Design of a specific phenyllactate dehydrogenase by peptide loop exchange on the Bacillus stearothermophilus lactate dehydrogenase framework

Better library design: data-driven protein engineering

Data-driven protein engineering is increasingly used as an alternative to rational design and combinatorial engineering because it uses available knowledge to limit library size, while still allowing for the identification of unpredictable substitutions that lead to large effects. Recent advances in computational modeling and bioinformatics, as well as an increasing databank of experiments on functional variants, have led to new strategies to choose particular amino acid residues to vary in order to increase the chances of obtaining a variant protein with the desired property. Strategies for limiting diversity at each position, design of small sub-libraries, and the performance of scouting experiments, have also been developed or even automated, further reducing the library size.

Protein engineering 20 years on

It is 20 years since site-directed mutagenesis was first used to modify the active site of an enzyme of known structure and mechanism. Since then, this method has contributed far-reaching insights into catalysis, specificity, stability and folding of proteins. Engineered proteins are now being used in industry and for the improved treatment of human disease.

The kinetic properties and sensitivities to inhibitors of lactate dehydrogenases (LDH1 and LDH2) from Toxoplasma gondii: comparisons with pLDH from Plasmodium falciparum

Toxoplasma gondii differentially expresses two forms of lactate dehydrogenase in tachyzoites and bradyzoites, respectively, designated LDH1 and LDH2. Previously it was demonstrated that LDH1 and LDH2 share a unique structural feature with LDH from the malarial parasite Plasmodium falciparum (pLDH), namely, the addition of a five-amino acid insert into the substrate specificity loops. pLDH exhibits a number of kinetic properties that previously were thought to be unique to pLDH. In the present study, kinetic properties of LDH1 and LDH2 were compared with those of pLDH. LDH1 and LDH2 exhibit broader substrate specificity than pLDH. For both LDH1 and LDH2, 3-phenylpyruvate is an excellent substrate. For LDH2, 3-phenylpyruvate is a better substrate even than pyruvate. By comparison, pLDH does not utilize 3-phenylpyruvate. Both LDH1 and LDH2 can utilize the NAD analog 3-acetylpyridine adenine dinucleotide (APAD) efficiently, similar to pLDH. LDH1 and LDH2 are inhibited competitively by a range of compounds that also inhibit pLDH, including gossypol and derivatives, dihydroxynaphthoic acids, and N-substituted oxamic acids. The lack of substrate inhibition observed with pLDH is also observed with LDH2. By comparison, LDH1 differs from LDH2 in exhibiting substrate inhibition in spite of an identical residue (M163) at a cofactor binding site that is thought to be critical for production of substrate inhibition. For gossypol and gossylic iminolactone, but not the other gossypol derivatives tested, the in vitro inhibition of T. gondii LDH activity correlated with specific inhibition of T. gondii tachyzoite growth in fibroblast cultures.

Introduction of a (poly)histidine tag in L-lactate dehydrogenase produces a mixture of active and inactive molecules

A (poly)histidine tag was fused to either the N- or the C-terminus of L-lactate dehydrogenase (LDH) of Bacillus stearothermophilus to facilitate purification and immobilization of these enzymes. The C-terminally tagged enzyme displayed lower activity compared both to the wild-type and to the N-terminally tagged variant. The reason for this loss of activity was investigated by affinity chromatography of the enzymes on a 5'-AMP-Sepharose resin and by size-exclusion chromatography. The C-terminally tagged enzyme could be separated into an inactive, unbound fraction and an active, bound fraction. Further differences between the C-terminally tagged enzyme and the N-terminally tagged and wild-type LDH were observed on size-exclusion chromatography of the three enzymes. These data suggest that the introduction of a "his-tag" at the C-terminus may induce misfolding of the LDH and serve as a warning that the introduction of a (poly)histidine tag can produce unforseen changes in a protein.

