Structure and activity of methylated horse liver alcohol dehydrogenase

Chemical modification of Saccharomycopsis fibuligera R64 α-amylase to improve its stability against thermal, chelator, and proteolytic inactivation

α-Amylase catalyzes hydrolysis of starch to oligosaccharides, which are further degraded to simple sugars. The enzyme has been widely used in food and textile industries and recently, in generation of renewable energy. An α-amylase from yeast Saccharomycopsis fibuligera R64 (Sfamy) is active at 50 °C and capable of degrading raw starch, making it attractive for the aforementioned applications. To improve its characteristics as well as to provide information for structural study ab initio, the enzyme was chemically modified by acid anhydrides (nonpolar groups), glyoxylic acid (GA) (polar group), dimethyl adipimidate (DMA) (cross-linking), and polyethylene glycol (PEG) (hydrophilization). Introduction of nonpolar groups increased enzyme stability up to 18 times, while modification by a cross-linking agent resulted in protection of the calcium ion, which is essential for enzyme activity and integrity. The hydrophilization with PEG resulted in protection against tryptic digestion. The chemical modification of Sfamy by various modifiers has thereby resulted in improvement of its characteristics and provided systematic information beneficial for structural study of the enzyme. An in silico structural study of the enzyme improved the interpretation of the results.

Lysine methylation strategies for characterizing protein conformations by NMR

In the presence of formaldehyde and a mild reducing agent, reductive methylation is known to achieve near complete dimethylation of protein amino groups under non-denaturing conditions, in aqueous media. Amino methylation of proteins is employed in mass spectrometric, crystallographic, and NMR studies. Where biosynthetic labeling is prohibitive, amino (13)C-methylation provides an attractive option for monitoring folding, kinetics, protein-protein and protein-DNA interactions by NMR. Here, we demonstrate two improvements over traditional (13)C-reductive methylation schemes: (1) By judicious choice of stoichiometry and pH, ε-aminos can be preferentially monomethylated. Monomethyl tags are less perturbing and generally exhibit improved resolution over dimethyllysines, and (2) By use of deuterated reducing agents and (13)C-formaldehyde, amino groups can be labeled with (13)CH(2)D tags. Use of deutero-(13)C-formaldehyde affords either (13)CHD(2), or (13)CD(3) probes depending on choice of reducing agent. Making use of (13)C-(2)H scalar couplings, we demonstrate a filtering scheme that eliminates natural abundance (13)C signal.

Extensive modification of protein amino groups by reductive addition of different sized substituents

The amino groups of ovomucoid, lysozyme and ovotransferrin have been extensively alkylated by reacting the proteins with various carbonyl reagents in the presence of sodim borohydride. The extent of modification ranged from 40 to 100%. Essentially monosubstitution was obtained with acetone, cyclopentanone, cyclohexanone and benzaldehyde, while 20--50% disubstitution was obtained with N-butanal and nearby 100% disubstitution was obtained with formaldehyde. Both the methylated and isopropylated derivatives of all three proteins were soluble and retained almost full biochemical activities, but introduction of the larger substituents caused precipitation with lysozyme and ovotransferrin.

A Hg (II) induced conformational change in penicillinase

Penicillinase (E.C. 3.5.2.6) from Bacillus cereus 569/H is inhibited by Hg(II). The inhibition is characterized by non-competitive kinetics and can be reversed by EDTA. A Hg(II) induced conformational change is indicated because: (1) The EDTA regenerated activity is unstable and is rapidly converted to an iodine-sensitive state, and (2) An irreversible change in the circular dichroism spectrum at 222 nm is found.

The radius of gyration of native and reductively methylated myosin subfragment-1 from neutron scattering

Reductive methylation of nearly all lysine groups of myosin subfragment-1 (S1) was required for crystallization and solution of its structure at atomic resolution. Possible effects of such methylation on the radius of gyration of chicken skeletal muscle myosin S1 have been investigated by using small-angle neutron scattering. In addition, we have investigated the effect of MgADP.Vi, which is thought to produce an analog of the S1.ADP.Pi state, on the S1 radius of gyration. We find that although methylation of S1, with or without SO42- ion addition, does not significantly alter the structure, addition of ADP plus vanadate does decrease the radius of gyration significantly. The S1 crystal structure predicts a radius of gyration close to that measured here by neutron scattering. These results suggest that the overall shape by crystallography resembles nucleotide-free S1 in solution. In order to estimate the effect of residues missing from the crystal structure, the structure of missing loops was estimated by secondary-structure prediction methods. Calculations using the complete crystal structure show that a simple closure of the nucleotide cleft by a rigid-body torsional rotation of residues (172-180 to 670) around an axis running along the base of the cleft alone does not produce changes as large as seen here and in x-ray scattering results. On the other hand, a rigid body rotation of either the light-chain binding domain (767 to 843 plus light chains) or of a portion of 20-kDa peptide plus this domain (706 to 843 plus light chains) is more readily capable of producing such changes.

