Thermally induced changes in the structure and activity of yeast hexokinase B

Yeast hexokinase has been poorly characterized in regard with its stability. In the present study, various spectroscopic techniques were employed to investigate thermal stability of the monomeric form of yeast hexokinase B (YHB). The enzyme underwent a conformational transition with a T(m) of about 41.9 degrees C. The structural transition proved to be significantly reversible below 55 degrees C and irreversible at higher temperatures. Thermoinactivation studies revealed that enzymatic activity diminished significantly at high temperatures, with greater loss of activity observed above 55 degrees C. Release of ammonia upon deamidation of YHB obeyed a similar temperature-dependence pattern. Dynamic light scattering and size exclusion-HPLC indicated formation of stable aggregates. Taking various findings on the influence of osmolytes and chaperone-like agents on YHB thermal denaturation together, it is proposed that the purely conformational transition of YHB is reversible, and irreversibility is due to aggregation, as a major cause. Deamidation of a critical Asn or Gln residue(s) may also play an important role.     

Probing protein hydration and conformational states in solution.

The addition of polyethylene glycol (PEG), of various molecular weights, to solutions bathing yeast hexokinase increases the affinity of the enzyme for its substrate glucose. The results can be interpreted on the basis that PEG acts directly on the protein or indirectly through water activity. The nature of the effects suggests to us that PEG's action is indirect. Interpretation of the results as an osmotic effect yields a decrease in the number of water molecules, delta Nw, associated with the glucose binding reaction. delta Nw is the difference in the number of PEG-inaccessible water molecules between the glucose-bound and glucose-free conformations of hexokinase. At low PEG concentrations, delta Nw increases from 50 to 326 with increasing MW of the PEG from 300 to 1000, and then remains constant for MW-PEG up to 10,000. This suggests that up to MW 1000, solutes of increasing size are excluded from ever larger aqueous compartments around the protein. Three hundred and twenty-six waters is larger than is estimated from modeling solvent volumes around the crystal structures of the two hexokinase conformations. For PEGs of MW > 1000, delta Nw falls from 326 to about 25 waters with increasing PEG concentration, i.e., PEG alone appears to "dehydrate" the unbound conformation of hexokinase in solution. Remarkably, the osmotic work of this dehydration would be on the order of only one k T per hexokinase molecule. We conclude that under thermal fluctuations, hexokinase in solution has a conformational flexibility that explores a wide range of hydration states not seen in the crystal structure.     

Polarised pulse fluorimetry study on the conformational properties of wheat germ hexokinase LI

The conformational properties of wheat germ hexokinase LI, a monomeric enzyme showing non-Michaelian kinetics, have been studied by polarised pulse fluorimetry using synchrotron radiation as an excitation light source.The fluorescence decays and the fluorescence anisotropy decays of tryptophyl residues were measured with excitation at 300 nm. At pH 8.5, we found that the mnemonical temperature-dependent transition did not induce any detectable structural change in the protein. This rules out modifications of the aggregation state of hexokinase during the transition as well as important conformational changes in the tertiary structure. At pH 6.1, a temperature-dependent transition of the enzyme-glucose binary complex is observed: rapid, large amplitude, internal motions appear in the structure when the temperature is raised from-1°C to 30°C. Full standard activity is retained during this dynamic change.In the experiments described here we obtained an active fluorescent derivative by reacting hexokinase with N-(iodoacetylaminoethyl)-5-naphtylamine-1-sulfonic acid (1,5-IAEDANS), in the presence of glucose. Polarised fluorescence decay measurements indicate that the label is exposed to the solvent and very mobile, which makes it ineffective as a probe for the conformational properties of hexokinase.Abbreviations 1,5-IAEDANS N-(iodoacetylaminoethyl)-5-napthylamine-1-sulfonic acid - DTNB 5,5-dithiobis(2-nitrobenzoic acid)     

