Marlen Schmidt

Strategies for the discovery and engineering of enzymes for biocatalysis

Protein engineering is the most important method to overcome the limitations of natural enzymes as biocatalysts. The past few years have seen a tremendous increase in novel concepts to facilitate the design of mutant libraries for focused directed evolution mostly guided by advanced bioinformatic tools. In addition, advanced high-throughput methods were developed using, for example, FACS analysis or microfluidic systems. These achievements significantly facilitate the tailor-made design of enzymes to make them suitable for industrial applications.

Directed Evolution of an Esterase from Pseudomonas fluorescens Yields a Mutant with Excellent Enantioselectivity and Activity for the Kinetic Resolution of a Chiral Building Block

A triple mutant of an esterase from Pseudomonas fluorescens (PFE) that was created by directed evolution exhibited high enantioselectivity (E=89) in a kinetic resolution and yielded the building block (S)‐but‐3‐yn‐2‐ol. Surprisingly, a mutation close to the active site caused the formation of inclusion bodies, but remote mutations were found to be responsible for the high selectivity. Back mutations gave a variant (double mutant PFE Ile76Val/Val175Ala) that showed excellent selectivity (E=96) and activity (20 min for 50 % conversion, which corresponds to 1.25 U per mg of protein).

The Metagenome-Derived Enzymes LipS and LipT Increase the Diversity of Known Lipases

Triacylglycerol lipases (EC 3.1.1.3) catalyze both hydrolysis and synthesis reactions with a broad spectrum of substrates rendering them especially suitable for many biotechnological applications. Most lipases used today originate from mesophilic organisms and are susceptible to thermal denaturation whereas only few possess high thermotolerance. Here, we report on the identification and characterization of two novel thermostable bacterial lipases identified by functional metagenomic screenings. Metagenomic libraries were constructed from enrichment cultures maintained at 65 to 75°C and screened resulting in the identification of initially 10 clones with lipolytic activities. Subsequently, two ORFs were identified encoding lipases, LipS and LipT. Comparative sequence analyses suggested that both enzymes are members of novel lipase families. LipS is a 30.2 kDa protein and revealed a half-life of 48 h at 70°C. The lipT gene encoded for a multimeric enzyme with a half-life of 3 h at 70°C. LipS had an optimum temperature at 70°C and LipT at 75°C. Both enzymes catalyzed hydrolysis of long-chain (C12 and C14) fatty acid esters and additionally hydrolyzed a number of industry-relevant substrates. LipS was highly specific for (R)-ibuprofen-phenyl ester with an enantiomeric excess (ee) of 99%. Furthermore, LipS was able to synthesize 1-propyl laurate and 1-tetradecyl myristate at 70°C with rates similar to those of the lipase CalB from Candida antarctica. LipS represents the first example of a thermostable metagenome-derived lipase with significant synthesis activities. Its X-ray structure was solved with a resolution of 1.99 Å revealing an unusually compact lid structure.

Use of ‘small but smart’ libraries to enhance the enantioselectivity of an esterase from Bacillus stearothermophilus towards tetrahydrofuran‐3‐yl acetate

Two libraries of simultaneous double mutations in the active site region of an esterase from Bacillus stearothermophilus were constructed to improve the enantioselectivity in the hydrolysis of tetrahydrofuran‐3‐yl acetate. As screening of large mutant libraries is hampered by the necessity for GC/MS analysis, mutant libraries were designed according to a ‘small but smart’ concept. The design of focused libraries was based on data derived from a structural alignment of 3317 amino acid sequences of α/β‐hydrolase fold enzymes with the bioinformatic tool 3dm. In this way, the number of mutants to be screened was substantially reduced as compared with a standard site‐saturation mutagenesis approach. Whereas the wild‐type esterase showed only poor enantioselectivity (E = 4.3) in the hydrolysis of (S)‐tetrahydrofuran‐3‐yl acetate, the best variants obtained with this approach showed increased E‐values of up to 10.4. Furthermore, some variants with inverted enantiopreference were found.

Directed Evolution of Lipases and Esterases

Publisher Summary This chapter describes the directed evolution of lipases and esterases. Directed evolution has emerged as a powerful tool to improve biocatalysts as well as to broaden our understanding of the underlying principles for substrate specificity, stereoselectivity, and mechanism. Lipases and esterases are important biocatalysts and are especially suitable for industrial applications as they are very stable and also active in organic solvents. A high-throughput screening system (HTS) was developed that allows the direct determination of synthetic activity in a microtiter plate format. The method is based on transesterification between an alcohol and a vinyl ester of a carboxylic acid. Acetaldehyde generated from the vinyl alcohol by keto-enol tautomerization is reacted with a hydrazine to produce the corresponding hydrazone, which is then quantified by fluorimetric measurement. It is found that the most important key to success is the availability of suitable HTS systems, and the methods developed allows for the rapid and reliable identification of active lipase and esterase variants, but also with improved enantioselectivity toward chiral carboxylic acids and alcohols.

