Interaction between pullulanase from Klebsiella pneumoniae and cyclodextrins

Development of pullulanase mutants to enhance starch substrate utilization for efficient production of β-CD

The inhibitory effect of β-CD on pullulanase which hydrolyzes α-1,6 glycosidic bond in starch to release more available linear substrates, limited substrate utilization thus influencing the yield of β-CD. Here, an aspartic acid residue (D465) which interacted with cyclodextrin ligand by hydrogen bond, was mutated to explore its contribution to bind inhibitors and obtain mutants with lower affinity to β-CD. Enzyme activity results showed that mutants D465E and D465N retained higher activity than wild-type pullulanase in presence of 10 mM β-CD. Circular dichroism spectra and fluorescence spectra results showed that D465 was related to structure stability. Chain length distribution results confirmed the improvement of substrate utilization by the addition of D465E. The conversion rate from potato starch, cassava starch, and corn starch into β-CD, increased to 56.9%, 55.4% and 54.7%, respectively, when synchronous using β-CGTase and D465E in the production process.

Relationship between the induced-fit loop and the activity of Klebsiella pneumoniae pullulanase

Klebsiella pneumoniae pullulanase (KPP) belongs to glycoside hydrolase family 13 subfamily 13 (GH13_13) and is the only enzyme that is reported to perform an induced-fit motion of the active-site loop (residues 706–710). Comparison of pullulanase structures indicated that only KPP has Leu680 present behind the loop, in contrast to the glycine found in other GH13_13 members. Analysis of the structure and activity of recombinant pullulanase from K. pneumoniae ATCC 9621 (rKPP) and its mutant (rKPP-G680L) indicated that the side chain of residue 680 is important for the induced-fit motion of the loop 706–710 and alters the binding affinity of the substrate.

Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin

Crystal structures of Klebsiella pneumoniae pullulanase (KPP) in complex with α-cyclodextrin (α-CD), β-cyclodextrin (β-CD) and γ-cyclodextrin (γ-CD) were refined at around 1.98–2.59 Å resolution from data collected at SPring-8. In the structures of the complexes obtained with 1 mM α-CD or γ-CD, one molecule of CD was found at carbohydrate-binding module 41 only (CBM41). In the structures of the complexes obtained with 1 mM β-CD or with 10 mM α-CD or γ-CD, two molecules of CD were found at CBM41 and in the active-site cleft, where the hydrophobic residue of Phe746 occupies the inside cavity of the CD rings. In contrast to α-CD and γ-CD, one β-CD molecule was found at the active site only in the presence of 0.1 mM β-CD. These results were coincident with the solution experiments, which showed that β-CD inhibits this enzyme more than a thousand times more potently than α-CD and γ-CD. The strong inhibition of β-CD is caused by the optimized interaction between β-CD and the side chain of Phe746. The increased K i values of the F746A mutant for β-CD supported the importance of Phe746 in the strong interaction of pullulanase with β-CD.

R-α lipoic acid γ-cyclodextrin complex increases energy expenditure: a 4-month feeding study in mice

OBJECTIVE

A high-fat diet (HFD) affects energy expenditure in laboratory rodents. R-α lipoic acid cyclodextrin (RALA-CD) complex is a stable form of lipoic acid (LA) and may improve energy expenditure. The aim of this study was to determine the effect of RALA-CD on energy expenditure and underlying molecular targets in female laboratory mice.

METHODS

Female C57BL/6J mice were fed a HFD containing 0.1% LA for about 16 wk. The effects on energy expenditure, gene and protein expression were assessed using indirect calorimetry, real-time reverse transcriptase polymerase chain reaction, and Western blot, respectively.

RESULTS

Supplementing mice with RALA-CD resulted in a significant increase in energy expenditure. However, both RALA per se (without γ-cyclodextrin) and S-α lipoic acid cyclodextrin did not significantly alter energy expenditure. Furthermore RALA-CD changed expression of genes encoding proteins centrally involved in energy metabolism. Transcriptional key regulators sirtuin 3 and peroxisome proliferator-activated receptor-γ, coactivator 1 alpha, as well as thyroid related enzyme type 2 iodothyronine deiodinase were up-regulated in brown adipose tissue (BAT) of RALA-CD-fed mice. Importantly, mRNA and/or protein expression of downstream effectors uncoupling protein (Ucp) 1 and 3 also were elevated in BAT from RALA-CD-supplemented mice.

CONCLUSION

Overall, present data suggest that RALA-CD is a regulator of energy expenditure in laboratory mice.