Mitochondrial hexokinase and cardioprotection of the intact heart

The interaction of hexokinase with mitochondria has emerged as a powerful mechanism in protecting many cell types against cell death. However, the role of mitochondrial hexokinase (mitoHK) in cardiac ischemia-reperfusion injury has as of yet received little attention. In this review we examine whether increased binding of hexokinase to the mitochondrion is also an integral component of cardioprotective signalling. We discuss observations in cardiac mitochondrial activation that directed us to the hypothesis of hexokinase cellular redistribution with reversible, cardioprotective ischemia, summarize the data showing that many cardioprotective interventions, such as ischemic preconditioning, insulin, morphine and volatile anesthetics, increase mitochondrial hexokinase binding within the intact heart, and discuss similarities between mitochondrial hexokinase association and ischemic preconditioning. Although most data indicate that mitochondrial hexokinase may indeed be an integral part of cardioprotection, a definitive proof for a causal relation between the amount of mitoHK and cardiac ischemia-reperfusion injury in the intact heart is eagerly awaited. When such relationship is indeed observed, the association of hexokinase with mitochondria will offer an opportunity to develop new therapies to combat ischemic cardiac diseases.     

A designed apoplastocyanin variant that shows reversible folding

Plastocyanin, like many other metalloproteins, does not undergo reversible folding, which is thought to be due to an irreversible conformational change in the copper-binding site. Moreover, apoplastocyanin's ability to adopt a native tertiary structure is highly salt-dependent, and even in high salt, it has an irreversible thermal denaturation. Here, we report a designed apoplastocyanin variant, PCV, that is well folded and has reversible folding in both high and low salt conditions. This variant provides a tractable model for understanding and designing protein beta-sheets.     

Crystal structures of an ATP-dependent hexokinase with broad substrate specificity from the hyperthermophilic archaeon Sulfolobus tokodaii

Hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate by using ATP as a phosphoryl donor. Recently, we identified and characterized an ATP-dependent hexokinase (StHK) from the hyperthermophilic archaeon Sulfolobus tokodaii, which can phosphorylate a broad range of sugar substrates, including glucose, mannose, glucosamine, and N-acetylglucosamine. Here we present the crystal structures of StHK in four different forms: (i) apo-form, (ii) binary complex with glucose, (iii) binary complex with ADP, and (iv) quaternary complex with xylose, Mg(2+), and ADP. Forms i and iii are in the open state, and forms ii and iv are in the closed state, indicating that sugar binding induces a large conformational change, whereas ADP binding does not. The four different crystal structures of the same enzyme provide "snapshots" of the conformational changes during the catalytic cycle. StHK exhibits a core fold characteristic of the hexokinase family, but the structures of several loop regions responsible for substrate binding are significantly different from those of other known hexokinase family members. Structural comparison of StHK with human N-acetylglucosamine kinase and other hexokinases provides an explanation for the ability of StHK to phosphorylate both glucose and N-acetylglucosamine. A Mg(2+) ion and coordinating water molecules are well defined in the electron density of the quaternary complex structure. This structure represents the first direct visualization of the binding mode for magnesium to hexokinase and thus allows for a better understanding of the catalytic mechanism proposed for the entire hexokinase family.     

Can conformational change be described by only a few normal modes?

We suggest a simple method to assess how many normal modes are needed to map a conformational change. By projecting the conformational change onto a subspace of the normal-mode vectors and using root mean square deviation as a test of accuracy, we find that the first 20 modes only contribute 50% or less of the total conformational change in four test cases (myosin, calmodulin, NtrC, and hemoglobin). In some allosteric systems, like the molecular switch NtrC, the conformational change is localized to a limited number of residues. We find that many more modes are necessary to accurately map this collective displacement. In addition, the normal-mode "spectra" can provide useful information about the details of the conformational change, especially when comparing structures with different bound ligands, in this case, calmodulin. Indeed, this approach presents normal-mode analysis as a useful basis in which to capture the mechanism of conformational change, and shows that the number of normal modes needed to capture the essential collective motions of atoms should be chosen according to the required accuracy.     