Effect of reductive alkylation on thermal stability of ribonuclease A and chymotrypsinogen A

In order to probe changes in the structural stability induced by the introduction of hydrophobic groups into proteins, the amino groups of ribonuclease A and chymotrypsinogen A were reductively alkylated by reaction with various aliphatic aldehydes, formaldehyde, acetaldehyde, n-butylaldehyde and n-hexylaldehyde, and their thermal stabilities were investigated by differential scanning calorimetry (DSC) at different acidic pH values. Ribonuclease A was thermally unstabilized by reductive alkylation, while chymotrypsinogen A was slightly stabilized, depending on both the size of the introduced alkyl groups and the extent of modification. These observations suggest that the effects induced by alkylation involve not only steric hindrance due to the entering bulky groups but also certain other factors such as the participation of the chemically introduced alkyl groups in hydrophobic interactions.

Modification of alpha-amylase from Bacillus licheniformis by the polyaldehyde derived from beta-cyclodextrine and alpha-amylase thermostability

The cleavage of beta-cyclodextrine by sodium periodate at the seven 2-3 diols of the glucose unit gives rise to the polyaldehyde 1, used to modify alpha-amylase. The reductive modification of alpha-amylase from Bacillus licheniformis reduced the number of reactive lysine groups from 8 to 3.5 per mol of enzyme with an activity loss of 25% and increased the half-life at 80 degrees C from 4.7 to 7.0 minutes.

Irreversible thermoinactivation of glucoamylase from Aspergillus niger and thermostabilization by chemical modification of carboxyl groups

The incubation of glucoamylase from Aspergillus niger at 70 degrees C induced its rapid and irreversible inactivation. The covalent modifications of the protein structure involved in the thermoinactivation depended on the pH of the medium. We observed the formation of a low amount of disulfide-linked oligomers showing that disulfide exchange takes place at pH 5.5. Hydrolysis of peptide bonds at pH 3.5 and 4.5 was also detected. The chemical modification of carboxyl groups with a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) decreased the rate of appearance of low-molecular-weight peptides at pH 3.5 and 4.5 upon heating at 70 degrees C. However, the rate of inactivation at such pH values was not modified. Modification of carboxyl groups with EDC in the presence of ethylenediamine leading to the transformation of three carboxyl groups to amino groups increased the thermostability of the enzyme for temperatures above the temperature of compensation, Tc, which is 60 degrees C.

The active site composition of porcine pancreatic lipase: possible involvement of lysine

A mechanism is proposed wherein an essential lysine in porcine pancreatic lipase is the acylable residue in the catalytic mechanism of the enzyme. This mechanism involves an initial interfacial activation step were acylation first takes place in a rate-limiting step on a serine residue assisted by histidine and a carboxyl-containing residue, aspartic acid or glutamic acid, and then in a fast subsequent step the acyl group is transferred to the essential lysine residue at the catalytic site. Indirect support for the mechanism is presented. When the essential lysine is made inactive by reductive methylation, the lipase is functionally converted to a proteinase, as predicted by the mechanism.

Structure-stability relationship in proteins: fundamental tasks and strategy for the development of stabilized enzyme catalysts for biotechnology

The problem of relationships between the protein structure and its stability comprises two major questions. First, how to elucidate the peculiarities of the protein structure responsible for its stability. Second, knowing the general molecular basis of protein stability, how to change the structure of a given protein in order to increase its stability. This review is an attempt to show the modern state of the first (fundamental) and the second (applied) aspects of the problem.

Activation of liver alcohol dehydrogenase by glycosylation

D-Fructose and D-glucose activate alcohol dehydrogenase from horse liver to oxidize ethanol. One mol of D-[U-14C]fructose or D-[U-14C]glucose is covalently incorporated per mol of the maximally activated enzyme. Amino acid and N-terminal analyses of the 14C-labelled glycopeptide isolated from a proteolytic digest of the [14C]glycosylated enzyme implicate lysine-315 as the site of the glycosylation. 13C-n.m.r.-spectroscopic studies indicate that D-[13C]glucose is covalently linked in N-glucosidic and Amadori-rearranged structures in the [13C]glucosylated alcohol dehydrogenase. Experimental results are consistent with the formation of the N-glycosylic linkage between glycose and lysine-315 of liver alcohol dehydrogenase in the initial step that results in an enhanced catalytic efficiency to oxidize ethanol.