Crystal structure of pullulanase: evidence for parallel binding of oligosaccharides in the active site

The crystal structures of Klebsiella pneumoniae pullulanase and its complex with glucose (G1), maltose (G2), isomaltose (isoG2), maltotriose (G3), or maltotetraose (G4), have been refined at around 1.7-1.9A resolution by using a synchrotron radiation source at SPring-8. The refined models contained 920-1052 amino acid residues, 942-1212 water molecules, four or five calcium ions, and the bound sugar moieties. The enzyme is composed of five domains (N1, N2, N3, A, and C). The N1 domain was clearly visible only in the structure of the complex with G3 or G4. The N1 and N2 domains are characteristic of pullulanase, while the N3, A, and C domains have weak similarity with those of Pseudomonas isoamylase. The N1 domain was found to be a new type of carbohydrate-binding domain with one calcium site (CBM41). One G1 bound at subsite -2, while two G2 bound at -1 approximately -2 and +2 approximately +1, two G3, -1 approximately -3 and +2 approximately 0', and two G4, -1 approximately -4 and +2 approximately -1'. The two bound G3 and G4 molecules in the active cleft are almost parallel and interact with each other. The subsites -1 approximately -4 and +1 approximately +2, including catalytic residues Glu706 and Asp677, are conserved between pullulanase and alpha-amylase, indicating that pullulanase strongly recognizes branched point and branched sugar residues, while subsites 0' and -1', which recognize the non-reducing end of main-chain alpha-1,4 glucan, are specific to pullulanase and isoamylase. The comparison suggested that the conformational difference around the active cleft, together with the domain organization, determines the different substrate specificities between pullulanase and isoamylase.

Pullulan degrading enzymes of bacterial origin

Pullulan degrading enzymes belong to a group of glycosylhydrolases that are widely distributed in nature and are produced by an extremely wide variety of species. Among them the thermophilic and mesophilic bacteria are a rich source of these enzymes. There are many biotechnological applications for these enzymes and a rapidly growing amount of information about their diversity, genetic as well as biochemical and biophysical characteristics. The properties of these enzymes vary and are somewhat linked to the natural environment inhabited by the producing organisms. Genes for these enzymes have been cloned from several strains and their amino acid sequences show highly conserved regions common to the enzymes of the amylase family. Molecular studies have greatly extended our knowledge on pullulan degrading enzymes and their biosynthesis. However, enzyme production levels have usually not been as high as had been assumed possible, and the properties of some enzymes are less than optimal for their industrial applications. Some of these problems can be overcome with the use of good producer organisms, optimized expression/secretion vectors, and site-directed mutagenesis. The molecular biology of pullulan degrading enzymes has been and continues to be a valuable system for studying basic questions of cell biology, such as mechanisms of gene regulation and secretion, and the structure-function relationships of proteins.

Reaction mechanism of electron transfer from FeII(CN)6(4-) or W(IV)(CN)8(4-) to the cupric ions in human copper, zinc superoxide dismutase

The electron transfer reactions from FeII(CN)6(4-) and W(IV)(CN)8(4-) to the cupric ions in human copper, zinc superoxide dismutase were followed by the micro-stopped-flow method. The kinetic rate data clearly indicate that FeII(CN)6(4-) or W(IV)(CN)8(4-) first forms an adduct with the enzyme through the interaction with Arg143 of the active cavity and then an electron from FeII(CN)6(4-) or W(IV)(CN)8(4-) of the adduct transfers to the cupric ion in the enzyme. The dissociation constants of the adducts of FeII(CN)6(4-) and W(IV)(CN)8(4-) were 4.0(+/-0.3) x 10(-3) and 2.2(+/-0.3) x 10(-3) M, respectively. In spite of the difference between the standard redox potentials of FeIII(CN)6(3-)/FeII(CN)6(4-) (468 mV) and W(V)(CN)8(3-)/W(IV)(CN)8(4-) (556 mV), the electron transfer rate constant (0.148(+/-0.005) s(-1) of FeII(CN)6(4-) at 25 degrees C is very similar to that of W(IV)(CN)8(4-) (0.072(+/-0.011) s(-1)). The entropy values of the adduct formations and the activation energies of the electron transfer rates were determined by the temperature dependence of the dissociation constants of the adducts and the electron transfer rates. The enthalpy values of the formation of adducts are almost zero, so that the driving forces to form the adducts are mainly derived from the entropy. The activation energy of the electron transfer rate of FeII(CN)6(4-) is very similar to that of W(IV)(CN)8(4-). The formation of the adduct between FeII(CN)6(4-) and the enzyme was inhibited by the presence of various anions (ClO4-, SO4(2-), SCN-, and N3-). The bulky anions SO4(2-) and ClO4- behave as competitive inhibitors for FeII(CN)6(4-); these anions should interact mainly with Arg143, as it has a positive charge at the entrance of the active cavity. The competitive inhibition constants of ClO4-, SO4(2-), and SCN- were 0.010, 0.012, and 0.008 M. The azide ion, which is smaller than SO4(2-) or ClO4-, shows mixed inhibition, because N3- can interact with Arg143 (competitive inhibition) and also directly binds to the cupric ion in h-SOD (noncompetitive inhibition). The competitive and noncompetitive inhibition constants of N3- were 0.004 and 0.016 M, respectively.