Structural basis for altered activity of M- and H-isozyme forms of human lactate dehydrogenase

Lactate dehydrogenase (LDH) interconverts pyruvate and lactate with concomitant interconversion of NADH and NAD(+). Although crystal structures of a variety of LDH have previously been described, a notable absence has been any of the three known human forms of this glycolytic enzyme. We have now determined the crystal structures of two isoforms of human LDH-the M form, predominantly found in muscle; and the H form, found mainly in cardiac muscle. Both structures have been crystallized as ternary complexes in the presence of the NADH cofactor and oxamate, a substrate-like inhibitor. Although each of these isoforms has different kinetic properties, the domain structure, subunit association, and active-site regions are indistinguishable between the two structures. The pK(a) that governs the K(M) for pyruvate for the two isozymes is found to differ by about 0.94 pH units, consistent with variation in pK(a) of the active-site histidine. The close similarity of these crystal structures suggests the distinctive activity of these enzyme isoforms is likely to result directly from variation of charged surface residues peripheral to the active site, a hypothesis supported by electrostatic calculations based on each structure. Proteins 2001;43:175-185.

2-Hydroxyacid dehydrogenase from Haloferax mediterranei, a D-isomer-specific member of the 2-hydroxyacid dehydrogenase family

An NAD-dependent D-2-hydroxyacid dehydrogenase (EC 1.1.1.) was isolated and characterized from the halophilic Archaeon Haloferax mediterranei. The enzyme is a dimer with a molecular mass of 101.4 +/- 3.3 kDa. It is strictly NAD-dependent and exhibits its highest activity in 4 M NaCl. The enzyme is characterized by a broad substrate specificity 2-ketoisocaproate and 2-ketobutyrate being the substrates with the higher Vmax/Km. When pyruvate and 2-ketobutyrate were the substrates the optimal pH was acidic (pH 5) meanwhile for 2-ketoisocaproate maximum activity was achieved at basic pH between 7.5 and 8.5. The optimum temperature was 52 degrees C and at 65 degrees C there was a pronounced activity decrease. This new enzyme can be used for the production of D-2-hydroxycarboxylic acid.

From malate dehydrogenase to phenyllactate dehydrogenase. Incorporation of unnatural amino acids to generate an improved enzyme-catalyzed activity

Malate dehydrogenase (MDH) from Escherichia coli is highly specific for its keto acid substrate. The placement of the active site-binding groups in MDH effectively discriminates against both the shorter and the longer keto dicarboxylic acids that could potentially serve as alternative substrates. A notable exception to this specificity is the alternative substrate phenylpyruvate. This aromatic keto acid can be reduced by MDH, albeit at a somewhat slower rate and with greatly diminished affinity, despite the presence of several substrate-binding arginyl residues and the absence of a hydrophobic pocket in the active site. The specificity of MDH for phenylpyruvate has now been enhanced, and that for the physiological substrate oxaloacetate has been diminished, through the replacement of one of the binding arginyl residues with several unnatural alkyl and aryl amino acid analogs. This approach, called site-specific modulation, incorporates systematic structural variations at a site of interest. Molecular modeling studies have suggested a structural basis for the affinity of native MDH for phenylpyruvate and a rationale for the improved catalytic activity that is observed with these new, modified phenyllactate dehydrogenases.

The pepsin residue glycine-76 contributes to active-site loop flexibility and participates in catalysis

Glycine residues are known to contribute to conformational flexibility of polypeptide chains, and have been found to contribute to flexibility of some loops associated with enzymic catalysis. A comparison of porcine pepsin in zymogen, mature and inhibited forms revealed that a loop (a flap), consisting of residues 71--80, located near the active site changed its position upon substrate binding. The loop residue, glycine-76, has been implicated in the catalytic process and thought to participate in a hydrogen-bond network aligning the substrate. This study investigated the role of glycine-76 using site-directed mutagenesis. Three mutants, G76A, G76V and G76S, were constructed to increase conformational restriction of a polypeptide chain. In addition, the serine mutant introduced a hydrogen-bonding potential at position 76 similar to that observed in human renin. All the mutants, regardless of amino acid size and polarity, had lower catalytic efficiency and activated more slowly than the wild-type enzyme. The slower activation process was associated directly with altered proteolytic activity. Consequently, it was proposed that a proteolytic cleavage represents a limiting step of the activation process. Lower catalytic efficiency of the mutants was explained as a decrease in the flap flexibility and, therefore, a different pattern of hydrogen bonds responsible for substrate alignment and flap conformation. The results demonstrated that flap flexibility is essential for efficient catalytic and activation processes.

