁺ entry and adding cyclic AMP were simply additive.The Ca²⁺ dependence of the natriferic effect could have reflected either a direct action of cytosolic Ca²⁺ on PKC or an indirect action on the final receptor site (the Na⁺ channel). To distinguish between these possibilities, the TPA- and phospholipid-dependent kinase activity of broken-cell preparations was assayed. The kinase activity was not stimulated by physiological levels of Ca²⁺, and in fact was inhibited at millimolar concentrations of Ca²⁺.We conclude that the effects of Ca²⁺ on the natriferic response to PKC activators are indirect. Reducing cytosolic uptake of Ca²⁺ may have stimulated Na⁺ transport by a chemical modification of the apical channels observed in other tight epithelia. The usual stimulation of Na⁺ transport produced by PKC activators in frog skin may reflect the operation of a nonconventional form of PKC. This enzyme is Ca²⁺ independent and seems related to thenPKC or PKC observed in other systems.     

Determinants of human glucokinase activation and implications for small molecule allosteric control

Glucokinase (GK) is an enzyme that catalyzes the ATP-dependent phosphorylation of glucose to form glucose-6-phosphate, and it is a tightly regulated checkpoint in glucose homeostasis. GK is known to undergo substantial conformational changes upon glucose binding. The monomeric enzyme possesses a highly exotic kinetic activity profile with an unusual sigmoidal dependence on glucose concentration. In this interdisciplinary study, which draws on small angle X-ray scattering (SAXS) integrated with 250?ns of atomistic molecular dynamics (MD) simulations and experimental glucose binding thermodynamics, we reveal that the critical regulation of this glucose sensor is due to a solvent controlled “switch”. We demonstrate that the “solvent switch” is driven by specific protein structural dynamics, which leads to an enzyme structure that has a much more favorable solvation energy than most of the protein ensemble. These findings uncover the physical workings of an agile and flexible protein scaffold, which derives its long-range allosteric control through specific regions with favorable solvation energy. The physiological framework presented herein provides insights that have direct implications for the design of small molecule GK activators as anti-diabetes therapeutics as well as for understanding how proteins can be designed to have built-in regulatory functions via solvation energy dynamics.     

A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase

¹⁹F NMR has recently emerged as an efficient, sensitive tool for analyzing protein binding to small molecules, and surface plasmon resonance (SPR) is also a popular tool for this purpose. Herein a combination of ¹⁹F NMR and SPR was used to find novel binders to the ATP-binding pocket of MAP kinase extracellular regulated kinase 2 (ERK2) by fragment screening with an original fluorinated-fragment library. The ¹⁹F NMR screening yielded a high primary hit rate of binders to the ERK2 ATP-binding pocket compared with the rate for the SPR screening. Hit compounds were evaluated and categorized according to their ability to bind to different binding sites in the ATP-binding pocket. The binding manner was characterized by using isothermal titration calorimetry and docking simulation. Combining ¹⁹F NMR with other biophysical methods allows the identification of multiple types of hit compounds, thereby increasing opportunities for drug design using preferred fragments.     

Heterodinuclear Cu(II)Zn(II) complexes: F NMR as a versatile tool to control the synthesis

The dinucleating ligands 2,6-bis[(bis(2-pyridylmethyl)amino)methyl]-4-methylphenol (H-BPMP) and 2,6-bis[(bis(2-pyridylmethyl)amino)methyl]-4-fluorophenol (H-BPFP) were used to synthesize heterodinuclear (μ-phenoxo)(μ-hydroxo) Cu(II)Zn(II) complexes. The labeled ligand with a fluorine atom allows the use of ¹⁹F NMR spectroscopy, which turned to be a rapid and powerful tool to tune the synthesis of the heterodinuclear paramagnetic complex [CuZnBPFP(μOH)](ClO₄)₂ and avoid mixing of complexes with statistical distribution. When applied to the non-fluorinated ligand, this experimental procedure leads to prepare and isolate easily the complex [CuZnBPMP(μOH)](ClO₄)₂. The X-ray structure is described.     