The effect of pH and methylation on the interaction of deoxycholate with rat liver alcohol dehydrogenase

The activation of rat liver alcohol dehydrogenase by deoxycholate depends on the anionic form of the steroid. Methylation of the enzyme protein leads to an increase of both turnover number and Km for ethanol and to a change in the effect of deoxycholate, which behaves as an inhibitor. It is suggested that the steroid and methylation effects depend on the same basic mechanism, in which one or more Lys groups are involved.

Kinetic and mechanistic studies of methylated liver alcohol dehydrogenase

Reductive methylation of lysine residues activates liver alcohol dehydrogenase in the oxidation of primary alcohols, but decreases the activity of the enzyme towards secondary alcohols. The modification also desensitizes the dehydrogenase to substrate inhibition at high alcohol concentrations. Steady-state kinetic studies of methylated liver alcohol dehydrogenase over a wide range of alcohol concentrations suggest that alcohol oxidation proceeds via a random addition of coenzyme and substrate with a pathway for the formation of the productive enzyme-NADH-alcohol complex. To facilitate the analyses of the effects of methylation on liver alcohol dehydrogenase and factors affecting them, new operational kinetic parameters to describe the results at high substrate concentration were introduced. The changes in the dehydrogenase activity on alkylation were found to be associated with changes in the maximum velocities that are affected by the hydrophobicity of alkyl groups introduced at lysine residues. The desensitization of alkylated liver alcohol dehydrogenase to substrate inhibition is identified with a decrease in inhibitory Michaelis constants for alcohols and this is favoured by the steric effects of substituents at the lysine residues.

Structural and kinetic studies on the activators of succinate dehydrogenase

1. Diverse classes of compounds such as dicarboxylates, pyrophosphates, quinols and nitrophenols are known to activate mitochondrial succinate dehydrogenase (EC 1.3.99.1). Examples in each class -- malonate, pyrophosphate, ubiquinol and 2,4-dinitrophenol -- are selected for comparative studies on the kinetic constants and structural relationship. 2. The activated forms of the enzyme obtained on preincubating mitochondria with the effectors exhibited Michaelian kinetics and gave double-reciprocal plots which are nearly parallel to that of the basal form. On activation, Km for the substrate also increased along with V. The effectors activated the enzyme at low concentrations and inhibited, in a competitive fashion, at high concentrations. The binding constant for activation was lower than that for inhibition for each effector. 3. These compounds possess ionizable twin oxygens separated by a distance of 5.5 +/- 0.8 A and having fractional charges in the range of -0.26 to -0.74 e. The common twin-oxygen feature of the substrate and the effectors suggested the presence of corresponding counter charges in the binding domain. The competitive nature of effectors with the substrate for inhibition further indicated the close structural resemblance of the activation and catalytic sites.

The reaction of horse-liver alcohol dehydrogenase with glyoxal

Horse liver alcohol dehydrogenase was reacted with glyoxal at different pH values ranging from 6.0 to 9.0. At pH 9.0 the enzyme undergoes a rapid activation over the first minutes of reaction, followed by a decline of activity, which reaches 10% of that of the native enzyme. Chemical analysis of the inactivated enzyme after sodium borohydride reduction shows that 11 argi-ine and 11 lysine residues per mole are modified. At pH 7.7 the enzyme activity increases during the first hour of the reaction with glyoxal and then decreases slowly. Chemical analysis shows that 4 arginine and 3 lysine residues per mole are modified in the enzyme at the maximum of activation. At pH 7.0 the enzyme undergoes a 4-fold activation. Chemical analysis shows that in this activated enzyme 3 lysine and no arginine residues per mole have been modified. Steady-state kinetic analysis suggests that the activated enzyme is not subjected to substrate inhibition and that its Michaelis constant for ethanol is three times larger than that of the native enzyme. The possible role of arginine and lysine residues in the catalytic function of liver alcohol dehydrogenase is discussed.

Identification of the lysine residue modified during the activation of acetimidylation of horse liver alcohol dehydrogenase

A single amino group in horse liver alcohol dehydrogenase was modified with methyl(14C)acetimidate by a differential labeling procedure. Lysine residues outside the active site were modified with ethyl acetimidate while a lysine residue in the active site was protected by the formation of an enzyme-NAD+-pyrazole complex. After the protecting reagents were removed, the enzyme was treated with methyl(14C)acetimidate. Enzyme activity was enhanced 13-fold as 1.1 (14C)acetimidyl group was incorporated per active site. A labeled peptide was isolated from a tryptic-chymotryptic digest of the modified enzyme in 35% overall yield. Amino acid composition and sequential Edman degradations identified the peptide as residues 219-229; lysine residue 228 was modified with the radioactive acetimidyl group.