Hybrid enzymes: manipulating enzyme design

Hybrid enzymes are engineered to contain elements of two or more enzymes. Hybrid-enzyme approaches, by taking advantage of the vast array of enzymatic properties that nature has evolved, as well as the strategies that nature has used to evolve them, are becoming an increasingly important avenue for obtaining novel enzymes with desired activities and properties.

Substrate and cofactor specificity and selective inhibition of lactate dehydrogenase from the malarial parasite P. falciparum

Lactate dehydrogenase from the malarial parasite Plasmodium falciparum has many amino acid residues that are unique compared to any other known lactate dehydrogenase. This includes residues that define the substrate and cofactor binding sites. Nevertheless, parasite lactate dehydrogenase exhibits high specificity for pyruvic acid, even more restricted than the specificity of human lactate dehydrogenases M4 and H4. Parasite lactate dehydrogenase exhibits high catalytic efficiency in the reduction of pyruvate, kcat/Km = 9.0 x 10(8) min(-1) M(-1). Parasite lactate dehydrogenase also exhibits similar cofactor specificity to the human isoforms in the oxidation of L-lactate with NAD+ and with a series of NAD+ analogs, suggesting a similar cofactor binding environment in spite of the numerous amino acid differences. Parasite lactate dehydrogenase exhibits an enhanced kcat with the analog 3-acetylpyridine adenine dinucleotide (APAD+) whereas the human isoforms exhibit a lower kcat. This differential response to APAD+ provides the kinetic basis for the enzyme-based detection of malarial parasites. A series of inhibitors structurally related to the natural product gossypol were shown to be competitive inhibitors of the binding of NADH. Slight changes in structure produced marked changes in selectivity of inhibition of lactate dehydrogenase. 7-p-Trifluoromethylbenzyl-8-deoxyhemigossylic acid inhibited parasite lactate dehydrogenase, Ki = 0.2 microM, which was 65- and 400-fold tighter binding compared to the M4 and H4 isoforms of human lactate dehydrogenase. The results suggest that the cofactor site of parasite lactate dehydrogenase may be a potential target for structure-based drug design.

Alternating arginine-modulated substrate specificity in an engineered tyrosine aminotransferase

Mutation of six residues of Escherichia coli aspartate aminotransferase results in substantial acquisition of the transamination properties of tyrosine amino-transferase without loss of aspartate transaminase activity. X-ray crystallographic analysis of key inhibitor complexes of the hexamutant reveals the structural basis for this substrate selectivity. It appears that tyrosine aminotransferase achieves nearly equal affinities for a wide range of amino acids by an unusual conformational switch. An active-site arginine residue either shifts its position to electrostatically interact with charged substrates or moves aside to allow access of aromatic ligands.

Novel enzymes as reagents

Enzymes are now used in a wide range of analytical methods, primarily for the measurement of substrates and as labels in immunoassays. Enzymes from microbial sources are becoming the preferred choice because of ease of extraction, catabolic activities and opportunities for enhancing yields. Protein engineering of bacterial enzymes will also play a role in future enzyme design with respect to improvements in specificity, reaction kinetics and stability.

NAD(+)-dependent D-2-hydroxyisocaproate dehydrogenase of Lactobacillus delbrueckii subsp. bulgaricus. Gene cloning and enzyme characterization

A genomic library from Lactobacillus delbrueckii subsp. bulgaricus was used to complement an Escherichia coli mutant strain deficient for both lactate dehydrogenase and pyruvate formate lyase, and thus unable to grow anaerobically. One recombinant clone was found to display a broad specificity NAD(+)-dependent D-2-hydroxyacid dehydrogenase activity. The corresponding gene (named hdhD) was subcloned and sequenced. The deduced amino acid sequence of the encoded enzyme indicates a 333-residue protein closely related to D-2-hydroxyisocaproate (i.e. 2-hydroxy-4-methyl-pentanoate) dehydrogenase (D-HO-HxoDH) of Lactobacillus casei and other NAD(+)-dependent D-lactate dehydrogenases (D-LDH) from several other bacterial species. The hdhD gene was overexpressed under the control of the lambda phage PL promoter and the enzyme was purified with a two-step method. The L. delbrueckii subsp. bulgaricus enzyme, like that of L. casei, was shown to be active on a wide variety of 2-oxoacid substrates except those having a branched beta-carbon.