Review: cyclodextrins and their interaction with amylolytic enzymes

This review is concerned with inhibition of amylases by cyclodextrins (cyclic maltooligosaccharides), the interaction that occurs between amylases and cyclodextrins and the application of cyclodextrin affinity chromatography in the purification of amylases. In many cases, amylases that are competitively inhibited by cyclodextrins can be purified by cyclodextrin affinity chromatography with the cyclodextrins interacting with the active site on such enzymes. Interestingly amylases that are not competitively inhibited by cyclodextrins may also be purified by cyclodextrin affinity chromatography. Therefore, cyclodextrin affinity chromatography can function in the purification of such amylolytic enzymes with the interaction occurring at a site removed from the active site. In such cases it appears that the cyclodextrin is interacting with an affinity site or binding site that is present on some amylolytic enzymes. It seems that certain similarities occur among the binding sites of such enzymes. Literature concerning amylases, and their subsequent purification using cyclodextrin affinity chromatography is reviewed and the fundamental basis of the interaction of the cyclodextrin with amylolytic enzymes is discussed here.

Pullulanase from the hyperthermophilic bacterium Thermotoga maritima: purification by beta-cyclodextrin affinity chromatography

This is the first report about the isolation of a type I pullulanase from a hyperthermophilic bacterium, Thermotoga maritima strain MSB8. Purification of the enzyme from a cleared cell-free extract was achieved by anion-exchange chromatography and beta-cyclodextrin affinity chromatography. Using this convenient two-step method we have purified the pullulanase 406-fold with a 26% yield. The purified enzyme displayed maximum pullulan hydrolysis at pH 5.9 and 90 degrees C (15-min assay) and was remarkably resistant against thermoinactivation, having a half-life at 90 degrees C of about 3.5 h. To our knowledge, the T. maritima pullulanase is the most thermostable type I pullulanase known to date. The affinity-based purification protocol described here may be useful for the efficient isolation of other pullulanases.

Thermodynamics of ligand binding to the starch-binding domain of glucoamylase from Aspergillus niger

The thermodynamics of ligand binding to the starch-binding domain (SBD) of glucoamylase from Aspergillus niger has been studied using titration calorimetry. The ligand binding was studied both with the SBD fragment as well as glucoamylase G1 which contains both a catalytic domain and SBD. The ligands were beta-cyclodextrin and three thiopanose analogues [panose = alpha-D-Glcp-(1-->6)-alpha-D-Glcp-(1-->4)-D-Glcp] each including an alpha-(1-->6) thioglycosidic linkage at the non-reducing end. beta-Cyclodextrin binds more strongly than the thiopanose analogues and these have a slightly increasing binding constant with chain length. The reactions are enthalpy-driven with unfavourable contributions from entropy and the variations in enthalpy and entropy compensate each other linearly. SBD was shown to have two binding sites that appear to bind identically and independently in the isolated binding domain, whereas they interact with each other in a negatively cooperative fashion when the catalytic domain of glucoamylase is present (glucoamylase G1). In glucoamylase G1 one site of SBD has an increased binding constant compared to the SBD fragment, whereas the other has the same association constant. The change in binding constant and induced cooperativity were not due to interactions with the catalytic binding site, since binding of beta-cyclodextrin was the same both when the catalytic site was occupied by the strong inhibitor acarbose and when the catalytic site was free.

Interaction of some anti-hypoxia drugs with hydroxypropyl-beta-cyclodextrin studied by means of charge transfer chromatography

The interaction of 12 anti-hypoxia drugs with hydroxypropyl-beta-cyclodextrin (HPBCD) and the influence of LiCl, NaCl and KCl on the strength of interaction was studied by charge transfer chromatography. Most of the drugs form inclusion complexes with HPBCD and the relative strength of interaction varies markedly according to the structure of the drugs. Salts exert a considerable influence on the inclusion complex formation and the effect depends on the radii of the cation. The significant correlations between the lipophilicity of drugs and their capacity to form inclusion complexes with HPBCD indicate the involvement of hydrophobic forces in the interaction.