Synthesis, characterisation and solution behaviour of fluoroalkyl phosphoryl complexes of tin tetrachloride

The synthesis, characterisation and solution behaviour of a series of octahedral complexes SnCl₄·2L (L = R₂NP(O)(OCH₂CF₃)₂; R = Me (1); Et (2) or L = P(O)(OCH₂R_f)₃; R_f = CF₃ (3); C₂F₅ (4)) are described. Complexes 1-4 were prepared from SnCl₄ and 2 equiv. of the ligand, L, in anhydrous CH₂Cl₂ solution. The adducts have been characterised by multinuclear (¹H, ³¹P and ¹¹⁹Sn) NMR, IR spectroscopy and elemental analysis. In dichloromethane solution, the NMR data showed the presence of a mixture of cis and trans isomers for 1 and 2 and only the cis isomer for 3 and 4. The difference could be interpreted in terms of the electronic effects of the substituents on the phosphorus atom of the ligand. In addition, the solution structure of the complexes studied by variable temperature ³¹P-{¹H} and ¹H NMR in the presence of excess ligand indicated that the ligand exchange on the cis isomer dominates the chemistry. The metal-ligand exchange barriers were estimated to be 13.38 and 11.39 kcal/mol for 1 and 3, respectively. The results are discussed and compared with those previously reported for the related hexamethylphosphoramide adduct, SnCl₄·2HMPA.     

Effect of γ-radiation on the ratio of [18F]2-fluoro-2-deoxy-D-glucose to glucose utilization in human glioblastoma cellsin vitro

The glucose consumption in tumoursin vivo as reflected by uptake of [¹⁸F]2-fluoro-2-deoxy-D-glucose (¹⁸FDG) using positron emission tomography (PET) is currently under investigation as a measure of tumour response to radiotherapy. The calculation of cerebral metabolic rate of glucose from¹⁸FDG-PET data requires a proportionality factor referred to as the lumped constant. In the presentin vitro study, the utilizations of¹⁸FDG and glucose have been measured in a human glioblastoma cell line (86HG-39) as a function of γ-radiation dose with various post-irradiation times and of different fractionation modes. The ratio of utilization of¹⁸FDG to that of glucose (R_F/G), assumed to correspond to the lumped constant, was observed to increase 12 and 24 h after single fraction γ-exposure by factors ranging from 1.2 to 1.5 compared with the non-irradiated controls. It decreased after multiple fraction γ-exposure (4 × 2 Gy) by a factor of 0.7 compared with the single fraction schedule (1 × 8 Gy). The results suggest that the affinities of glucose transporters or hexokiriase enzyme or both for¹⁸FDG and glucose could be influenced by γ-irradiation in this tumour cell linein vitro. Apparent changes of the glucose consumption determined with PET in human tumours following radiotherapy may, therefore, not be solely due to changes in cellular metabolism or cell number but may also be due to changes in R _F/G .     

Neutral and cationic Fe(II) β-diketiminate complexes

The three-coordinate, 12-valence electron complexes [(^MeBDK)FeR] (^MeBDK = [HC(C(Me)NAr)₂]⁻, Ar = 2,6-iPr₂C₆H₃, R = CH₂Ph, CH₂SiMe₃) are reported as well as their reactivity towards Lewis bases. With perfluoroaryl borane and -borate type activators, the monoalkyls react to give alkyl-free paramagnetic cationic iron species counterbalanced by perfluorinated arylborate anions. The paramagnetic nature of the cations permits the observation of weak and dynamic interactions with these anions via ¹⁹F NMR spectroscopy.     

A TROSY relayed HCCH-COSY experiment for correlating adenine H2/H8 resonances in uniformly 13C-labeled RNA molecules

A new TROSY relayed HCCH-COSY pulse sequence is introduced for correlating adenine H2 and H8 resonances in ¹³C-labeled RNA molecules. The pulse scheme provides substantial improvements in signal-to-noise compared to previously suggested experiments, and therefore will be suitable for NMR studies of larger RNA molecules. The experiment provides ¹³C chemical shifts for all carbon nuclei in the adenine base. This is advantageous for resolving spectral overlap in larger RNA molecules and provides a starting point for measuring additional parameters for these carbons in the adenine spin system.     

Two-dimensional structure of phospholipase induced crystals of Ca2+-ATPase from sarcoplasmic reticulum

A two-dimensional projection map was computed of the Ca²⁺-ATPase molecules in sarcoplasmic reticulum, isolated from rabbit skeletal muscle. Crystalline arrays of Ca²⁺-ATPase molecules were formed by incubating the membrane vesicles with phospholipase A₂ and dialysing against Tris/HCl buffer. Ca²⁺-ATPase molecules appear as quasi-triangular blobs in the projection map and seem to form dimers. The projection map seems to indicate an enzyme conformation somewhat similar to vanadate-induced crystals but different from lanthanide-induced crystals of Ca^2*-ATPase.     