Deletion variants of L-hydroxyisocaproate dehydrogenase. Probing substrate specificity

The substrate specificity and catalytic activity of the dinucleotide-dependent L-2-hydroxyisocaproate dehydrogenase from Lactobacillus confusus (L-HicDH) have been altered by modifying an enzyme region which is assumed to be involved in substrate recognition. The design of the variant enzymes was based on an amino acid alignment of the modified region with the functionally related L-lactate dehydrogenases. The best absolute sequence similarity for a protein with known tertiary structure was found for L-lactate dehydrogenase from dogfish (23%). In this study, the coenzyme loop, a functional element which is essential for catalysis and substrate specificity, was modified in order to identify the residues involved in the catalytic reaction and observe the effect on the substrate specificity. Deletions were introduced into the L-hydroxyisocaproate gene by site-directed mutagenesis. Several deletion-variant enzymes Ile100A delta, Lys100B delta, Leu101 delta, Asn105A delta and Pro105B delta showed an altered substrate specificity. For the variant enzyme with the deletion of Asn/Pro105A/B, 2-oxo carboxylic acids branched at C4 proved to be better substrates than 2-oxocaproate, the substrate with the best kcat/KM ratio known for the wild-type enzyme. The mutation resulted in a 5.2-fold increased catalytic efficiency towards 2-oxoisocaproate compared to the wild-type enzyme. After deleting Ile/Lys100A/B, 2-phenylpyruvate is the only substrate which is still converted at a significant catalytic rate. The kcat ratios of 2-oxocaproate versus 2-phenylpyruvate changed by a factor of 6500 when comparing wild-type enzyme and deletion-variant enzyme data. The single amino acid deletions in position 100A and 100B caused drastic reductions in the catalytic activity for all tested substrates, whereas the deletion of Lys100B, Leu101, Asn105A as well as Pro105B showed more specific modifications in catalytic rates and substrate recognition for each tested substrate.

Engineering surface loops of proteins--a preferred strategy for obtaining new enzyme function

A prerequisite for the rational redesign of enzymes is that altering amino acids in an attempt to obtain new biological function does not unexpectedly alter the globular, natural framework of the native protein on which the design is being executed. The results of combinatorial-mutagenesis strategies suggest that random variation of amino acid sequence is most easily tolerated at the solvent-exposed surfaces of a protein. This review analyses effective redesigns of Bacillus stearothermophilus lactate dehydrogenase (bsLDH), in which all residue variations are at solvent-exposed surfaces. The majority of these variations were located within surface loops, which interconnect stable secondary structures traversing the globular core of the protein.

Protein engineering for unusual environments

The ability to use proteins in unusual or non-natural environments greatly expands their potential applications in biotechnology. Because natural selection has neither maximized the stability of proteins nor optimized them to function under unusual conditions, there is considerable room for their improvement by protein engineering. Significant advances reported within the past year include a dramatic demonstration of a protein's ability to tolerate changes in its amino acid sequence, large increases in protein stability, and the use of random mutagenesis to obtain novel enzymatic properties. Approaches using random or site-directed mutagenesis have been successful in generating proteins able to function in an extended range of environments.

Movable lobes and flexible loops in proteins. Structural deformations that control biochemical activity

Two classes of protein whose structure is modified by small ligands are reviewed. Proteins of one group contain two massive domains joined by a flexible link; in response to small molecules, the two lobes approach and enclose the ligand. In the other, a short segment of amino acids moves as a flexible loop over the ligand which often is trapped in a non-aqueous environment. Biochemical reaction rates are altered dramatically by these movements.