Rational Protein Design of Paenibacillus barcinonensis Esterase EstA for Kinetic Resolution of Tertiary Alcohols

Protein engineering is a very powerful tool to optimize enzymes for specific applications and thus provide important chiral building blocks such as tertiary alcohols. By use of structural comparisons, esterase from Paenibacillus barcinonensis (EstA) was engineered to convert tertiary alcohol esters with excellent enantioselectivity. Whereas the wild‐type enzyme converts 1,1,1‐trifluoro‐2‐phenylbut‐3‐yn‐2‐yl acetate with very low activity and enantioselectivity (E=12, at 4 °C), several mutants show a significantly increased enantioselectivity, for example E>100 for mutant EstA–AGA, under the same reaction conditions. Furthermore, the range of tertiary alcohols obtained in enantiopure form was also broadened for EstA mutants.

Investigation of the Cosolvent Effect on Six Isoenzymes of PLE in the Enantioselective Hydrolysis of Selected α,α‐Disubstituted Malonate Esters

Pig liver esterase (PLE) is among the most widely utilized enzymes in organic synthesis. PLE has demonstrated its versatility in performing enantioselective hydrolysis of a vast variety of esters in moderate to excellent enantiomeric excess. This esterase has proven to be extremely useful for the generation of chiral quaternary carbon centers by hydrolysis of appropriately substituted a,a-disubstituted malonate esters. The acid-ester products obtained from the hydrolysis of prochiral a,a-disubstituted malonate esters have been successfully used for the generation of novel unnatural amino acids as illustrated in Scheme 1. b, g]

Protein Engineering of Carboxyl Esterases by Rational Design and Directed Evolution

In the past few years a considerable number of mutagenesis methods and high-throughput screening (HTS) systems have been developed and improved. In parallel, computer programs or software packages for molecular modeling have been further investigated. Thus, the number of examples for successful directed evolution and rational design is increasing constantly. In this review the essential mutagenesis methods and HTS systems, especially for esterases, are described and various examples for the application of these protein engineering tools are provided.

Recombinant expression and purification of the 2,5-diketocamphane 1,2-monooxygenase from the camphor metabolizing Pseudomonas putida strain NCIMB 10007

Three different Baeyer-Villiger monooxygenases (BVMOs) were reported to be involved in the camphor metabolism by Pseudomonas putida NCIMB 10007. During (+)-camphor degradation, 2,5-diketocamphane is formed serving as substrate for the 2,5-diketocamphane 1,2-monooxygenase. This enzyme is encoded on the CAM plasmid and depends on the cofactors FMN and NADH and hence belongs to the group of type II BVMOs. We have cloned and recombinantly expressed the oxygenating subunit of the 2,5-diketocamphane 1,2-monooxygenase (2,5-DKCMO) in E. coli followed by His-tag-based affinity purification. A range of compounds representing different BVMO substrate classes were then investigated, but only bicyclic ketones were converted by 2,5-DKCMO used as crude cell extract or after purification. Interestingly, also (-)-camphor was oxidized, but conversion was about 3-fold lower compared to (+)-camphor. Moreover, activity of purified 2,5-DKCMO was observed in the absence of an NADH-dehydrogenase subunit.

The role of the GGGX motif in determining the activity and enantioselectivity of pig liver esterase towards tertiary alcohols

Abstract The GGG(A)X motif has been reported to determine the activity of esterases or lipases towards tertiary alcohols. The γ-isoenzyme of pig liver esterase (γ-PLE, PLE 1) contains a GGGX motif; this motif was systematically mutated to the corresponding AGGX, GAGX, GGAX, AAAX, AAGX, AGAX and GAAX motifs to investigate its influence on the activity and especially enantioselectivity in the kinetic resolution of three acetates of tertiary alcohols. None of the mutants showed higher enantioselectivity than the starting enzyme (E=17), and mutation of the central glycine to alanine completely destroyed activity and selectivity. Hence, only subtle changes of this crucial motif lead to substantial changes in esterase properties. These findings were analyzed and interpreted by computer modeling.