FoldX as Protein Engineering Tool: Better Than Random Based Approaches?

Improving protein stability is an important goal for basic research as well as for clinical and industrial applications but no commonly accepted and widely used strategy for efficient engineering is known. Beside random approaches like error prone PCR or physical techniques to stabilize proteins, e.g. by immobilization, in silico approaches are gaining more attention to apply target-oriented mutagenesis. In this review different algorithms for the prediction of beneficial mutation sites to enhance protein stability are summarized and the advantages and disadvantages of FoldX are highlighted. The question whether the prediction of mutation sites by the algorithm FoldX is more accurate than random based approaches is addressed.

Enantiomer discrimination in ß-phenylalanine degradation by a newly isolated Paraburkholderia strain BS115 and type strain PsJN.

Despite their key role in numerous natural compounds, ß-amino acids have rarely been studied as substrates for microbial degradation. Fermentation of the newly isolated Paraburkholderia strain BS115 and the type strain P. phytofirmans PsJN with ß-phenylalanine (ß-PA) as sole nitrogen source revealed (S)-selective transamination of ß-PA to the corresponding ß-keto acid by both strains, accompanied by substantial formation of acetophenone (AP) from spontaneous decarboxylation of the emerging ß-keto acid. While the PsJN culture became stationary after entire (S)-ß-PA consumption, BS115 showed further growth at a considerably slower rate, consuming (R)-ß-PA without generation of AP which points to a different degradation mechanism for this enantiomer. This is the first report on degradation of both enantiomers of any ß-amino acid by one single bacterial strain.

ß-Phenylalanine Ester Synthesis from Stable ß-Keto Ester Substrate Using Engineered ω-Transaminases.

The successful synthesis of chiral amines from ketones using ω-transaminases has been shown in many cases in the last two decades. In contrast, the amination of ß-keto acids is a special and relatively new challenge, as they decompose easily in aqueous solution. To avoid this, transamination of the more stable ß-keto esters would be an interesting alternative. For this reason, ω-transaminases were tested in this study, which enabled the transamination of the ß-keto ester substrate ethyl benzoylacetate. Therefore, a ω-transaminase library was screened using a coloring o-xylylenediamine assay. The ω-transaminase mutants 3FCR_4M and ATA117 11Rd show great potential for further engineering experiments aiming at the synthesis of chiral (S)- and (R)-ß-phenylalanine esters. This alternative approach resulted in the conversion of 32% and 13% for the (S)- and (R)-enantiomer, respectively. Furthermore, the (S)-ß-phenylalanine ethyl ester was isolated by performing a semi-preparative synthesis.

The ω-transaminase engineering database (oTAED): A navigation tool in protein sequence and structure space.

The ω-Transaminase Engineering Database (oTAED) was established as a publicly accessible resource on sequences and structures of the biotechnologically relevant ω-transaminases (ω-TAs) from Fold types I and IV. The oTAED integrates sequence and structure data, provides a classification based on fold type and sequence similarity, and applies a standard numbering scheme to identify equivalent positions in homologous proteins. The oTAED includes 67 210 proteins (114 655 sequences) which are divided into 169 homologous families based on global sequence similarity. The 44 and 39 highly conserved positions which were identified in Fold type I and IV, respectively, include the known catalytic residues and a large fraction of glycines and prolines in loop regions, which might have a role in protein folding and stability. However, for most of the conserved positions the function is still unknown. Literature information on positions that mediate substrate specificity and stereoselectivity was systematically examined. The standard numbering schemes revealed that many positions which have been described in different enzymes are structurally equivalent. For some positions, multiple functional roles have been suggested based on experimental data in different enzymes. The proposed standard numbering schemes for Fold type I and IV ω-TAs assist with analysis of literature data, facilitate annotation of ω-TAs, support prediction of promising mutation sites, and enable navigation in ω-TA sequence space. Thus, it is a useful tool for enzyme engineering and the selection of novel ω-TA candidates with desired biochemical properties.

Improvement in the Thermostability of a ß-Amino Acid Converting ω-Transaminase by Using FoldX.

ω-Transaminases (ω-TAs) are important biocatalysts for the synthesis of active, chiral pharmaceutical ingredients containing amino groups, such as ß-amino acids, which are important in peptidomimetics and as building blocks for drugs. However, the application of ω-TAs is limited by the availability and stability of enzymes with high conversion rates. One strategy for the synthesis and optical resolution of ß-phenylalanine and other important aromatic ß-amino acids is biotransformation by utilizing an ω-transaminase from Variovorax paradoxus. We designed variants of this ω-TA to gain higher process stability on the basis of predictions calculated by using the FoldX software. We herein report the first thermostabilization of a nonthermostable S-selective ω-TA by FoldX-guided site-directed mutagenesis. The melting point (Tm ) of our best-performing mutant was increased to 59.3 °C, an increase of 4.0 °C relative to the Tm value of the wild-type enzyme, whereas the mutant fully retained its specific activity.