Analysis of Aluminum—Yeast Hexokinase Interaction: Modifications on Protein Structure and Functionality

The aluminum and yeast hexokinase interaction was studied. Structural changes were correlated with variations in protein functionality. Results show two different behaviors: At low metal concentrations preferential adsorption of metal (and water exclusion) induces aggregate formation. No significant changes in the protein structure occur, but there is a continuous loss of activity (from the first concentration). At large salt concentrations a monomerization process and a conformational change in the secondary structure as well as in the three-dimensional structure take place. This change reduces the percentage of α-helix conformation, gives thermal stability to the protein, and allows the exposure of some tryptophan residue and hydrophobic regions. The protein inhibition increases. Conformational change and monomerization may allow access of the metal to the substrate site, mainly the ATP site. The inhibition in any case is of mixed type with a competitive component.     

Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance

BACKGROUND: The human immunodeficiency virus type 1 (HIV-1) protease is an essential viral protein that is a major drug target in the fight against Acquired Immune Deficiency Syndrome (AIDS). Access to the active site of this homodimeric enzyme is gained when two large flaps, one from each monomer, open. The flap movements are therefore central to the function of the enzyme, yet determining how these flaps move at an atomic level has not been experimentally possible. RESULTS: In the present study, we observe the flaps of HIV-1 protease completely opening during a 10 ns solvated molecular dynamics simulation starting from the unliganded crystal structure. This movement is on the time scale observed by Nuclear Magnetic Resonance (NMR) relaxation data. The highly flexible tips of the flaps, with the sequence Gly-Gly-Ile-Gly-Gly, are seen curling back into the protein and thereby burying many hydrophobic residues. CONCLUSIONS: This curled-in conformational change has never been previously described. Previous models of this movement, with the flaps as rigid levers, are not consistent with the experimental data. The residues that participate in this hydrophobic cluster as a result of the conformational change are highly sensitive to mutation and often contribute to drug resistance when they do change. However, several of these residues are not part of the active site cavity, and their essential role in causing drug resistance could possibly be rationalized if this conformational change actually occurs. Trapping HIV-1 protease in this inactive conformation would provide a unique opportunity for future drug design.     

Sugar induced cell death in yeast is dependent on the rate of sugar phosphorylation as determined by Arabidopsis thaliana hexokinase

Sugars like glucose and fructose induce death of yeast cells within a few hours, in the absence of additional nutrients to support growth, while cells incubated in water remain viable for weeks. This sugar-induced cell death (SICD) by glucose and fructose required glucose or fructose phosphorylation since yeast cells deficient in hexose phosphorylation did not die. However, when hexose phosphorylation is restored by complementation with Arabidopsis thaliana hexokinase, the cells died. The affinity of A. thaliana hexokinase is about 400 times higher for glucose than for fructose, therefore, A. thaliana hexokinase was further utilized to study the role of hexose phosphorylation in SICD. The rate of SICD of hexokinase-deficient yeast cells expressing A. thaliana hexokinase was significantly slower in fructose than in glucose, indicating that SICD is determined by the rate of hexose phosphorylation. The significance of hexose phosphorylation and its role in SICD is discussed.     

Mechanistic origin of the kinetic cooperativity of hexokinase type L1 from wheat germ

A theoretical analysis is presented which shows that initial velocity data for hexokinase L1 catalysis of glucose phosphorylation by MgATP cannot be reconciled with the observed rate of the 'mnemonical' conformational transition which has been proposed to account for the kinetic cooperativity of the enzyme. The basic kinetic properties of hexokinase L1 and other allegedly 'mnemonical' enzymes appear to be fully consistent with an ordered ternary-complex mechanism in which the leading substrate participates in abortive-complex formation. It is concluded that, so far, no enzyme displaying kinetic cooperativity has been convincingly demonstrated to operate by a 'mnemonical' type of reaction mechanism.     