A NMR method to determine the anomeric specificity of glucose phosphorylation

A NMR method related to 2D CH correlation with an additional double quantum filter for ³¹P spin coupling was employed to follow the reaction kinetics of the two anomers of glucose during phosphorylation catalyzed by the enzyme yeast hexokinase. The kinetic parameters according to Michaelis–Menten for these reactions have been determined and it is shown that the β-anomer of glucose is phosphorylated faster by a factor of 1.4 versus the α-anomer. Use of human liver glucokinase as an enzyme yields more complex kinetics.     

Activation and translocation of glucokinase in rat primary hepatocytes monitored by high content image analysis

In the liver, glucokinase (GK) regulatory protein (GKRP) negatively modulates the metabolic enzyme GK by locking it in an inactive state in the nucleus. Here, the authors established a high content screening assay in the 384-well microplate format to measure the nucleus-to-cytoplasm translocation of GK by reagents that destabilize the interaction between GK and GKRP. As a cellular model system, primary rat hepatocytes endogenously expressing both GK and GKRP at physiological levels were used. The GK translocation assay was robust, displayed limited day-to-day variability, and delivered good Z' statistics. The increase of the glucose concentration in the extracellular medium from a low glucose situation (2.8 mM) to beyond its physiological set point value of 5 mM was found to drive GK from the nucleus into the cytoplasm. Likewise, both fructose (converted intracellularly into fructose-1-phosphate) and a known allosteric GK activator were found to induce the export of GK from the nucleus and to synergistically enhance the effects of medium or high glucose concentrations with respect to GK translocation. Transfer of the high content screening format to a semiautomated medium throughput screening platform enabled the profiling of large compound numbers with respect to allosteric activation of GK.     

Purification and characterization of D-glycerate-3-kinase from maize leaves

Glycerate kinase (GK; EC 2.7.1.31) from maize (Zea mays L.) leaves was purified by a sequence of ammonium-sulfate precipitations and chromatography on diethylaminoethyl-cellulose, hydroxyapatite, Sephadex G-75SF and dye ligand (Green A) columns. The purest preparation was almost 1300-fold enriched and had a specific activity of 68 mol · min^-1 · (mg protein) ^-1. The enzyme was a monomer of a relative molecular mass (M_r) of 44 kDa (kdalton) as determined by gel filtration, electrophoresis in dissociating conditions and by immunoblots. The enzyme was only weakly recognized by polyclonal antibodies against purified spinach GK, indicating substantial differences in molecular structure of the two proteins. Highly reducing conditions stabilized GK activity and were required for activation of crude leaf enzyme. The enzyme had a broad pH optimum of 6.8–8.5, and formed 3-phosphoglycerate and ADP as reaction products. Apparent K _ms for D-glycerate and Mg-ATP were 0.11 and 0.25 mM, respectively. The enzyme was strongly affected by a number of phosphoesters, especially by 3-phosphoglycerate (K _i= 0.36 mM), fructose bisphosphates and nucleoside bisphosphates. Inhibition by 3-phosphoglycerate was competitive to Mg-ATP and noncompetitive to D-glycerate. Pyruvate was found noncompetitive to D-glycerate (K _is=4 mM). The ratio of stromal concentration of Mg-ATP to phosphoesters, particularly to 3-phosphoglycerate, may be of importance in the regulation of GK during C₄-photosynthesis.Abbreviations DEAE diethylaminoethyl - kDa kdalton - GAP-DH glyceraldehyde phosphate dehydrogenase - GK glycerate kinase - LDH lactate dehydrogenase - 2-ME 2-mercaptoethanol - M_r relative molecular mass - PEP phosphoenolpyruvate - PGA(PK) phosphoglycerate (phosphokinase) - PK pyruvate kinase - SDS-PAGE sodium dodecyl sulfatepolyacrylamide gel electrophoresis     

Measuring <Superscript>13</Superscript>C<Superscript>β</Superscript> chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy

A labeling scheme is introduced that facilitates the measurement of accurate ¹³C^β chemical shifts of invisible, excited states of proteins by relaxation dispersion NMR spectroscopy. The approach makes use of protein over-expression in a strain of E. coli in which the TCA cycle enzyme succinate dehydrogenase is knocked out, leading to the production of samples with high levels of ¹³C enrichment (30–40%) at C^β side-chain carbon positions for 15 of the amino acids with little ¹³C label at positions one bond removed (≈5%). A pair of samples are produced using [1-¹³C]-glucose/NaH¹²CO₃ or [2-¹³C]-glucose as carbon sources with isolated and enriched (>30%) ¹³C^β positions for 11 and 4 residues, respectively. The efficacy of the labeling procedure is established by NMR spectroscopy. The utility of such samples for measurement of ¹³C^β chemical shifts of invisible, excited states in exchange with visible, ground conformations is confirmed by relaxation dispersion studies of a protein–ligand binding exchange reaction in which the extracted chemical shift differences from dispersion profiles compare favorably with those obtained directly from measurements on ligand free and fully bound protein samples.     

Conformational isomerism of the binuclear N,N-pentamethylenedithiocarbamate cadmium(II) complex, [Cd2{S2CN(CH2)5}4] on multinuclear (N, Cd) CP/MAS NMR and single-crystal X-ray diffraction data

Crystalline N,N-cyclo-pentamethylenedithiocarbamate (PmDtc) cadmium(II) complex was prepared and studied by means of ¹⁵N, ¹¹³Cd CP/MAS NMR spectroscopy and single-crystal X-ray diffraction. The unit cell of the cadmium(II) compound comprises two centrosymmetric isomeric binuclear molecules [Cd₂{S₂CN(CH₂)₅}₄], which display structural inequivalence in both ¹⁵N and ¹¹³Cd NMR and XRD data. There are pairs of the dithiocarbamate ligands exhibiting different structural functions in both isomeric molecules. Each of the terminal ligands is bidentately coordinated to the cadmium atom and forms a planar four-membered chelate ring [CdS₂C]; whereas pairs of the tridentate bridging ligands combine two neighbouring cadmium atoms forming an extended eight-membered tricyclic moieties [Cd₂S₄C₂], whose geometry can be approximated by a ‘chair’ conformation. The structural states of cadmium atoms were characterised by almost axially symmetric ¹¹³Cd chemical shift tensors. All experimental ¹⁵N resonance lines were assigned to the nitrogen structural sites in both isomeric binuclear molecules.     

Na+−K+-ATPase activity of glial,neuronal, and synaptosomal enriched fractions from normal and freezing-injured rabbit cerebral cortex

This paper investigates the kinetic parameters of Na⁺–K⁺-ATPase in glial, neuronal, and synaptosomal enriched fractions isolated from rabbit cerebral cortex. Under normal conditions, kinetic parameters-V_max and K _0.5 ^K+ -of Na⁺–K⁺-ATPase are the same in the three fractions, suggesting that this enzyme behaves as the same molecular entity. Following a cryogenic lesion, the alterations of these parameters appear to be different in the different fractions. These data suggest that the same enzyme exhibits various responses when exposed to the same pathological event. The dissimilar lipid composition of the Na⁺–K⁺-ATPase environment, and/or different adaptative responses to abnormal ion concentrations in glial, neuronal, and synaptosomal fractions could account for these different responses.     

Mapping the ligand binding site at protein side-chains in protein-ligand complexes through NOE difference spectroscopy

This report describes a novel NMR approach for mapping the interaction surface between an unlabeled ligand and a ¹³C,¹⁵N-labeled protein. The method relies on the spin inversion properties of the dipolar relaxation pathways and records the differential relaxation of two spin modes, where ligand and protein ¹H magnetizations are aligned either in a parallel or anti-parallel manner. Selective inversion of protein protons is achieved in a straightforward manner by exploiting the one-bond heteronuclear scalar couplings (¹J_CH, ¹J_NH). Suppression of indirect relaxation pathways mediated by bulk water or rapidly exchanging protons is achieved by selective inversion of the water signal in the middle of the NOESY mixing period. The method does not require deuteration of the protein or well separated spectral regions for the protein and the ligand, respectively. Additionally, in contrast to previous methods, the new experiment identifies side-chain enzyme ligand interactions along the intermolecular binding interface. The method is demonstrated with an application to the B₁₂-binding subunit of glutamate mutase from Clostridium tetanomorphum for which NMR chemical shift changes upon B₁₂-nucleotide loop binding and a high-resolution solution structure are available.