Stereoselectivity and Expanded Substrate Scope of an Engineered PLP-Dependent Aldolase

Enzymatic asymmetric synthesis of chiral amino acids

This review summarizes the progress achieved in the enzymatic asymmetric synthesis of chiral amino acids from prochiral substrates.

Biomimetic Chirality Sensing with Pyridoxal-5'-phosphate

Pyridoxal-5'-phosphate (PLP) is introduced to a biomimetic indicator displacement assay for simultaneous determination of the absolute configuration, enantiomeric composition and concentration of unprotected amino acids, amino alcohols and amines. The chiroptical assay is based on fast imine metathesis with a PLP aryl imine probe to capture the target compound for circular dichroism and fluorescence sensing analysis. The substrate binding yields characteristic Cotton effects that provide information about the target compound ee and the synchronous release of the indicator results in a nonenantioselective off-on fluorescence response that is independent of the enantiomeric sample composition and readily correlated to the total analyte concentration.

Benchmarking pKa Prediction Methods for Residues in Proteins

Methods for estimation of pKa values of residues in proteins were tested on a set of benchmark proteins with experimentally known pKa values. The benchmark set includes 80 different residues (20 each for Asp, Glu, Lys, and His), half of which consists of significantly variant cases (ΔpKa ≥ 1 pKa unit from the amino acid in solution). The method introduced by Case and co-workers [J. Am. Chem. Soc. 2004, 126, 4167-4180], referred to as the molecular dynamics/generalized-Born/thermodynamic integration (MD/GB/TI) technique, gives a root-mean-square deviation (rmsd) of 1.4 pKa units on the benchmark set. The use of explicit waters in the immediate region surrounding the residue was shown to generally reduce high errors for this method. Longer simulation time was also shown to increase the accuracy of this method. The empirical approach developed by Jensen and co-workers [Proteins 2005, 61, 704-721], PROPKA, also gives an overall rmsd of 1.4 pKa units and is more or less accurate based on residue type-the method does very well for Lys and Glu, but less so for Asp and His. Likewise, the absolute deviation is quite similar for the two methods-5.2 for PROPKA and 5.1 for MD/GB/TI. A comparison of these results with several prediction methods from the literature is presented. The error in pKa prediction is analyzed as a function of variation of the pKa from that in water and the solvent accessible surface area (SASA) of the residue. A case study of the catalytic lysine residue in 2-deoxyribose-5-phosphate aldolase (DERA) is also presented.

Threonine aldolases

Threonine aldolases catalyze the pyridoxal phosphate-dependent condensation between small amino acids (principally glycine) and aldehydes such as acetaldehyde. Carbon-carbon bond formation involves forming two adjacent chiral centers. As a rule, threonine aldolases are very stereoselective for α-carbon configuration but show modest selectivity at the β-carbon. On the other hand, these enzymes accept a wide variety of synthetically useful acceptor aldehydes, making them important additions to the synthetic toolkit. This review briefly summarizes the reaction mechanism and then lists all published synthetic reactions by threonine aldolases as of early 2014. The current state of the art in crystallographic and protein engineering studies of these enzymes is also presented.

Recent advances in rational approaches for enzyme engineering

Enzymes are an attractive alternative in the asymmetric syntheses of chiral building blocks. To meet the requirements of industrial biotechnology and to introduce new functionalities, the enzymes need to be optimized by protein engineering. This article specifically reviews rational approaches for enzyme engineering and de novo enzyme design involving structure-based approaches developed in recent years for improvement of the enzymes’ performance, broadened substrate range, and creation of novel functionalities to obtain products with high added value for industrial applications.

Rational approaches for engineering novel functionalities in carbon-carbon bond forming enzymes

Enzymes that catalyze carbon-carbon bond formation can be exploited as biocatalyst for synthetic organic chemistry. However, natural enzymes frequently do not possess the required properties or specificities to catalyze industrially useful transformations. This mini-review describes recent work using knowledge-guided site-specific mutagenesis of key active site residues to alter substrate specificity, stereospecificity and reaction specificity of these enzymes. In addition, examples of de novo designed enzymes that catalyze C-C bond reactions not found in nature will be discussed.

Controlling reaction specificity in pyridoxal phosphate enzymes

Pyridoxal 5'-phosphate enzymes are ubiquitous in the nitrogen metabolism of all organisms. They catalyze a wide variety of reactions including racemization, transamination, decarboxylation, elimination, retro-aldol cleavage, Claisen condensation, and others on substrates containing an amino group, most commonly α-amino acids. The wide variety of reactions catalyzed by PLP enzymes is enabled by the ability of the covalent aldimine intermediate formed between substrate and PLP to stabilize carbanionic intermediates at Cα of the substrate. This review attempts to summarize the mechanisms by which reaction specificity can be achieved in PLP enzymes by focusing on three aspects of these reactions: stereoelectronic effects, protonation state of the external aldimine intermediate, and interaction of the carbanionic intermediate with the protein side chains present in the active site. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.

Molecular dynamics simulations of the intramolecular proton transfer and carbanion stabilization in the pyridoxal 5'-phosphate dependent enzymes L-dopa decarboxylase and alanine racemase

Molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) potential have been carried out to investigate the internal proton transfer equilibrium of the external aldimine species in l-dopa decarboxylase, and carbanion stabilization by the enzyme cofactor in the active site of alanine racemase. Solvent effects lower the free energy of the O-protonated PLP tautomer both in aqueous solution and in the active site, resulting a free energy difference of about -1 kcal/mol relative to the N-protonated Schiff base in the enzyme. The external aldimine provides the dominant contribution to lowering the free energy barrier for the spontaneous decarboxylation of l-dopa in water, by a remarkable 16 kcal/mol, while the enzyme l-dopa decarboxylase further lowers the barrier by 8 kcal/mol. Kinetic isotope effects were also determined using a path integral free energy perturbation theory on the primary (13)C and the secondary (2)H substitutions. In the case of alanine racemase, if the pyridine ring is unprotonated as that in the active site, there is destabilizing contribution to the formation of the α-carbanion in the gas phase, although when the pyridine ring is protonated the contribution is stabilizing. In aqueous solution and in alanine racemase, the α-carbanion is stabilized both when the pyridine ring is protonated and unprotonated. The computational studies illustrated in this article show that combined QM/MM simulations can help provide a deeper understanding of the mechanisms of PLP-dependent enzymes. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.

Minimalist active-site redesign: teaching old enzymes new tricks

Although nature evolves its catalysts over millions of years, enzyme engineers try to do it a bit faster. Enzyme active sites provide highly optimized microenvironments for the catalysis of biologically useful chemical transformations. Consequently, changes at these centers can have large effects on enzyme activity. The prediction and control of these effects provides a promising way to access new functions. The development of methods and strategies to explore the untapped catalytic potential of natural enzyme scaffolds has been pushed by the increasing demand for industrial biocatalysts. This Review describes the use of minimal modifications at enzyme active sites to expand their catalytic repertoires, including targeted mutagenesis and the addition of new reactive functionalities. Often, a novel activity can be obtained with only a single point mutation. The many successful examples of active-site engineering through minimal mutations give useful insights into enzyme evolution and open new avenues in biocatalyst research.