Conformational changes of the lecithin headgroup in monolayers at the air/water interface

The headgroup conformation of the phospholipid dipalmitoyl-glycero-phosphocholine (DPPC) in monolayers at the air/water interface has been studied by neutron reflection in the fluid like liquid-expanded (LE) and in the crystal like solid (S) phase. Information on the headgroup conformation in the two phases has been obtained by scattering contrast variation of the lipid monolayer using four differently deuterated species of DPPC: perdeuterated, chain perdeuterated, choline group perdeuterated and selectively headgroup deuterated. Since the measurements were done mainly on a subphase of null reflecting water (i.e. water scattering contrast matched to the air) there is no subphase contribution to reflectivity and the simplest one layer model can be employed for the data analysis, thus minimising the number of free parameters. A remarkable change of the headgroup orientation was observed between the LE and the S phase. We found that the phosphate-nitrogen dipole of the DPPC headgroup exhibits an in-plane orientation with respect to the monolayer in the LE phase but it assumes a more parallel orientation to the surface normal at lateral pressures above 30 mN/m (S phase). Moreover, this conformational change is accompanied by a significant alteration of the headgroup hydration.Abbreviations DPPC Dipalmitoyl-Phosphatidylcholine - DMPC Dimyristoyl-Phosphatidylcholine - DPPE Dipalmitoyl-Phosphatidylethanolamine - DMPE Dimyristoyl-Phosphatidylethanolamine - DMPA Dimyristoyl-Phosphatic Acid - DMPG Dimyristoyl-Phosphatidylglycerol Correspondence to: T M. Bayed     

Exploring the role of large conformational changes in the fidelity of DNA polymerase beta

The relationships between the conformational landscape, nucleotide insertion catalysis and fidelity of DNA polymerase beta are explored by means of computational simulations. The simulations indicate that the transition states for incorporation of right (R) and wrong (W) nucleotides reside in substantially different protein conformations. The protein conformational changes that reproduce the experimentally observed fidelity are significantly larger than the small rearrangements that usually accompany motions from the reactant state to the transition state in common enzymatic reactions. Once substrate binding has occurred, different constraints imposed on the transition states for insertion of R and W nucleotides render it highly unlikely that both transition states can occur in the same closed structure, because the predicted fidelity would then be many orders of magnitude too large. Since the conformational changes reduce the transition state energy of W incorporation drastically they decrease fidelity rather than increase it. Overall, a better agreement with experimental data is attained when the R is incorporated through a transition state in a closed conformation and W is incorporated through a transition state in one or perhaps several partially open conformations. The generation of free energy surfaces for R and W also allow us to analyze proposals about the relationship between induced fit and fidelity.     

Volumetric and spectroscopic characterizations of glucose-hexokinase association

The binding of D-glucose to hexokinase PII at 25 degrees C and pH 8.7 has been investigated by a combination of ultrasonic velocimetry, high precision densimetry, and fluorescence spectroscopy. The binding of glucose to the enzyme results in significant dehydration of the two interacting molecules, while the intrinsic coefficient of adiabatic compressibility of hexokinase slightly decreases. Glucose-hexokinase association is an entropy-driven process. The favorable change in entropy results from compensation between two large contributions. The binding-induced increase in hydrational entropy slightly prevails over the decrease in the configurational entropy of the enzyme. Taken together, our results emphasize the crucial role of water in modulating the energetics of protein recognition.     

Analysis of aluminum-yeast hexokinase interaction: modifications on protein structure and functionality

The aluminum and yeast hexokinase interaction was studied. Structural changes were correlated with variations in protein functionality. Results show two different behaviors: At low metal concentrations preferential adsorption of metal (and water exclusion) induces aggregate formation. No significant changes in the protein structure occur, but there is a continuous loss of activity (from the first concentration). At large salt concentrations a monomerization process and a conformational change in the secondary structure as well as in the three-dimensional structure take place. This change reduces the percentage of -helix conformation, gives thermal stability to the protein, and allows the exposure of some tryptophan residue and hydrophobic regions. The protein inhibition increases. Conformational change and monomerization may allow access of the metal to the substrate site, mainly the ATP site. The inhibition in any case is of mixed type with a competitive component.     

Ligand-induced conformations of rat brain hexokinase: effects of glucose-6-phosphate and inorganic phosphate

Binding of glucose-6-P induces conformational change in rat brain hexokinase (ATP:d-hexose 6-phosphotransferase, EC 2.7.1.1) as indicated by decreased susceptibility to digestion by chymotrypsin and an increased sedimentation coefficient on sucrose density gradients. These effects are competitively reversed by P_i, as are solubilization (of the mitochondrial form of hexokinase) and inhibition by glucose-6-P. Thus, the observed conformational changes are likely to be directly related to the effect of these ligands on catalytic activity and the interaction of the hexokinase with the mitochondrial membrane.Both glucose-6-P and P_i stabilize the enzyme against heat inactivation; this effect, as well as the effect of glucose-6-P on inactivation by chymotrypsin, have been used to estimate the dissociation constants for the complexes of hexokinase with glucose-6-P and P_i; the values are 7–8 μm, and 0.25 mm, respectively.These observations are consistent with a model in which brain hexokinase may exist in two distinct conformations, rapidly and reversibly interconvertible. The effect of glucose-6-P and P_i are explained by highly preferential binding to one or the other of these conformations.     

Function of interdomain α-helix in human brain hexokinase: covalent linkage and catalytic regulation between N- and C-terminal halves

Human brain relies on a steady supply of glucose as the source of fuel, and type I hexokinase is the major isozyme governing the introduction of glucose to glycolysis in the brain. One unique regulatory property associated with type I isozyme is the alleviation of product inhibition by inorganic phosphate which binds to the N-terminal half, and the conformational change induced by inorganic phosphate must be propagated to the active site in the C-terminal half. With a single interdomain α-helix as the only covalent connection between the N- and C-terminal halves, the question arises as what role the interdomain α-helix plays at the interdomain signal transduction. Two mutants were constructed in an attempt to answer this question. The first mutant, A464P/E465G, with a helix breaker embedded in the interdomain α-helix had a smaller magnitude of phosphate alleviation than the wild type. The second mutant, with an insertion of seven additional residues between Gln 466 and His 467, had this phosphate relief property further diminished. Neither mutant showed dramatic changes nor the other kinetic properties. It is speculated that the interdomain α-helix is important for keeping the proper non-covalent contact so that transmission of the conformational changes across the N- and C-terminal half boundary can be achieved.     

Sex or Sanctuary: How do Asexual Worms Survive the Winter?

The common and geographically widespread freshwater worm Stylaria lacustris (Linnaeus, 1767) (Oligochaeta: Naididae) typically reproduces asexually through transverse paratomic fission during the spring, summer, and autumn. With the onset of shorter days and colder conditions, S. lacustris becomes a sexually mature simultaneous hermaphrodite and produces resting eggs that are capable of overwintering. However, like many naidid species, S. lacustris shows widespread variation in reproductive mode with some populations never attaining sexual maturity and others apparently exhibiting both sexual and obligately asexual genotypes. How then do obligately asexual genotypes and populations survive the harsh winter conditions? Extensive winter sampling of two, largely obligately, asexual populations of S. lacustris in Oxfordshire, UK, demonstrate that adult individuals can survive over the winter, but at densities way below that normally detected by standard sampling procedures. Laboratory experiments confirm that asexual individuals can survive cold water conditions but not freezing (unlike sexually produced cocoons). The proposed advantage of this seemingly risky reproductive strategy is that naidids like Stylaria, with their remarkably fast asexual reproductive rate, can respond instantly to favourable change in conditions.